From 66368763085d02a67ff4809d6a850989140e224e Mon Sep 17 00:00:00 2001
From: pourzanj <pourzanj@gmail.com>
Date: Thu, 18 Jan 2024 15:05:27 -0800
Subject: [PATCH] Recompiled M2 notebook with recent Casey updates

---
 M2/Presentations/torsten_test.html | 11224 ++++++++++++++++++---------
 1 file changed, 7598 insertions(+), 3626 deletions(-)

diff --git a/M2/Presentations/torsten_test.html b/M2/Presentations/torsten_test.html
index 2974783..f532460 100644
--- a/M2/Presentations/torsten_test.html
+++ b/M2/Presentations/torsten_test.html
@@ -7,9 +7,9 @@
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
 <meta name="author" content="Casey Davis">
-<meta name="dcterms.date" content="2024-01-17">
+<meta name="dcterms.date" content="2024-01-18">
 
-<title>Torsten Issues</title>
+<title>Torsten Testing on an M2</title>
 <style>
 code{white-space: pre-wrap;}
 span.smallcaps{font-variant: small-caps;}
@@ -3062,7 +3062,7 @@ <h2 id="toc-title">Table of contents</h2>
 
 <header id="title-block-header" class="quarto-title-block default">
 <div class="quarto-title">
-<div class="quarto-title-block"><div><h1 class="title">Torsten Issues</h1><button type="button" class="btn code-tools-button dropdown-toggle" id="quarto-code-tools-menu" data-bs-toggle="dropdown" aria-expanded="false"><i class="bi"></i> Code</button><ul class="dropdown-menu dropdown-menu-end" aria-labelelledby="quarto-code-tools-menu"><li><a id="quarto-show-all-code" class="dropdown-item" href="javascript:void(0)" role="button">Show All Code</a></li><li><a id="quarto-hide-all-code" class="dropdown-item" href="javascript:void(0)" role="button">Hide All Code</a></li><li><hr class="dropdown-divider"></li><li><a id="quarto-view-source" class="dropdown-item" href="javascript:void(0)" role="button">View Source</a></li></ul></div></div>
+<div class="quarto-title-block"><div><h1 class="title">Torsten Testing on an M2</h1><button type="button" class="btn code-tools-button dropdown-toggle" id="quarto-code-tools-menu" data-bs-toggle="dropdown" aria-expanded="false"><i class="bi"></i> Code</button><ul class="dropdown-menu dropdown-menu-end" aria-labelelledby="quarto-code-tools-menu"><li><a id="quarto-show-all-code" class="dropdown-item" href="javascript:void(0)" role="button">Show All Code</a></li><li><a id="quarto-hide-all-code" class="dropdown-item" href="javascript:void(0)" role="button">Hide All Code</a></li><li><hr class="dropdown-divider"></li><li><a id="quarto-view-source" class="dropdown-item" href="javascript:void(0)" role="button">View Source</a></li></ul></div></div>
 </div>
 
 
@@ -3079,7 +3079,7 @@ <h2 id="toc-title">Table of contents</h2>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">January 17, 2024</p>
+      <p class="date">January 18, 2024</p>
     </div>
   </div>
   
@@ -3104,7 +3104,15 @@ <h2 id="toc-title">Table of contents</h2>
 <section id="introduction" class="level1" data-number="1">
 <h1 data-number="1"><span class="header-section-number">1</span> Introduction</h1>
 <p>I’ve been doing some testing with the new Torsten release (v0.91.0) on an M3 Macbook Pro. I brought up an issue with M3 compatibility <a href="https://discourse.mc-stan.org/t/problem-installing-torsten-0-90/27585/12">here</a>. Thank you for fixing that issue. Now I’m doing some more testing, and I’m finding some issues with the Torsten solvers.</p>
-<p>I’ve mostly done testing on my own models, but I’ve also worked on the <code>pk2cpt</code>, <code>pk2cpt_linode</code>, <code>pk2cpt_ode</code>, and <code>poppk2cpt</code> models, For the single subject models, the analytical solution didn’t work, the linear ODE solution worked, and the ODE solution didn’t work (although I’m not exactly sure why the ODE solution didn’t work. Still needs worked on, I guess.) For the population model, the analytical solution and the ODE solution worked with the model that you’ve written, but the linear ODE soolution didn’t work. So I then used the data in <code>poppk2cpt</code> and fit it with a model I’ve written, and the linear ODE and general ODE solutions worked, but the analytical solution didn’t.</p>
+<!-- I've mostly done testing on my own models, but I've also worked on the  -->
+<!-- ```pk2cpt```, ```pk2cpt_linode```, ```pk2cpt_ode```, and ```poppk2cpt``` models, -->
+<!-- For the single subject models, the analytical solution didn't work, the linear  -->
+<!-- ODE solution worked, and the ODE solution didn't work (although I'm not exactly  -->
+<!-- sure why the ODE solution didn't work. Still needs worked on, I guess.) For the  -->
+<!-- population model, the analytical solution and the ODE solution worked with the -->
+<!-- model that you've written, but the linear ODE soolution didn't work. So I then -->
+<!-- used the data in ```poppk2cpt``` and fit it with a model I've written, and the -->
+<!-- linear ODE and general ODE solutions worked, but the analytical solution didn't. -->
 </section>
 <section id="some-examples" class="level1" data-number="2">
 <h1 data-number="2"><span class="header-section-number">2</span> Some Examples</h1>
@@ -3540,7 +3548,7 @@ <h3 data-number="2.1.1" class="anchored" data-anchor-id="one-compartment-oral-wi
 </div>
 </div>
 </div>
-<p>So you can see that the analytical solution spits out a vector of 0s, while the linear ODE, general ODE, and mrgsolve simulations are all the same.</p>
+<p>So you can see for the M2, the analytical soultion, linear ODE, general ODE, and mrgsolve simulations are all the same, in contrast with the M3 where the analytical solution was a vector of zeros.</p>
 </section>
 <section id="two-compartment-iv-with-proportional-error" class="level3" data-number="2.1.2">
 <h3 data-number="2.1.2" class="anchored" data-anchor-id="two-compartment-iv-with-proportional-error"><span class="header-section-number">2.1.2</span> Two-Compartment IV with Proportional Error</h3>
@@ -4073,7 +4081,7 @@ <h3 data-number="2.1.2" class="anchored" data-anchor-id="two-compartment-iv-with
 </div>
 </div>
 </div>
-<p>So you can see that the analytical solution spits out a vector of 0s, while the linear ODE, general ODE, and mrgsolve simulations are all the same.</p>
+<p>So you can see for the M2, the analytical soultion, linear ODE, general ODE, and mrgsolve simulations are all the same, in contrast with the M3 where the analytical solution was a vector of zeros.</p>
 </section>
 </section>
 <section id="fitting-pk2cpt-pk2cpt_linode-pk2cpt_ode-from-example-models" class="level2" data-number="2.2">
@@ -4086,63 +4094,17 @@ <h3 data-number="2.2.1" class="anchored" data-anchor-id="pk2cpt"><span class="he
 <details>
 <summary>Code</summary>
 <div class="sourceCode cell-code" id="cb17"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb17-1"><a href="#cb17-1" aria-hidden="true" tabindex="-1"></a>model_analytical <span class="ot">&lt;-</span> <span class="fu">cmdstan_model</span>(</span>
-<span id="cb17-2"><a href="#cb17-2" aria-hidden="true" tabindex="-1"></a>  here<span class="sc">::</span><span class="fu">here</span>(<span class="st">&quot;M3/example_models_metrum/pk2cpt/pk2cpt.stan&quot;</span>))</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
-</details>
-<div class="cell-output cell-output-stderr">
-<pre><code>In file included from /var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-7925944e9cd.hpp:1:
-In file included from /Users/Arya/Torsten/cmdstan/stan/src/stan/model/model_header.hpp:4:
-In file included from /Users/Arya/Torsten/cmdstan/stan/lib/stan_math/stan/math.hpp:19:
-In file included from /Users/Arya/Torsten/cmdstan/stan/lib/stan_math/stan/math/rev.hpp:10:
-In file included from /Users/Arya/Torsten/cmdstan/stan/lib/stan_math/stan/math/rev/fun.hpp:200:
-In file included from /Users/Arya/Torsten/cmdstan/stan/lib/stan_math/stan/math/prim/functor.hpp:16:
-In file included from /Users/Arya/Torsten/cmdstan/stan/lib/stan_math/stan/math/prim/functor/integrate_ode_rk45.hpp:6:
-In file included from /Users/Arya/Torsten/cmdstan/stan/lib/stan_math/stan/math/prim/functor/ode_rk45.hpp:9:
-In file included from /Users/Arya/Torsten/cmdstan/stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint.hpp:76:
-In file included from /Users/Arya/Torsten/cmdstan/stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint/integrate/observer_collection.hpp:23:
-In file included from /Users/Arya/Torsten/cmdstan/stan/lib/stan_math/lib/boost_1.78.0/boost/function.hpp:30:
-In file included from /Users/Arya/Torsten/cmdstan/stan/lib/stan_math/lib/boost_1.78.0/boost/function/detail/prologue.hpp:17:
-In file included from /Users/Arya/Torsten/cmdstan/stan/lib/stan_math/lib/boost_1.78.0/boost/function/function_base.hpp:21:
-In file included from /Users/Arya/Torsten/cmdstan/stan/lib/stan_math/lib/boost_1.78.0/boost/type_index.hpp:29:
-In file included from /Users/Arya/Torsten/cmdstan/stan/lib/stan_math/lib/boost_1.78.0/boost/type_index/stl_type_index.hpp:47:
-/Users/Arya/Torsten/cmdstan/stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:132:33: warning: &#39;unary_function&lt;const std::error_category *, unsigned long&gt;&#39; is deprecated [-Wdeprecated-declarations]
-        struct hash_base : std::unary_function&lt;T, std::size_t&gt; {};
-                                ^
-/Users/Arya/Torsten/cmdstan/stan/l</code></pre>
-</div>
-<div class="cell-output cell-output-stderr">
-<pre><code>ib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:692:18: note: in instantiation of template class &#39;boost::hash_detail::hash_base&lt;const std::error_category *&gt;&#39; requested here
-        : public boost::hash_detail::hash_base&lt;T*&gt;
-                 ^
-/Users/Arya/Torsten/cmdstan/stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:420:24: note: in instantiation of template class &#39;boost::hash&lt;const std::error_category *&gt;&#39; requested here
-        boost::hash&lt;T&gt; hasher;
-                       ^
-/Users/Arya/Torsten/cmdstan/stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:551:9: note: in instantiation of function template specialization &#39;boost::hash_combine&lt;const std::error_category *&gt;&#39; requested here
-        hash_combine(seed, &amp;v.category());
-        ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/unary_function.h:23:29: note: &#39;unary_function&lt;const std::error_category *, unsigned long&gt;&#39; has been explicitly marked deprecated here
-struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function
-                            ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:825:41: note: expanded from macro &#39;_LIBCPP_DEPRECATED_IN_CXX11&#39;
-#    define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
-                                        ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro &#39;_LIBCPP_DEPRECATED&#39;
-#      define _LIBCPP_DEPRECATED __attribute__((deprecated))
-                                                ^</code></pre>
-</div>
-<div class="cell-output cell-output-stderr">
-<pre><code>1 warning generated.</code></pre>
-</div>
-<details>
-<summary>Code</summary>
-<div class="sourceCode cell-code" id="cb21"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb21-1"><a href="#cb21-1" aria-hidden="true" tabindex="-1"></a>fit_analytical <span class="ot">&lt;-</span> model_analytical<span class="sc">$</span><span class="fu">sample</span>(</span>
-<span id="cb21-2"><a href="#cb21-2" aria-hidden="true" tabindex="-1"></a>  <span class="at">data =</span> here<span class="sc">::</span><span class="fu">here</span>(<span class="st">&quot;M3/example_models_metrum/pk2cpt/pk2cpt.data.R&quot;</span>), </span>
-<span id="cb21-3"><a href="#cb21-3" aria-hidden="true" tabindex="-1"></a>  <span class="at">init =</span> here<span class="sc">::</span><span class="fu">here</span>(<span class="st">&quot;M3/example_models_metrum/pk2cpt/pk2cpt.init.R&quot;</span>), </span>
-<span id="cb21-4"><a href="#cb21-4" aria-hidden="true" tabindex="-1"></a>  <span class="at">seed =</span> <span class="dv">3191951</span>,</span>
-<span id="cb21-5"><a href="#cb21-5" aria-hidden="true" tabindex="-1"></a>  <span class="at">chains =</span> <span class="dv">1</span>,</span>
-<span id="cb21-6"><a href="#cb21-6" aria-hidden="true" tabindex="-1"></a>  <span class="at">parallel_chains =</span> <span class="dv">1</span>,</span>
-<span id="cb21-7"><a href="#cb21-7" aria-hidden="true" tabindex="-1"></a>  <span class="at">iter_warmup =</span> <span class="dv">500</span>,</span>
-<span id="cb21-8"><a href="#cb21-8" aria-hidden="true" tabindex="-1"></a>  <span class="at">iter_sampling =</span> <span class="dv">1000</span>,</span>
-<span id="cb21-9"><a href="#cb21-9" aria-hidden="true" tabindex="-1"></a>  <span class="at">adapt_delta =</span> <span class="fl">0.80</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<span id="cb17-2"><a href="#cb17-2" aria-hidden="true" tabindex="-1"></a>  here<span class="sc">::</span><span class="fu">here</span>(<span class="st">&quot;M3/example_models_metrum/pk2cpt/pk2cpt.stan&quot;</span>))</span>
+<span id="cb17-3"><a href="#cb17-3" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb17-4"><a href="#cb17-4" aria-hidden="true" tabindex="-1"></a>fit_analytical <span class="ot">&lt;-</span> model_analytical<span class="sc">$</span><span class="fu">sample</span>(</span>
+<span id="cb17-5"><a href="#cb17-5" aria-hidden="true" tabindex="-1"></a>  <span class="at">data =</span> here<span class="sc">::</span><span class="fu">here</span>(<span class="st">&quot;M3/example_models_metrum/pk2cpt/pk2cpt.data.R&quot;</span>), </span>
+<span id="cb17-6"><a href="#cb17-6" aria-hidden="true" tabindex="-1"></a>  <span class="at">init =</span> here<span class="sc">::</span><span class="fu">here</span>(<span class="st">&quot;M3/example_models_metrum/pk2cpt/pk2cpt.init.R&quot;</span>), </span>
+<span id="cb17-7"><a href="#cb17-7" aria-hidden="true" tabindex="-1"></a>  <span class="at">seed =</span> <span class="dv">3191951</span>,</span>
+<span id="cb17-8"><a href="#cb17-8" aria-hidden="true" tabindex="-1"></a>  <span class="at">chains =</span> <span class="dv">1</span>,</span>
+<span id="cb17-9"><a href="#cb17-9" aria-hidden="true" tabindex="-1"></a>  <span class="at">parallel_chains =</span> <span class="dv">1</span>,</span>
+<span id="cb17-10"><a href="#cb17-10" aria-hidden="true" tabindex="-1"></a>  <span class="at">iter_warmup =</span> <span class="dv">500</span>,</span>
+<span id="cb17-11"><a href="#cb17-11" aria-hidden="true" tabindex="-1"></a>  <span class="at">iter_sampling =</span> <span class="dv">1000</span>,</span>
+<span id="cb17-12"><a href="#cb17-12" aria-hidden="true" tabindex="-1"></a>  <span class="at">adapt_delta =</span> <span class="fl">0.80</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 </details>
 <div class="cell-output cell-output-stdout">
 <pre><code>Running MCMC with 1 chain...
@@ -4229,11 +4191,11 @@ <h3 data-number="2.2.1" class="anchored" data-anchor-id="pk2cpt"><span class="he
 Chain 1 Iteration: 1300 / 1500 [ 86%]  (Sampling) 
 Chain 1 Iteration: 1400 / 1500 [ 93%]  (Sampling) 
 Chain 1 Iteration: 1500 / 1500 [100%]  (Sampling) 
-Chain 1 finished in 8.3 seconds.</code></pre>
+Chain 1 finished in 8.0 seconds.</code></pre>
 </div>
 </div>
 </div>
-<p>In particular, <code>Chain 1 Exception: normal_lpdf: Location parameter[1] is -inf, but must be finite!</code> implies that the prediction is 0.</p>
+<p>This seems to work, in contrast to the M3 where we had a vector of zeros.</p>
 </section>
 <section id="pk2cpt_linode" class="level3" data-number="2.2.2">
 <h3 data-number="2.2.2" class="anchored" data-anchor-id="pk2cpt_linode"><span class="header-section-number">2.2.2</span> <code>pk2cpt_linode</code></h3>
@@ -4241,8 +4203,8 @@ <h3 data-number="2.2.2" class="anchored" data-anchor-id="pk2cpt_linode"><span cl
 <div class="cell" data-hash="torsten_test_cache/html/unnamed-chunk-10_638a076275d1ba4722ad894eb6b4f1bd">
 <details>
 <summary>Code</summary>
-<div class="sourceCode cell-code" id="cb45"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb45-1"><a href="#cb45-1" aria-hidden="true" tabindex="-1"></a>model_mat_exp <span class="ot">&lt;-</span> <span class="fu">cmdstan_model</span>(</span>
-<span id="cb45-2"><a href="#cb45-2" aria-hidden="true" tabindex="-1"></a>  here<span class="sc">::</span><span class="fu">here</span>(<span class="st">&quot;M3/example_models_metrum/pk2cpt_linode/pk2cpt_linode.stan&quot;</span>))</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<div class="sourceCode cell-code" id="cb41"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb41-1"><a href="#cb41-1" aria-hidden="true" tabindex="-1"></a>model_mat_exp <span class="ot">&lt;-</span> <span class="fu">cmdstan_model</span>(</span>
+<span id="cb41-2"><a href="#cb41-2" aria-hidden="true" tabindex="-1"></a>  here<span class="sc">::</span><span class="fu">here</span>(<span class="st">&quot;M3/example_models_metrum/pk2cpt_linode/pk2cpt_linode.stan&quot;</span>))</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 </details>
 <div class="cell-output cell-output-stderr">
 <pre><code>In file included from /var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-7921fca1428.hpp:1:
@@ -4292,16 +4254,16 @@ <h3 data-number="2.2.2" class="anchored" data-anchor-id="pk2cpt_linode"><span cl
 </div>
 <details>
 <summary>Code</summary>
-<div class="sourceCode cell-code" id="cb50"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb50-1"><a href="#cb50-1" aria-hidden="true" tabindex="-1"></a>fit_mat_exp <span class="ot">&lt;-</span> model_mat_exp<span class="sc">$</span><span class="fu">sample</span>(</span>
-<span id="cb50-2"><a href="#cb50-2" aria-hidden="true" tabindex="-1"></a>  <span class="at">data =</span> here<span class="sc">::</span><span class="fu">here</span>(<span class="st">&quot;M3/example_models_metrum/pk2cpt_linode/pk2cpt_linode.data.R&quot;</span>), </span>
-<span id="cb50-3"><a href="#cb50-3" aria-hidden="true" tabindex="-1"></a>  <span class="at">init =</span> here<span class="sc">::</span><span class="fu">here</span>(<span class="st">&quot;M3/example_models_metrum/pk2cpt_linode/pk2cpt_linode.init.R&quot;</span>), </span>
-<span id="cb50-4"><a href="#cb50-4" aria-hidden="true" tabindex="-1"></a>  <span class="at">seed =</span> <span class="dv">3191951</span>,</span>
-<span id="cb50-5"><a href="#cb50-5" aria-hidden="true" tabindex="-1"></a>  <span class="at">chains =</span> <span class="dv">4</span>,</span>
-<span id="cb50-6"><a href="#cb50-6" aria-hidden="true" tabindex="-1"></a>  <span class="at">parallel_chains =</span> <span class="dv">4</span>,</span>
-<span id="cb50-7"><a href="#cb50-7" aria-hidden="true" tabindex="-1"></a>  <span class="at">iter_warmup =</span> <span class="dv">500</span>,</span>
-<span id="cb50-8"><a href="#cb50-8" aria-hidden="true" tabindex="-1"></a>  <span class="at">iter_sampling =</span> <span class="dv">1000</span>,</span>
-<span id="cb50-9"><a href="#cb50-9" aria-hidden="true" tabindex="-1"></a>  <span class="at">refresh =</span> <span class="dv">0</span>,</span>
-<span id="cb50-10"><a href="#cb50-10" aria-hidden="true" tabindex="-1"></a>  <span class="at">adapt_delta =</span> <span class="fl">0.80</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<div class="sourceCode cell-code" id="cb46"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb46-1"><a href="#cb46-1" aria-hidden="true" tabindex="-1"></a>fit_mat_exp <span class="ot">&lt;-</span> model_mat_exp<span class="sc">$</span><span class="fu">sample</span>(</span>
+<span id="cb46-2"><a href="#cb46-2" aria-hidden="true" tabindex="-1"></a>  <span class="at">data =</span> here<span class="sc">::</span><span class="fu">here</span>(<span class="st">&quot;M3/example_models_metrum/pk2cpt_linode/pk2cpt_linode.data.R&quot;</span>), </span>
+<span id="cb46-3"><a href="#cb46-3" aria-hidden="true" tabindex="-1"></a>  <span class="at">init =</span> here<span class="sc">::</span><span class="fu">here</span>(<span class="st">&quot;M3/example_models_metrum/pk2cpt_linode/pk2cpt_linode.init.R&quot;</span>), </span>
+<span id="cb46-4"><a href="#cb46-4" aria-hidden="true" tabindex="-1"></a>  <span class="at">seed =</span> <span class="dv">3191951</span>,</span>
+<span id="cb46-5"><a href="#cb46-5" aria-hidden="true" tabindex="-1"></a>  <span class="at">chains =</span> <span class="dv">4</span>,</span>
+<span id="cb46-6"><a href="#cb46-6" aria-hidden="true" tabindex="-1"></a>  <span class="at">parallel_chains =</span> <span class="dv">4</span>,</span>
+<span id="cb46-7"><a href="#cb46-7" aria-hidden="true" tabindex="-1"></a>  <span class="at">iter_warmup =</span> <span class="dv">500</span>,</span>
+<span id="cb46-8"><a href="#cb46-8" aria-hidden="true" tabindex="-1"></a>  <span class="at">iter_sampling =</span> <span class="dv">1000</span>,</span>
+<span id="cb46-9"><a href="#cb46-9" aria-hidden="true" tabindex="-1"></a>  <span class="at">refresh =</span> <span class="dv">0</span>,</span>
+<span id="cb46-10"><a href="#cb46-10" aria-hidden="true" tabindex="-1"></a>  <span class="at">adapt_delta =</span> <span class="fl">0.80</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 </details>
 <div class="cell-output cell-output-stdout">
 <pre><code>Running MCMC with 4 parallel chains...</code></pre>
@@ -4480,7 +4442,7 @@ <h3 data-number="2.2.2" class="anchored" data-anchor-id="pk2cpt_linode"><span cl
 </div>
 </div>
 </div>
-<p>Works fine. I also fit the <code>pk2cpt</code> and <code>pk2cpt_ode</code> data with this model with no issues.</p>
+<p>Works fine.</p>
 </section>
 <section id="pk2cpt_ode" class="level3" data-number="2.2.3">
 <h3 data-number="2.2.3" class="anchored" data-anchor-id="pk2cpt_ode"><span class="header-section-number">2.2.3</span> <code>pk2cpt_ode</code></h3>
@@ -4488,8 +4450,8 @@ <h3 data-number="2.2.3" class="anchored" data-anchor-id="pk2cpt_ode"><span class
 <div class="cell" data-hash="torsten_test_cache/html/unnamed-chunk-11_10565859ccbdac0deb9cd949bf11b015">
 <details>
 <summary>Code</summary>
-<div class="sourceCode cell-code" id="cb107"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb107-1"><a href="#cb107-1" aria-hidden="true" tabindex="-1"></a>model_rk45 <span class="ot">&lt;-</span> <span class="fu">cmdstan_model</span>(</span>
-<span id="cb107-2"><a href="#cb107-2" aria-hidden="true" tabindex="-1"></a>  here<span class="sc">::</span><span class="fu">here</span>(<span class="st">&quot;M3/example_models_metrum/pk2cpt_ode/pk2cpt_ode.stan&quot;</span>))</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<div class="sourceCode cell-code" id="cb103"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb103-1"><a href="#cb103-1" aria-hidden="true" tabindex="-1"></a>model_rk45 <span class="ot">&lt;-</span> <span class="fu">cmdstan_model</span>(</span>
+<span id="cb103-2"><a href="#cb103-2" aria-hidden="true" tabindex="-1"></a>  here<span class="sc">::</span><span class="fu">here</span>(<span class="st">&quot;M3/example_models_metrum/pk2cpt_ode/pk2cpt_ode.stan&quot;</span>))</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 </details>
 <div class="cell-output cell-output-stderr">
 <pre><code>In file included from /var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-792260b064d.hpp:1:
@@ -4539,20 +4501,20 @@ <h3 data-number="2.2.3" class="anchored" data-anchor-id="pk2cpt_ode"><span class
 </div>
 <details>
 <summary>Code</summary>
-<div class="sourceCode cell-code" id="cb112"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb112-1"><a href="#cb112-1" aria-hidden="true" tabindex="-1"></a>stan_data_rk45 <span class="ot">&lt;-</span> rstan<span class="sc">::</span><span class="fu">read_rdump</span>(</span>
-<span id="cb112-2"><a href="#cb112-2" aria-hidden="true" tabindex="-1"></a>  here<span class="sc">::</span><span class="fu">here</span>(<span class="st">&quot;M3/example_models_metrum/pk2cpt_ode/pk2cpt_ode.data.R&quot;</span>))</span>
-<span id="cb112-3"><a href="#cb112-3" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb112-4"><a href="#cb112-4" aria-hidden="true" tabindex="-1"></a>stan_data_rk45<span class="sc">$</span>prior_only <span class="ot">&lt;-</span> <span class="dv">1</span></span>
-<span id="cb112-5"><a href="#cb112-5" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb112-6"><a href="#cb112-6" aria-hidden="true" tabindex="-1"></a>fit_rk45 <span class="ot">&lt;-</span> model_rk45<span class="sc">$</span><span class="fu">sample</span>(</span>
-<span id="cb112-7"><a href="#cb112-7" aria-hidden="true" tabindex="-1"></a>  <span class="at">data =</span> stan_data_rk45, </span>
-<span id="cb112-8"><a href="#cb112-8" aria-hidden="true" tabindex="-1"></a>  <span class="at">init =</span> here<span class="sc">::</span><span class="fu">here</span>(<span class="st">&quot;M3/example_models_metrum/pk2cpt_ode/pk2cpt_ode.init.R&quot;</span>), </span>
-<span id="cb112-9"><a href="#cb112-9" aria-hidden="true" tabindex="-1"></a>  <span class="at">seed =</span> <span class="dv">3191951</span>,</span>
-<span id="cb112-10"><a href="#cb112-10" aria-hidden="true" tabindex="-1"></a>  <span class="at">chains =</span> <span class="dv">1</span>,</span>
-<span id="cb112-11"><a href="#cb112-11" aria-hidden="true" tabindex="-1"></a>  <span class="at">parallel_chains =</span> <span class="dv">1</span>,</span>
-<span id="cb112-12"><a href="#cb112-12" aria-hidden="true" tabindex="-1"></a>  <span class="at">iter_warmup =</span> <span class="dv">1</span>,</span>
-<span id="cb112-13"><a href="#cb112-13" aria-hidden="true" tabindex="-1"></a>  <span class="at">iter_sampling =</span> <span class="dv">1</span>,</span>
-<span id="cb112-14"><a href="#cb112-14" aria-hidden="true" tabindex="-1"></a>  <span class="at">adapt_delta =</span> <span class="fl">0.80</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<div class="sourceCode cell-code" id="cb108"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb108-1"><a href="#cb108-1" aria-hidden="true" tabindex="-1"></a>stan_data_rk45 <span class="ot">&lt;-</span> rstan<span class="sc">::</span><span class="fu">read_rdump</span>(</span>
+<span id="cb108-2"><a href="#cb108-2" aria-hidden="true" tabindex="-1"></a>  here<span class="sc">::</span><span class="fu">here</span>(<span class="st">&quot;M3/example_models_metrum/pk2cpt_ode/pk2cpt_ode.data.R&quot;</span>))</span>
+<span id="cb108-3"><a href="#cb108-3" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb108-4"><a href="#cb108-4" aria-hidden="true" tabindex="-1"></a>stan_data_rk45<span class="sc">$</span>prior_only <span class="ot">&lt;-</span> <span class="dv">1</span></span>
+<span id="cb108-5"><a href="#cb108-5" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb108-6"><a href="#cb108-6" aria-hidden="true" tabindex="-1"></a>fit_rk45 <span class="ot">&lt;-</span> model_rk45<span class="sc">$</span><span class="fu">sample</span>(</span>
+<span id="cb108-7"><a href="#cb108-7" aria-hidden="true" tabindex="-1"></a>  <span class="at">data =</span> stan_data_rk45, </span>
+<span id="cb108-8"><a href="#cb108-8" aria-hidden="true" tabindex="-1"></a>  <span class="at">init =</span> here<span class="sc">::</span><span class="fu">here</span>(<span class="st">&quot;M3/example_models_metrum/pk2cpt_ode/pk2cpt_ode.init.R&quot;</span>), </span>
+<span id="cb108-9"><a href="#cb108-9" aria-hidden="true" tabindex="-1"></a>  <span class="at">seed =</span> <span class="dv">3191951</span>,</span>
+<span id="cb108-10"><a href="#cb108-10" aria-hidden="true" tabindex="-1"></a>  <span class="at">chains =</span> <span class="dv">1</span>,</span>
+<span id="cb108-11"><a href="#cb108-11" aria-hidden="true" tabindex="-1"></a>  <span class="at">parallel_chains =</span> <span class="dv">1</span>,</span>
+<span id="cb108-12"><a href="#cb108-12" aria-hidden="true" tabindex="-1"></a>  <span class="at">iter_warmup =</span> <span class="dv">1</span>,</span>
+<span id="cb108-13"><a href="#cb108-13" aria-hidden="true" tabindex="-1"></a>  <span class="at">iter_sampling =</span> <span class="dv">1</span>,</span>
+<span id="cb108-14"><a href="#cb108-14" aria-hidden="true" tabindex="-1"></a>  <span class="at">adapt_delta =</span> <span class="fl">0.80</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 </details>
 <div class="cell-output cell-output-stdout">
 <pre><code>Running MCMC with 1 chain...
@@ -4627,7 +4589,7 @@ <h3 data-number="2.2.3" class="anchored" data-anchor-id="pk2cpt_ode"><span class
 </div>
 </div>
 </div>
-<p>As you can see, it’s returning a vector of 0s as the solution.</p>
+<p>Works fine, in contrast to the one from the M3, where it was returning a vector of zeros.</p>
 </section>
 </section>
 <section id="fitting-poppk2cpt-from-example-models" class="level2" data-number="2.3">
@@ -4639,8 +4601,8 @@ <h3 data-number="2.3.1" class="anchored" data-anchor-id="analytical-solution"><s
 <div class="cell" data-hash="torsten_test_cache/html/unnamed-chunk-12_aa3fd938a2cc8da7db18b340f0074584">
 <details>
 <summary>Code</summary>
-<div class="sourceCode cell-code" id="cb126"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb126-1"><a href="#cb126-1" aria-hidden="true" tabindex="-1"></a>model <span class="ot">&lt;-</span> <span class="fu">cmdstan_model</span>(</span>
-<span id="cb126-2"><a href="#cb126-2" aria-hidden="true" tabindex="-1"></a>  here<span class="sc">::</span><span class="fu">here</span>(<span class="st">&quot;M3/example_models_metrum/poppk2cpt/poppk2cpt.stan&quot;</span>))</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<div class="sourceCode cell-code" id="cb122"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb122-1"><a href="#cb122-1" aria-hidden="true" tabindex="-1"></a>model <span class="ot">&lt;-</span> <span class="fu">cmdstan_model</span>(</span>
+<span id="cb122-2"><a href="#cb122-2" aria-hidden="true" tabindex="-1"></a>  here<span class="sc">::</span><span class="fu">here</span>(<span class="st">&quot;M3/example_models_metrum/poppk2cpt/poppk2cpt.stan&quot;</span>))</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 </details>
 <div class="cell-output cell-output-stderr">
 <pre><code>In file included from /var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.hpp:1:
@@ -4690,20 +4652,20 @@ <h3 data-number="2.3.1" class="anchored" data-anchor-id="analytical-solution"><s
 </div>
 <details>
 <summary>Code</summary>
-<div class="sourceCode cell-code" id="cb131"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb131-1"><a href="#cb131-1" aria-hidden="true" tabindex="-1"></a>stan_data <span class="ot">&lt;-</span> rstan<span class="sc">::</span><span class="fu">read_rdump</span>(</span>
-<span id="cb131-2"><a href="#cb131-2" aria-hidden="true" tabindex="-1"></a>  here<span class="sc">::</span><span class="fu">here</span>(<span class="st">&quot;M3/example_models_metrum/poppk2cpt/poppk2cpt.data.R&quot;</span>))</span>
-<span id="cb131-3"><a href="#cb131-3" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb131-4"><a href="#cb131-4" aria-hidden="true" tabindex="-1"></a>stan_data<span class="sc">$</span>solver <span class="ot">&lt;-</span> <span class="dv">1</span></span>
-<span id="cb131-5"><a href="#cb131-5" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb131-6"><a href="#cb131-6" aria-hidden="true" tabindex="-1"></a>fit_analytical <span class="ot">&lt;-</span> model<span class="sc">$</span><span class="fu">sample</span>(</span>
-<span id="cb131-7"><a href="#cb131-7" aria-hidden="true" tabindex="-1"></a>  <span class="at">data =</span> stan_data, </span>
-<span id="cb131-8"><a href="#cb131-8" aria-hidden="true" tabindex="-1"></a>  <span class="at">init =</span> here<span class="sc">::</span><span class="fu">here</span>(<span class="st">&quot;M3/example_models_metrum/poppk2cpt/poppk2cpt.init.R&quot;</span>), </span>
-<span id="cb131-9"><a href="#cb131-9" aria-hidden="true" tabindex="-1"></a>  <span class="at">seed =</span> <span class="dv">3191951</span>,</span>
-<span id="cb131-10"><a href="#cb131-10" aria-hidden="true" tabindex="-1"></a>  <span class="at">chains =</span> <span class="dv">4</span>,</span>
-<span id="cb131-11"><a href="#cb131-11" aria-hidden="true" tabindex="-1"></a>  <span class="at">parallel_chains =</span> <span class="dv">4</span>,</span>
-<span id="cb131-12"><a href="#cb131-12" aria-hidden="true" tabindex="-1"></a>  <span class="at">iter_warmup =</span> <span class="dv">500</span>,</span>
-<span id="cb131-13"><a href="#cb131-13" aria-hidden="true" tabindex="-1"></a>  <span class="at">iter_sampling =</span> <span class="dv">500</span>,</span>
-<span id="cb131-14"><a href="#cb131-14" aria-hidden="true" tabindex="-1"></a>  <span class="at">adapt_delta =</span> <span class="fl">0.80</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<div class="sourceCode cell-code" id="cb127"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb127-1"><a href="#cb127-1" aria-hidden="true" tabindex="-1"></a>stan_data <span class="ot">&lt;-</span> rstan<span class="sc">::</span><span class="fu">read_rdump</span>(</span>
+<span id="cb127-2"><a href="#cb127-2" aria-hidden="true" tabindex="-1"></a>  here<span class="sc">::</span><span class="fu">here</span>(<span class="st">&quot;M3/example_models_metrum/poppk2cpt/poppk2cpt.data.R&quot;</span>))</span>
+<span id="cb127-3"><a href="#cb127-3" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb127-4"><a href="#cb127-4" aria-hidden="true" tabindex="-1"></a>stan_data<span class="sc">$</span>solver <span class="ot">&lt;-</span> <span class="dv">1</span></span>
+<span id="cb127-5"><a href="#cb127-5" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb127-6"><a href="#cb127-6" aria-hidden="true" tabindex="-1"></a>fit_analytical <span class="ot">&lt;-</span> model<span class="sc">$</span><span class="fu">sample</span>(</span>
+<span id="cb127-7"><a href="#cb127-7" aria-hidden="true" tabindex="-1"></a>  <span class="at">data =</span> stan_data, </span>
+<span id="cb127-8"><a href="#cb127-8" aria-hidden="true" tabindex="-1"></a>  <span class="at">init =</span> here<span class="sc">::</span><span class="fu">here</span>(<span class="st">&quot;M3/example_models_metrum/poppk2cpt/poppk2cpt.init.R&quot;</span>), </span>
+<span id="cb127-9"><a href="#cb127-9" aria-hidden="true" tabindex="-1"></a>  <span class="at">seed =</span> <span class="dv">3191951</span>,</span>
+<span id="cb127-10"><a href="#cb127-10" aria-hidden="true" tabindex="-1"></a>  <span class="at">chains =</span> <span class="dv">4</span>,</span>
+<span id="cb127-11"><a href="#cb127-11" aria-hidden="true" tabindex="-1"></a>  <span class="at">parallel_chains =</span> <span class="dv">4</span>,</span>
+<span id="cb127-12"><a href="#cb127-12" aria-hidden="true" tabindex="-1"></a>  <span class="at">iter_warmup =</span> <span class="dv">500</span>,</span>
+<span id="cb127-13"><a href="#cb127-13" aria-hidden="true" tabindex="-1"></a>  <span class="at">iter_sampling =</span> <span class="dv">500</span>,</span>
+<span id="cb127-14"><a href="#cb127-14" aria-hidden="true" tabindex="-1"></a>  <span class="at">adapt_delta =</span> <span class="fl">0.80</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 </details>
 <div class="cell-output cell-output-stdout">
 <pre><code>Running MCMC with 4 parallel chains...
@@ -5060,26 +5022,23 @@ <h3 data-number="2.3.1" class="anchored" data-anchor-id="analytical-solution"><s
 <section id="linear-ode-solution" class="level3" data-number="2.3.2">
 <h3 data-number="2.3.2" class="anchored" data-anchor-id="linear-ode-solution"><span class="header-section-number">2.3.2</span> Linear ODE Solution</h3>
 <div class="scrolling_500">
-<div class="cell" data-hash="torsten_test_cache/html/unnamed-chunk-13_c49d3dddd64c26f93ce4ef2a3a1baf68">
+<div class="cell" data-hash="torsten_test_cache/html/unnamed-chunk-13_e318e5e25e36417926e2399a98cfb3de">
 <details>
 <summary>Code</summary>
-<div class="sourceCode cell-code" id="cb230"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb230-1"><a href="#cb230-1" aria-hidden="true" tabindex="-1"></a>stan_data<span class="sc">$</span>solver <span class="ot">&lt;-</span> <span class="dv">2</span></span>
-<span id="cb230-2"><a href="#cb230-2" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb230-3"><a href="#cb230-3" aria-hidden="true" tabindex="-1"></a>fit_mat_exp <span class="ot">&lt;-</span> model<span class="sc">$</span><span class="fu">sample</span>(</span>
-<span id="cb230-4"><a href="#cb230-4" aria-hidden="true" tabindex="-1"></a>  <span class="at">data =</span> stan_data, </span>
-<span id="cb230-5"><a href="#cb230-5" aria-hidden="true" tabindex="-1"></a>  <span class="at">init =</span> here<span class="sc">::</span><span class="fu">here</span>(<span class="st">&quot;M3/example_models_metrum/poppk2cpt/poppk2cpt.init.R&quot;</span>), </span>
-<span id="cb230-6"><a href="#cb230-6" aria-hidden="true" tabindex="-1"></a>  <span class="at">seed =</span> <span class="dv">3191951</span>,</span>
-<span id="cb230-7"><a href="#cb230-7" aria-hidden="true" tabindex="-1"></a>  <span class="at">chains =</span> <span class="dv">4</span>,</span>
-<span id="cb230-8"><a href="#cb230-8" aria-hidden="true" tabindex="-1"></a>  <span class="at">parallel_chains =</span> <span class="dv">4</span>,</span>
-<span id="cb230-9"><a href="#cb230-9" aria-hidden="true" tabindex="-1"></a>  <span class="at">iter_warmup =</span> <span class="dv">1</span>,</span>
-<span id="cb230-10"><a href="#cb230-10" aria-hidden="true" tabindex="-1"></a>  <span class="at">iter_sampling =</span> <span class="dv">1</span>,</span>
-<span id="cb230-11"><a href="#cb230-11" aria-hidden="true" tabindex="-1"></a>  <span class="at">adapt_delta =</span> <span class="fl">0.80</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<div class="sourceCode cell-code" id="cb226"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb226-1"><a href="#cb226-1" aria-hidden="true" tabindex="-1"></a>stan_data<span class="sc">$</span>solver <span class="ot">&lt;-</span> <span class="dv">2</span></span>
+<span id="cb226-2"><a href="#cb226-2" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb226-3"><a href="#cb226-3" aria-hidden="true" tabindex="-1"></a>fit_mat_exp <span class="ot">&lt;-</span> model<span class="sc">$</span><span class="fu">sample</span>(</span>
+<span id="cb226-4"><a href="#cb226-4" aria-hidden="true" tabindex="-1"></a>  <span class="at">data =</span> stan_data, </span>
+<span id="cb226-5"><a href="#cb226-5" aria-hidden="true" tabindex="-1"></a>  <span class="at">init =</span> here<span class="sc">::</span><span class="fu">here</span>(<span class="st">&quot;M3/example_models_metrum/poppk2cpt/poppk2cpt.init.R&quot;</span>), </span>
+<span id="cb226-6"><a href="#cb226-6" aria-hidden="true" tabindex="-1"></a>  <span class="at">seed =</span> <span class="dv">3191951</span>,</span>
+<span id="cb226-7"><a href="#cb226-7" aria-hidden="true" tabindex="-1"></a>  <span class="at">chains =</span> <span class="dv">4</span>,</span>
+<span id="cb226-8"><a href="#cb226-8" aria-hidden="true" tabindex="-1"></a>  <span class="at">parallel_chains =</span> <span class="dv">4</span>,</span>
+<span id="cb226-9"><a href="#cb226-9" aria-hidden="true" tabindex="-1"></a>  <span class="at">iter_warmup =</span> <span class="dv">300</span>,</span>
+<span id="cb226-10"><a href="#cb226-10" aria-hidden="true" tabindex="-1"></a>  <span class="at">iter_sampling =</span> <span class="dv">100</span>,</span>
+<span id="cb226-11"><a href="#cb226-11" aria-hidden="true" tabindex="-1"></a>  <span class="at">adapt_delta =</span> <span class="fl">0.80</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 </details>
 <div class="cell-output cell-output-stdout">
-<pre><code>Running MCMC with 4 parallel chains...
-
-Chain 1 WARNING: No variance estimation is 
-Chain 1          performed for num_warmup &lt; 20 </code></pre>
+<pre><code>Running MCMC with 4 parallel chains...</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
 <pre><code>Chain 1 Warning: file &#39;/Users/Arya/R-Projects/torsten_test/M3/example_models_metrum/poppk2cpt/poppk2cpt.init.R&#39; is being read as an &#39;RDump&#39; file.</code></pre>
@@ -5090,10 +5049,6 @@ <h3 data-number="2.3.2" class="anchored" data-anchor-id="linear-ode-solution"><s
 <div class="cell-output cell-output-stderr">
 <pre><code>Chain 1     Consider saving your data in JSON format instead.</code></pre>
 </div>
-<div class="cell-output cell-output-stdout">
-<pre><code>Chain 2 WARNING: No variance estimation is 
-Chain 2          performed for num_warmup &lt; 20 </code></pre>
-</div>
 <div class="cell-output cell-output-stderr">
 <pre><code>Chain 2 Warning: file &#39;/Users/Arya/R-Projects/torsten_test/M3/example_models_metrum/poppk2cpt/poppk2cpt.init.R&#39; is being read as an &#39;RDump&#39; file.</code></pre>
 </div>
@@ -5103,10 +5058,6 @@ <h3 data-number="2.3.2" class="anchored" data-anchor-id="linear-ode-solution"><s
 <div class="cell-output cell-output-stderr">
 <pre><code>Chain 2     Consider saving your data in JSON format instead.</code></pre>
 </div>
-<div class="cell-output cell-output-stdout">
-<pre><code>Chain 3 WARNING: No variance estimation is 
-Chain 3          performed for num_warmup &lt; 20 </code></pre>
-</div>
 <div class="cell-output cell-output-stderr">
 <pre><code>Chain 3 Warning: file &#39;/Users/Arya/R-Projects/torsten_test/M3/example_models_metrum/poppk2cpt/poppk2cpt.init.R&#39; is being read as an &#39;RDump&#39; file.</code></pre>
 </div>
@@ -5116,10 +5067,6 @@ <h3 data-number="2.3.2" class="anchored" data-anchor-id="linear-ode-solution"><s
 <div class="cell-output cell-output-stderr">
 <pre><code>Chain 3     Consider saving your data in JSON format instead.</code></pre>
 </div>
-<div class="cell-output cell-output-stdout">
-<pre><code>Chain 4 WARNING: No variance estimation is 
-Chain 4          performed for num_warmup &lt; 20 </code></pre>
-</div>
 <div class="cell-output cell-output-stderr">
 <pre><code>Chain 4 Warning: file &#39;/Users/Arya/R-Projects/torsten_test/M3/example_models_metrum/poppk2cpt/poppk2cpt.init.R&#39; is being read as an &#39;RDump&#39; file.</code></pre>
 </div>
@@ -5130,7 +5077,7 @@ <h3 data-number="2.3.2" class="anchored" data-anchor-id="linear-ode-solution"><s
 <pre><code>Chain 4     Consider saving your data in JSON format instead.</code></pre>
 </div>
 <div class="cell-output cell-output-stdout">
-<pre><code>Chain 1 Iteration: 1 / 2 [ 50%]  (Warmup) </code></pre>
+<pre><code>Chain 1 Iteration:   1 / 400 [  0%]  (Warmup) </code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
 <pre><code>Chain 1 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
@@ -5162,9 +5109,6 @@ <h3 data-number="2.3.2" class="anchored" data-anchor-id="linear-ode-solution"><s
 <div class="cell-output cell-output-stderr">
 <pre><code>Chain 1 </code></pre>
 </div>
-<div class="cell-output cell-output-stdout">
-<pre><code>Chain 2 Iteration: 1 / 2 [ 50%]  (Warmup) </code></pre>
-</div>
 <div class="cell-output cell-output-stderr">
 <pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
 </div>
@@ -5211,8 +5155,7 @@ <h3 data-number="2.3.2" class="anchored" data-anchor-id="linear-ode-solution"><s
 <pre><code>Chain 2 </code></pre>
 </div>
 <div class="cell-output cell-output-stdout">
-<pre><code>Chain 3 Iteration: 1 / 2 [ 50%]  (Warmup) 
-Chain 3 Iteration: 2 / 2 [100%]  (Sampling) </code></pre>
+<pre><code>Chain 3 Iteration:   1 / 400 [  0%]  (Warmup) </code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
 <pre><code>Chain 3 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
@@ -5244,9 +5187,6 @@ <h3 data-number="2.3.2" class="anchored" data-anchor-id="linear-ode-solution"><s
 <div class="cell-output cell-output-stderr">
 <pre><code>Chain 3 </code></pre>
 </div>
-<div class="cell-output cell-output-stdout">
-<pre><code>Chain 4 Iteration: 1 / 2 [ 50%]  (Warmup) </code></pre>
-</div>
 <div class="cell-output cell-output-stderr">
 <pre><code>Chain 4 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
 </div>
@@ -5292,9 +5232,6 @@ <h3 data-number="2.3.2" class="anchored" data-anchor-id="linear-ode-solution"><s
 <div class="cell-output cell-output-stderr">
 <pre><code>Chain 4 </code></pre>
 </div>
-<div class="cell-output cell-output-stdout">
-<pre><code>Chain 1 Iteration: 2 / 2 [100%]  (Sampling) </code></pre>
-</div>
 <div class="cell-output cell-output-stderr">
 <pre><code>Chain 1 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
 </div>
@@ -5311,31 +5248,28 @@ <h3 data-number="2.3.2" class="anchored" data-anchor-id="linear-ode-solution"><s
 <pre><code>Chain 1 </code></pre>
 </div>
 <div class="cell-output cell-output-stdout">
-<pre><code>Chain 2 Iteration: 2 / 2 [100%]  (Sampling) </code></pre>
-</div>
-<div class="cell-output cell-output-stderr">
-<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 324] is -2.06377e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+<pre><code>Chain 2 Iteration:   1 / 400 [  0%]  (Warmup) </code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+<pre><code>Chain 3 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 2 Exception: normal_lpdf: Location parameter[1] is -inf, but must be finite! (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 176, column 2 to column 40)</code></pre>
+<pre><code>Chain 3 Exception: poppk2cpt_model_namespace::log_prob: thetaM[1, 3] is nan, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 81, column 2 to column 44)</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+<pre><code>Chain 3 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+<pre><code>Chain 3 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 2 </code></pre>
+<pre><code>Chain 3 </code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
 <pre><code>Chain 3 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 3 Exception: poppk2cpt_model_namespace::log_prob: thetaM[1, 3] is nan, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 81, column 2 to column 44)</code></pre>
+<pre><code>Chain 3 Exception: normal_lpdf: Location parameter[1] is -inf, but must be finite! (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 176, column 2 to column 40)</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
 <pre><code>Chain 3 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
@@ -5347,7 +5281,7 @@ <h3 data-number="2.3.2" class="anchored" data-anchor-id="linear-ode-solution"><s
 <pre><code>Chain 3 </code></pre>
 </div>
 <div class="cell-output cell-output-stdout">
-<pre><code>Chain 4 Iteration: 2 / 2 [100%]  (Sampling) </code></pre>
+<pre><code>Chain 4 Iteration:   1 / 400 [  0%]  (Warmup) </code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
 <pre><code>Chain 4 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
@@ -5364,105 +5298,86 @@ <h3 data-number="2.3.2" class="anchored" data-anchor-id="linear-ode-solution"><s
 <div class="cell-output cell-output-stderr">
 <pre><code>Chain 4 </code></pre>
 </div>
-<div class="cell-output cell-output-stdout">
-<pre><code>Chain 1 finished in 0.1 seconds.
-Chain 2 finished in 0.1 seconds.
-Chain 3 finished in 0.0 seconds.
-Chain 4 finished in 0.0 seconds.
-
-All 4 chains finished successfully.
-Mean chain execution time: 0.1 seconds.
-Total execution time: 0.4 seconds.</code></pre>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 1 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Warning: 4 of 4 (100.0%) transitions ended with a divergence.
-See https://mc-stan.org/misc/warnings for details.</code></pre>
+<pre><code>Chain 1 Exception: normal_lpdf: Location parameter[1] is -inf, but must be finite! (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 176, column 2 to column 40)</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Warning: E-BFMI not computed because it is undefined for posterior chains of
-length less than 3.</code></pre>
+<pre><code>Chain 1 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
 </div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 1 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
 </div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 1 </code></pre>
 </div>
-<p>This one doesn’t work.</p>
-</section>
-<section id="general-ode-solution" class="level3" data-number="2.3.3">
-<h3 data-number="2.3.3" class="anchored" data-anchor-id="general-ode-solution"><span class="header-section-number">2.3.3</span> General ODE Solution</h3>
-<div class="scrolling_500">
-<div class="cell" data-hash="torsten_test_cache/html/unnamed-chunk-14_a612bf12bf9223eb5c0a9462682f3242">
-<details>
-<summary>Code</summary>
-<div class="sourceCode cell-code" id="cb328"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb328-1"><a href="#cb328-1" aria-hidden="true" tabindex="-1"></a>stan_data<span class="sc">$</span>solver <span class="ot">&lt;-</span> <span class="dv">3</span></span>
-<span id="cb328-2"><a href="#cb328-2" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb328-3"><a href="#cb328-3" aria-hidden="true" tabindex="-1"></a>fit_rk45 <span class="ot">&lt;-</span> model<span class="sc">$</span><span class="fu">sample</span>(</span>
-<span id="cb328-4"><a href="#cb328-4" aria-hidden="true" tabindex="-1"></a>  <span class="at">data =</span> stan_data, </span>
-<span id="cb328-5"><a href="#cb328-5" aria-hidden="true" tabindex="-1"></a>  <span class="at">init =</span> here<span class="sc">::</span><span class="fu">here</span>(<span class="st">&quot;M3/example_models_metrum/poppk2cpt/poppk2cpt.init.R&quot;</span>), </span>
-<span id="cb328-6"><a href="#cb328-6" aria-hidden="true" tabindex="-1"></a>  <span class="at">seed =</span> <span class="dv">3191951</span>,</span>
-<span id="cb328-7"><a href="#cb328-7" aria-hidden="true" tabindex="-1"></a>  <span class="at">chains =</span> <span class="dv">4</span>,</span>
-<span id="cb328-8"><a href="#cb328-8" aria-hidden="true" tabindex="-1"></a>  <span class="at">parallel_chains =</span> <span class="dv">4</span>,</span>
-<span id="cb328-9"><a href="#cb328-9" aria-hidden="true" tabindex="-1"></a>  <span class="at">iter_warmup =</span> <span class="dv">300</span>,</span>
-<span id="cb328-10"><a href="#cb328-10" aria-hidden="true" tabindex="-1"></a>  <span class="at">iter_sampling =</span> <span class="dv">100</span>,</span>
-<span id="cb328-11"><a href="#cb328-11" aria-hidden="true" tabindex="-1"></a>  <span class="at">adapt_delta =</span> <span class="fl">0.80</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
-</details>
-<div class="cell-output cell-output-stdout">
-<pre><code>Running MCMC with 4 parallel chains...</code></pre>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 1 Warning: file &#39;/Users/Arya/R-Projects/torsten_test/M3/example_models_metrum/poppk2cpt/poppk2cpt.init.R&#39; is being read as an &#39;RDump&#39; file.</code></pre>
+<pre><code>Chain 2 Exception: normal_lpdf: Location parameter[1] is -inf, but must be finite! (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 176, column 2 to column 40)</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 1     This format is deprecated and will not receive new features.</code></pre>
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 1     Consider saving your data in JSON format instead.</code></pre>
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 2 Warning: file &#39;/Users/Arya/R-Projects/torsten_test/M3/example_models_metrum/poppk2cpt/poppk2cpt.init.R&#39; is being read as an &#39;RDump&#39; file.</code></pre>
+<pre><code>Chain 2 </code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 2     This format is deprecated and will not receive new features.</code></pre>
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 2     Consider saving your data in JSON format instead.</code></pre>
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.12934e-12, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 3 Warning: file &#39;/Users/Arya/R-Projects/torsten_test/M3/example_models_metrum/poppk2cpt/poppk2cpt.init.R&#39; is being read as an &#39;RDump&#39; file.</code></pre>
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 3     This format is deprecated and will not receive new features.</code></pre>
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 3     Consider saving your data in JSON format instead.</code></pre>
+<pre><code>Chain 2 </code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 4 Warning: file &#39;/Users/Arya/R-Projects/torsten_test/M3/example_models_metrum/poppk2cpt/poppk2cpt.init.R&#39; is being read as an &#39;RDump&#39; file.</code></pre>
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 4     This format is deprecated and will not receive new features.</code></pre>
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -4.79036e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 4     Consider saving your data in JSON format instead.</code></pre>
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 1 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 1 Exception: Max number of iterations exceeded (1000000). (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 140, column 6 to line 151, column 46)</code></pre>
+<pre><code>Chain 2 </code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 1 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 1 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -4.50422e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 1 </code></pre>
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
 <pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 2 Exception: Max number of iterations exceeded (1000000). (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 140, column 6 to line 151, column 46)</code></pre>
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -1.49641e-12, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
 <pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
@@ -5474,55 +5389,55 @@ <h3 data-number="2.3.3" class="anchored" data-anchor-id="general-ode-solution"><
 <pre><code>Chain 2 </code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 3 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 3 Exception: Max number of iterations exceeded (1000000). (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 140, column 6 to line 151, column 46)</code></pre>
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -8.76041e-14, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 3 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 3 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 3 </code></pre>
+<pre><code>Chain 2 </code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 4 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 4 Exception: Max number of iterations exceeded (1000000). (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 140, column 6 to line 151, column 46)</code></pre>
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -8.55239e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 4 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 4 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 4 </code></pre>
+<pre><code>Chain 2 </code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 1 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 1 Exception: Max number of iterations exceeded (1000000). (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 140, column 6 to line 151, column 46)</code></pre>
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -8.55242e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 1 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 1 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 1 </code></pre>
+<pre><code>Chain 2 </code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
 <pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 2 Exception: Max number of iterations exceeded (1000000). (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 140, column 6 to line 151, column 46)</code></pre>
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.38163e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
 <pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
@@ -5534,25 +5449,25 @@ <h3 data-number="2.3.3" class="anchored" data-anchor-id="general-ode-solution"><
 <pre><code>Chain 2 </code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 3 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 3 Exception: Max number of iterations exceeded (1000000). (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 140, column 6 to line 151, column 46)</code></pre>
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -6.81513e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 3 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 3 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 3 </code></pre>
+<pre><code>Chain 2 </code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
 <pre><code>Chain 4 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 4 Exception: Max number of iterations exceeded (1000000). (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 140, column 6 to line 151, column 46)</code></pre>
+<pre><code>Chain 4 Exception: normal_lpdf: Location parameter[1] is -inf, but must be finite! (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 176, column 2 to column 40)</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
 <pre><code>Chain 4 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
@@ -5564,25 +5479,25 @@ <h3 data-number="2.3.3" class="anchored" data-anchor-id="general-ode-solution"><
 <pre><code>Chain 4 </code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 3 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 3 Exception: Max number of iterations exceeded (1000000). (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 140, column 6 to line 151, column 46)</code></pre>
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -7.91948e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 3 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 3 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 3 </code></pre>
+<pre><code>Chain 2 </code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
 <pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 2 Exception: Max number of iterations exceeded (1000000). (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 140, column 6 to line 151, column 46)</code></pre>
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -4.50602e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
 <pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
@@ -5593,78 +5508,71 @@ <h3 data-number="2.3.3" class="anchored" data-anchor-id="general-ode-solution"><
 <div class="cell-output cell-output-stderr">
 <pre><code>Chain 2 </code></pre>
 </div>
-<div class="cell-output cell-output-stdout">
-<pre><code>Chain 3 Iteration:   1 / 400 [  0%]  (Warmup) 
-Chain 2 Iteration:   1 / 400 [  0%]  (Warmup) </code></pre>
-</div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 3 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 3 Exception: PMX Variadic ODE System: initial state[2] is nan, but must be finite! (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 140, column 6 to line 151, column 46)</code></pre>
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.74077e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 3 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 3 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 3 </code></pre>
+<pre><code>Chain 2 </code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 1 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 1 Exception: Max number of iterations exceeded (1000000). (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 140, column 6 to line 151, column 46)</code></pre>
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -2.19468e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 1 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 1 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 1 </code></pre>
-</div>
-<div class="cell-output cell-output-stdout">
-<pre><code>Chain 1 Iteration:   1 / 400 [  0%]  (Warmup) </code></pre>
+<pre><code>Chain 2 </code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 1 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 1 Exception: PMX Variadic ODE System: initial state[2] is nan, but must be finite! (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 140, column 6 to line 151, column 46)</code></pre>
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -8.55241e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 1 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 1 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 1 </code></pre>
+<pre><code>Chain 2 </code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 3 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 3 Exception: Max number of iterations exceeded (1000000). (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 140, column 6 to line 151, column 46)</code></pre>
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.38163e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 3 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 3 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 3 </code></pre>
+<pre><code>Chain 2 </code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
 <pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 2 Exception: Max number of iterations exceeded (1000000). (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 140, column 6 to line 151, column 46)</code></pre>
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -8.91155e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
 <pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
@@ -5676,2443 +5584,6505 @@ <h3 data-number="2.3.3" class="anchored" data-anchor-id="general-ode-solution"><
 <pre><code>Chain 2 </code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 1 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 1 Exception: Max number of iterations exceeded (1000000). (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 140, column 6 to line 151, column 46)</code></pre>
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -4.50602e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 1 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 1 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 1 </code></pre>
+<pre><code>Chain 2 </code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 4 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 4 Exception: Max number of iterations exceeded (1000000). (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 140, column 6 to line 151, column 46)</code></pre>
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -4.60644e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 4 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 4 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 4 </code></pre>
-</div>
-<div class="cell-output cell-output-stdout">
-<pre><code>Chain 4 Iteration:   1 / 400 [  0%]  (Warmup) </code></pre>
+<pre><code>Chain 2 </code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 4 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 4 Exception: PMX Variadic ODE System: initial state[2] is nan, but must be finite! (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 140, column 6 to line 151, column 46)</code></pre>
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -6.81513e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 4 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 4 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 4 </code></pre>
+<pre><code>Chain 2 </code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 4 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 4 Exception: PMX Variadic ODE System: initial state[2] is nan, but must be finite! (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 140, column 6 to line 151, column 46)</code></pre>
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.38163e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 4 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 4 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>Chain 4 </code></pre>
+<pre><code>Chain 2 </code></pre>
 </div>
-<div class="cell-output cell-output-stdout">
-<pre><code>Chain 1 Iteration: 100 / 400 [ 25%]  (Warmup) 
-Chain 3 Iteration: 100 / 400 [ 25%]  (Warmup) 
-Chain 2 Iteration: 100 / 400 [ 25%]  (Warmup) 
-Chain 1 Iteration: 200 / 400 [ 50%]  (Warmup) 
-Chain 4 Iteration: 100 / 400 [ 25%]  (Warmup) 
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-Chain 1 Iteration: 400 / 400 [100%]  (Sampling) 
-Chain 1 finished in 3834.0 seconds.
-Chain 4 Iteration: 300 / 400 [ 75%]  (Warmup) 
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-Chain 3 Iteration: 300 / 400 [ 75%]  (Warmup) 
-Chain 3 Iteration: 301 / 400 [ 75%]  (Sampling) 
-Chain 2 Iteration: 400 / 400 [100%]  (Sampling) 
-Chain 2 finished in 3922.8 seconds.
-Chain 4 Iteration: 400 / 400 [100%]  (Sampling) 
-Chain 4 finished in 3916.5 seconds.
-Chain 3 Iteration: 400 / 400 [100%]  (Sampling) 
-Chain 3 finished in 3996.8 seconds.
-
-All 4 chains finished successfully.
-Mean chain execution time: 3917.5 seconds.
-Total execution time: 4013.2 seconds.</code></pre>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
 </div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -4.60644e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
 </div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
 </div>
-<p>This one works.</p>
-</section>
-</section>
-<section id="fitting-poppk2cpt-from-example-models-with-my-own-models" class="level2" data-number="2.4">
-<h2 data-number="2.4" class="anchored" data-anchor-id="fitting-poppk2cpt-from-example-models-with-my-own-models"><span class="header-section-number">2.4</span> Fitting <code>poppk2cpt</code> from <code>example-models/</code> With My Own Models</h2>
-<p>I’ve previously written this model to fit with the analytical, linear ODE, and general ODE solutions with proportional error, so I’m just going to use that, but it shouldn’t make a difference.</p>
-<section id="data-wrangling" class="level3" data-number="2.4.1">
-<h3 data-number="2.4.1" class="anchored" data-anchor-id="data-wrangling"><span class="header-section-number">2.4.1</span> Data Wrangling</h3>
-<p>My models should work from a NONMEM dataset in .csv format, so I’ll wrangle the data into something like that first.</p>
-<div class="cell">
-<details>
-<summary>Code</summary>
-<div class="sourceCode cell-code" id="cb441"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb441-1"><a href="#cb441-1" aria-hidden="true" tabindex="-1"></a>dv <span class="ot">&lt;-</span> <span class="fu">rep</span>(<span class="cn">NA</span>, stan_data<span class="sc">$</span>nt)</span>
-<span id="cb441-2"><a href="#cb441-2" aria-hidden="true" tabindex="-1"></a>dv[stan_data<span class="sc">$</span>iObs] <span class="ot">&lt;-</span> stan_data<span class="sc">$</span>cObs</span>
-<span id="cb441-3"><a href="#cb441-3" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb441-4"><a href="#cb441-4" aria-hidden="true" tabindex="-1"></a>nonmem_data <span class="ot">&lt;-</span> <span class="fu">with</span>(stan_data, </span>
-<span id="cb441-5"><a href="#cb441-5" aria-hidden="true" tabindex="-1"></a>                    <span class="fu">tibble</span>(<span class="at">ID =</span> <span class="fu">rep</span>(<span class="dv">1</span><span class="sc">:</span>stan_data<span class="sc">$</span>nSubj, <span class="at">each =</span> <span class="dv">54</span>),</span>
-<span id="cb441-6"><a href="#cb441-6" aria-hidden="true" tabindex="-1"></a>                           <span class="at">amt =</span> amt, </span>
-<span id="cb441-7"><a href="#cb441-7" aria-hidden="true" tabindex="-1"></a>                           <span class="at">ii =</span> ii,</span>
-<span id="cb441-8"><a href="#cb441-8" aria-hidden="true" tabindex="-1"></a>                           <span class="at">addl =</span> addl,</span>
-<span id="cb441-9"><a href="#cb441-9" aria-hidden="true" tabindex="-1"></a>                           <span class="at">rate =</span> rate,</span>
-<span id="cb441-10"><a href="#cb441-10" aria-hidden="true" tabindex="-1"></a>                           <span class="at">cmt =</span> cmt,</span>
-<span id="cb441-11"><a href="#cb441-11" aria-hidden="true" tabindex="-1"></a>                           <span class="at">evid =</span> evid, </span>
-<span id="cb441-12"><a href="#cb441-12" aria-hidden="true" tabindex="-1"></a>                           <span class="at">ss =</span> ss,</span>
-<span id="cb441-13"><a href="#cb441-13" aria-hidden="true" tabindex="-1"></a>                           <span class="at">lloq =</span> <span class="dv">0</span>,</span>
-<span id="cb441-14"><a href="#cb441-14" aria-hidden="true" tabindex="-1"></a>                           <span class="at">bloq =</span> <span class="dv">0</span>,</span>
-<span id="cb441-15"><a href="#cb441-15" aria-hidden="true" tabindex="-1"></a>                           <span class="at">time =</span> time,</span>
-<span id="cb441-16"><a href="#cb441-16" aria-hidden="true" tabindex="-1"></a>                           <span class="at">DV =</span> dv)) <span class="sc">%&gt;%</span> </span>
-<span id="cb441-17"><a href="#cb441-17" aria-hidden="true" tabindex="-1"></a>  <span class="fu">mutate</span>(<span class="at">DV =</span> <span class="fu">if_else</span>(<span class="fu">is.na</span>(DV), <span class="dv">5555555</span>, DV),    <span class="co"># This value can be anything except NA. It&#39;ll be indexed away </span></span>
-<span id="cb441-18"><a href="#cb441-18" aria-hidden="true" tabindex="-1"></a>         <span class="at">bloq =</span> <span class="fu">if_else</span>(<span class="fu">is.na</span>(bloq), <span class="sc">-</span><span class="dv">999</span>, bloq)) <span class="co"># This value can be anything except NA. It&#39;ll be indexed away </span></span>
-<span id="cb441-19"><a href="#cb441-19" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb441-20"><a href="#cb441-20" aria-hidden="true" tabindex="-1"></a>n_subjects <span class="ot">&lt;-</span> nonmem_data <span class="sc">%&gt;%</span>  <span class="co"># number of individuals</span></span>
-<span id="cb441-21"><a href="#cb441-21" aria-hidden="true" tabindex="-1"></a>  <span class="fu">distinct</span>(ID) <span class="sc">%&gt;%</span></span>
-<span id="cb441-22"><a href="#cb441-22" aria-hidden="true" tabindex="-1"></a>  <span class="fu">count</span>() <span class="sc">%&gt;%</span></span>
-<span id="cb441-23"><a href="#cb441-23" aria-hidden="true" tabindex="-1"></a>  <span class="fu">deframe</span>()</span>
-<span id="cb441-24"><a href="#cb441-24" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb441-25"><a href="#cb441-25" aria-hidden="true" tabindex="-1"></a>n_total <span class="ot">&lt;-</span> <span class="fu">nrow</span>(nonmem_data)   <span class="co"># total number of records</span></span>
-<span id="cb441-26"><a href="#cb441-26" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb441-27"><a href="#cb441-27" aria-hidden="true" tabindex="-1"></a>i_obs <span class="ot">&lt;-</span> nonmem_data <span class="sc">%&gt;%</span></span>
-<span id="cb441-28"><a href="#cb441-28" aria-hidden="true" tabindex="-1"></a>  <span class="fu">mutate</span>(<span class="at">row_num =</span> <span class="dv">1</span><span class="sc">:</span><span class="fu">n</span>()) <span class="sc">%&gt;%</span></span>
-<span id="cb441-29"><a href="#cb441-29" aria-hidden="true" tabindex="-1"></a>  <span class="fu">filter</span>(evid <span class="sc">==</span> <span class="dv">0</span>) <span class="sc">%&gt;%</span></span>
-<span id="cb441-30"><a href="#cb441-30" aria-hidden="true" tabindex="-1"></a>  <span class="fu">select</span>(row_num) <span class="sc">%&gt;%</span></span>
-<span id="cb441-31"><a href="#cb441-31" aria-hidden="true" tabindex="-1"></a>  <span class="fu">deframe</span>()</span>
-<span id="cb441-32"><a href="#cb441-32" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb441-33"><a href="#cb441-33" aria-hidden="true" tabindex="-1"></a>n_obs <span class="ot">&lt;-</span> <span class="fu">length</span>(i_obs)</span>
-<span id="cb441-34"><a href="#cb441-34" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb441-35"><a href="#cb441-35" aria-hidden="true" tabindex="-1"></a>subj_start <span class="ot">&lt;-</span> nonmem_data <span class="sc">%&gt;%</span></span>
-<span id="cb441-36"><a href="#cb441-36" aria-hidden="true" tabindex="-1"></a>  <span class="fu">mutate</span>(<span class="at">row_num =</span> <span class="dv">1</span><span class="sc">:</span><span class="fu">n</span>()) <span class="sc">%&gt;%</span></span>
-<span id="cb441-37"><a href="#cb441-37" aria-hidden="true" tabindex="-1"></a>  <span class="fu">group_by</span>(ID) <span class="sc">%&gt;%</span></span>
-<span id="cb441-38"><a href="#cb441-38" aria-hidden="true" tabindex="-1"></a>  <span class="fu">slice_head</span>(<span class="at">n =</span> <span class="dv">1</span>) <span class="sc">%&gt;%</span></span>
-<span id="cb441-39"><a href="#cb441-39" aria-hidden="true" tabindex="-1"></a>  <span class="fu">ungroup</span>() <span class="sc">%&gt;%</span></span>
-<span id="cb441-40"><a href="#cb441-40" aria-hidden="true" tabindex="-1"></a>  <span class="fu">select</span>(row_num) <span class="sc">%&gt;%</span></span>
-<span id="cb441-41"><a href="#cb441-41" aria-hidden="true" tabindex="-1"></a>  <span class="fu">deframe</span>()</span>
-<span id="cb441-42"><a href="#cb441-42" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb441-43"><a href="#cb441-43" aria-hidden="true" tabindex="-1"></a>subj_end <span class="ot">&lt;-</span> <span class="fu">c</span>(subj_start[<span class="sc">-</span><span class="dv">1</span>] <span class="sc">-</span> <span class="dv">1</span>, n_total)</span>
-<span id="cb441-44"><a href="#cb441-44" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb441-45"><a href="#cb441-45" aria-hidden="true" tabindex="-1"></a>stan_data <span class="ot">&lt;-</span> <span class="fu">list</span>(<span class="at">n_subjects =</span> n_subjects,</span>
-<span id="cb441-46"><a href="#cb441-46" aria-hidden="true" tabindex="-1"></a>                  <span class="at">n_total =</span> n_total,</span>
-<span id="cb441-47"><a href="#cb441-47" aria-hidden="true" tabindex="-1"></a>                  <span class="at">n_obs =</span> n_obs,</span>
-<span id="cb441-48"><a href="#cb441-48" aria-hidden="true" tabindex="-1"></a>                  <span class="at">i_obs =</span> i_obs,</span>
-<span id="cb441-49"><a href="#cb441-49" aria-hidden="true" tabindex="-1"></a>                  <span class="at">ID =</span> nonmem_data<span class="sc">$</span>ID,</span>
-<span id="cb441-50"><a href="#cb441-50" aria-hidden="true" tabindex="-1"></a>                  <span class="at">amt =</span> nonmem_data<span class="sc">$</span>amt,</span>
-<span id="cb441-51"><a href="#cb441-51" aria-hidden="true" tabindex="-1"></a>                  <span class="at">cmt =</span> nonmem_data<span class="sc">$</span>cmt,</span>
-<span id="cb441-52"><a href="#cb441-52" aria-hidden="true" tabindex="-1"></a>                  <span class="at">evid =</span> nonmem_data<span class="sc">$</span>evid,</span>
-<span id="cb441-53"><a href="#cb441-53" aria-hidden="true" tabindex="-1"></a>                  <span class="at">rate =</span> nonmem_data<span class="sc">$</span>rate,</span>
-<span id="cb441-54"><a href="#cb441-54" aria-hidden="true" tabindex="-1"></a>                  <span class="at">ii =</span> nonmem_data<span class="sc">$</span>ii,</span>
-<span id="cb441-55"><a href="#cb441-55" aria-hidden="true" tabindex="-1"></a>                  <span class="at">addl =</span> nonmem_data<span class="sc">$</span>addl,</span>
-<span id="cb441-56"><a href="#cb441-56" aria-hidden="true" tabindex="-1"></a>                  <span class="at">ss =</span> nonmem_data<span class="sc">$</span>ss,</span>
-<span id="cb441-57"><a href="#cb441-57" aria-hidden="true" tabindex="-1"></a>                  <span class="at">time =</span> nonmem_data<span class="sc">$</span>time,</span>
-<span id="cb441-58"><a href="#cb441-58" aria-hidden="true" tabindex="-1"></a>                  <span class="at">dv =</span> nonmem_data<span class="sc">$</span>DV,</span>
-<span id="cb441-59"><a href="#cb441-59" aria-hidden="true" tabindex="-1"></a>                  <span class="at">subj_start =</span> subj_start,</span>
-<span id="cb441-60"><a href="#cb441-60" aria-hidden="true" tabindex="-1"></a>                  <span class="at">subj_end =</span> subj_end,</span>
-<span id="cb441-61"><a href="#cb441-61" aria-hidden="true" tabindex="-1"></a>                  <span class="at">lloq =</span> nonmem_data<span class="sc">$</span>lloq,</span>
-<span id="cb441-62"><a href="#cb441-62" aria-hidden="true" tabindex="-1"></a>                  <span class="at">bloq =</span> nonmem_data<span class="sc">$</span>bloq,</span>
-<span id="cb441-63"><a href="#cb441-63" aria-hidden="true" tabindex="-1"></a>                  <span class="at">location_tvcl =</span> <span class="fl">0.75</span>,</span>
-<span id="cb441-64"><a href="#cb441-64" aria-hidden="true" tabindex="-1"></a>                  <span class="at">location_tvvc =</span> <span class="dv">18</span>,</span>
-<span id="cb441-65"><a href="#cb441-65" aria-hidden="true" tabindex="-1"></a>                  <span class="at">location_tvq =</span> <span class="dv">3</span>,</span>
-<span id="cb441-66"><a href="#cb441-66" aria-hidden="true" tabindex="-1"></a>                  <span class="at">location_tvvp =</span> <span class="dv">35</span>,</span>
-<span id="cb441-67"><a href="#cb441-67" aria-hidden="true" tabindex="-1"></a>                  <span class="at">location_tvka =</span> <span class="fl">0.8</span>,</span>
-<span id="cb441-68"><a href="#cb441-68" aria-hidden="true" tabindex="-1"></a>                  <span class="at">scale_tvcl =</span> <span class="dv">1</span>,</span>
-<span id="cb441-69"><a href="#cb441-69" aria-hidden="true" tabindex="-1"></a>                  <span class="at">scale_tvvc =</span> <span class="dv">1</span>,</span>
-<span id="cb441-70"><a href="#cb441-70" aria-hidden="true" tabindex="-1"></a>                  <span class="at">scale_tvq =</span> <span class="dv">1</span>,</span>
-<span id="cb441-71"><a href="#cb441-71" aria-hidden="true" tabindex="-1"></a>                  <span class="at">scale_tvvp =</span> <span class="dv">1</span>,</span>
-<span id="cb441-72"><a href="#cb441-72" aria-hidden="true" tabindex="-1"></a>                  <span class="at">scale_tvka =</span> <span class="dv">1</span>,</span>
-<span id="cb441-73"><a href="#cb441-73" aria-hidden="true" tabindex="-1"></a>                  <span class="at">scale_omega_cl =</span> <span class="fl">0.4</span>,</span>
-<span id="cb441-74"><a href="#cb441-74" aria-hidden="true" tabindex="-1"></a>                  <span class="at">scale_omega_vc =</span> <span class="fl">0.4</span>,</span>
-<span id="cb441-75"><a href="#cb441-75" aria-hidden="true" tabindex="-1"></a>                  <span class="at">scale_omega_q =</span> <span class="fl">0.4</span>,</span>
-<span id="cb441-76"><a href="#cb441-76" aria-hidden="true" tabindex="-1"></a>                  <span class="at">scale_omega_vp =</span> <span class="fl">0.4</span>,</span>
-<span id="cb441-77"><a href="#cb441-77" aria-hidden="true" tabindex="-1"></a>                  <span class="at">scale_omega_ka =</span> <span class="fl">0.4</span>,</span>
-<span id="cb441-78"><a href="#cb441-78" aria-hidden="true" tabindex="-1"></a>                  <span class="at">lkj_df_omega =</span> <span class="dv">2</span>,</span>
-<span id="cb441-79"><a href="#cb441-79" aria-hidden="true" tabindex="-1"></a>                  <span class="at">scale_sigma_p =</span> <span class="fl">0.5</span>,</span>
-<span id="cb441-80"><a href="#cb441-80" aria-hidden="true" tabindex="-1"></a>                  <span class="at">prior_only =</span> <span class="dv">0</span>)</span>
-<span id="cb441-81"><a href="#cb441-81" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb441-82"><a href="#cb441-82" aria-hidden="true" tabindex="-1"></a>model <span class="ot">&lt;-</span> <span class="fu">cmdstan_model</span>(</span>
-<span id="cb441-83"><a href="#cb441-83" aria-hidden="true" tabindex="-1"></a>  here<span class="sc">::</span><span class="fu">here</span>(<span class="st">&quot;M3/depot_2cmt_linear/Stan/Fit/depot_2cmt_prop_all_solvers.stan&quot;</span>),</span>
-<span id="cb441-84"><a href="#cb441-84" aria-hidden="true" tabindex="-1"></a>  <span class="at">cpp_options =</span> <span class="fu">list</span>(<span class="at">stan_threads =</span> <span class="cn">TRUE</span>))</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
-</details>
 <div class="cell-output cell-output-stderr">
-<pre><code>In file included from src/cmdstan/main.cpp:1:
-In file included from src/cmdstan/command.hpp:4:
-In file included from src/cmdstan/arguments/arg_data.hpp:6:
-In file included from src/cmdstan/arguments/arg_data_file.hpp:4:
-In file included from src/cmdstan/arguments/singleton_argument.hpp:5:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/lexical_cast.hpp:31:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/lexical_cast/bad_lexical_cast.hpp:28:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/throw_exception.hpp:24:
-stan/lib/stan_math/lib/boost_1.78.0/boost/assert/source_location.hpp:75:14: warning: &#39;sprintf&#39; is deprecated: This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
-        std::sprintf( buffer, &quot;:%ld&quot;, static_cast&lt;long&gt;( line() ) );
-             ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: &#39;sprintf&#39; has been explicitly marked deprecated here
-__deprecated_msg(&quot;This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.&quot;)
-^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro &#39;__deprecated_msg&#39;
-        #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
-                                                      ^</code></pre>
-</div>
-<div class="cell-output cell-output-stderr">
-<pre><code>In file included from src/cmdstan/main.cpp:1:
-In file included from src/cmdstan/command.hpp:4:
-In file included from src/cmdstan/arguments/arg_data.hpp:6:
-In file included from src/cmdstan/arguments/arg_data_file.hpp:4:
-In file included from src/cmdstan/arguments/singleton_argument.hpp:5:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/lexical_cast.hpp:31:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/lexical_cast/bad_lexical_cast.hpp:28:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/throw_exception.hpp:24:
-stan/lib/stan_math/lib/boost_1.78.0/boost/assert/source_location.hpp:80:18: warning: &#39;sprintf&#39; is deprecated: This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
-            std::sprintf( buffer, &quot;:%ld&quot;, static_cast&lt;long&gt;( column() ) );
-                 ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: &#39;sprintf&#39; has been explicitly marked deprecated here
-__deprecated_msg(&quot;This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.&quot;)
-^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro &#39;__deprecated_msg&#39;
-        #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
-                                                      ^</code></pre>
-</div>
-<div class="cell-output cell-output-stderr">
-<pre><code>In file included from src/cmdstan/main.cpp:1:
-In file included from src/cmdstan/command.hpp:4:
-In file included from src/cmdstan/arguments/arg_data.hpp:6:
-In file included from src/cmdstan/arguments/arg_data_file.hpp:4:
-In file included from src/cmdstan/arguments/singleton_argument.hpp:5:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/lexical_cast.hpp:32:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/lexical_cast/try_lexical_convert.hpp:44:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/lexical_cast/detail/converter_lexical.hpp:54:
-stan/lib/stan_math/lib/boost_1.78.0/boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: &#39;sprintf&#39; is deprecated: This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
-                    sprintf(begin,
-                    ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: &#39;sprintf&#39; has been explicitly marked deprecated here
-__deprecated_msg(&quot;This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.&quot;)
-^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro &#39;__deprecated_msg&#39;
-        #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
-                                                      ^
-In file included from src/cmdstan/main.cpp:1:
-In file included from src/cmdstan/command.hpp:4:
-In file included from src/cmdstan/arguments/arg_data.hpp:6:
-In file included from src/cmdstan/arguments/arg_data_file.hpp:4:
-In file included from src/cmdstan/arguments/singleton_argument.hpp:5:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/lexical_cast.hpp:32:
-In file included from stan/lib/s</code></pre>
-</div>
-<div class="cell-output cell-output-stderr">
-<pre><code>tan_math/lib/boost_1.78.0/boost/lexical_cast/try_lexical_convert.hpp:44:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/lexical_cast/detail/converter_lexical.hpp:54:
-stan/lib/stan_math/lib/boost_1.78.0/boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: &#39;sprintf&#39; is deprecated: This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
-                    sprintf(begin,
-                    ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: &#39;sprintf&#39; has been explicitly marked deprecated here
-__deprecated_msg(&quot;This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.&quot;)
-^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro &#39;__deprecated_msg&#39;</code></pre>
-</div>
-<div class="cell-output cell-output-stderr">
-<pre><code>        #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
-                                                      ^
-In file included from src/cmdstan/main.cpp:1:
-In file included from src/cmdstan/command.hpp:4:
-In file included from src/cmdstan/arguments/arg_data.hpp:6:
-In file included from src/cmdstan/arguments/arg_data_file.hpp:4:
-In file included from src/cmdstan/arguments/singleton_argument.hpp:5:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/lexical_cast.hpp:32:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/lexical_cast/try_lexical_convert.hpp:44:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/lexical_cast/detail/converter_lexical.hpp:54:
-stan/lib/stan_math/lib/boost_1.78.0/boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: &#39;sprintf&#39; is deprecated: This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
-                    sprintf(begin,
-                    ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: &#39;sprintf&#39; has been explicitly marked deprecated here
-__deprecated_msg(&quot;This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.&quot;)
-^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro &#39;__deprecated_msg&#39;
-        #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
-                                                      ^</code></pre>
-</div>
-<div class="cell-output cell-output-stderr">
-<pre><code>In file included from src/cmdstan/main.cpp:1:
-In file included from src/cmdstan/command.hpp:14:
-In file included from src/cmdstan/command_helper.hpp:20:
-In file included from stan/src/stan/io/dump.hpp:7:
-In file included from stan/lib/stan_math/stan/math/prim.hpp:15:
-In file included from stan/lib/stan_math/stan/math/prim/functor.hpp:16:
-In file included from stan/lib/stan_math/stan/math/prim/functor/integrate_ode_rk45.hpp:6:
-In file included from stan/lib/stan_math/stan/math/prim/functor/ode_rk45.hpp:9:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint.hpp:37:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint/stepper/dense_output_runge_kutta.hpp:40:
-stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint/integrate/max_step_checker.hpp:72:18: warning: &#39;sprintf&#39; is deprecated: This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
-            std::sprintf(error_msg, &quot;Max number of iterations exceeded (%d).&quot;, m_max_steps);
-                 ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: &#39;sprintf&#39; has been explicitly marked deprecated here
-__deprecated_msg(&quot;This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.&quot;)
-^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro &#39;__deprecated_msg&#39;
-        #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
-                                                      ^</code></pre>
-</div>
-<div class="cell-output cell-output-stderr">
-<pre><code>In file included from src/cmdstan/main.cpp:1:
-In file included from src/cmdstan/command.hpp:14:
-In file included from src/cmdstan/command_helper.hpp:20:
-In file included from stan/src/stan/io/dump.hpp:7:
-In file included from stan/lib/stan_math/stan/math/prim.hpp:15:
-In file included from stan/lib/stan_math/stan/math/prim/functor.hpp:16:
-In file included from stan/lib/stan_math/stan/math/prim/functor/integrate_ode_rk45.hpp:6:
-In file included from stan/lib/stan_math/stan/math/prim/functor/ode_rk45.hpp:9:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint.hpp:37:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint/stepper/dense_output_runge_kutta.hpp:40:
-stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint/integrate/max_step_checker.hpp:104:18: warning: &#39;sprintf&#39; is deprecated: This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
-            std::sprintf(error_msg, &quot;Max number of iterations exceeded (%d). A new step size was not found.&quot;, m_max_steps);
-                 ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: &#39;sprintf&#39; has been explicitly marked deprecated here
-__deprecated_msg(&quot;This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.&quot;)
-^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro &#39;__deprecated_msg&#39;
-        #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
-                                                      ^</code></pre>
-</div>
-<div class="cell-output cell-output-stderr">
-<pre><code>In file included from src/cmdstan/main.cpp:1:
-In file included from src/cmdstan/command.hpp:14:
-In file included from src/cmdstan/command_helper.hpp:20:
-In file included from stan/src/stan/io/dump.hpp:7:
-In file included from stan/lib/stan_math/stan/math/prim.hpp:15:
-In file included from stan/lib/stan_math/stan/math/prim/functor.hpp:16:
-In file included from stan/lib/stan_math/stan/math/prim/functor/integrate_ode_rk45.hpp:6:
-In file included from stan/lib/stan_math/stan/math/prim/functor/ode_rk45.hpp:9:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint.hpp:76:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint/integrate/observer_collection.hpp:23:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function.hpp:30:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/detail/prologue.hpp:17:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/function_base.hpp:21:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index.hpp:29:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index/stl_type_index.hpp:47:
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:132:33: warning: &#39;unary_function&lt;bool, unsigned long&gt;&#39; is deprecated [-Wdeprecated-declarations]
-        struct hash_base : std::unary_function&lt;T, std::size_t&gt; {};
-                                ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:609:5: note: in instantiation of template class &#39;boost::hash_detail::hash_base&lt;bool&gt;&#39; requested here
-    BOOST_HASH_SPECIALIZE(bool)
-    ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:581:19: note: expanded from macro &#39;BOOST_HASH_SPECIALIZE&#39;
-         : public boost::hash_detail::hash_base&lt;type&gt; \
-                  ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/unary_function.h:23:29: note: &#39;unary_function&lt;bool, unsigned long&gt;&#39; has been ex</code></pre>
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>plicitly marked deprecated here
-struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function
-                            ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:825:41: note: expanded from macro &#39;_LIBCPP_DEPRECATED_IN_CXX11&#39;
-#    define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
-                                        ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro &#39;_LIBCPP_DEPRECATED&#39;
-#      define _LIBCPP_DEPRECATED __attribute__((deprecated))
-                                                ^</code></pre>
+<pre><code>Chain 2 </code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>In file included from src/cmdstan/main.cpp:1:
-In file included from src/cmdstan/command.hpp:14:
-In file included from src/cmdstan/command_helper.hpp:20:
-In file included from stan/src/stan/io/dump.hpp:7:
-In file included from stan/lib/stan_math/stan/math/prim.hpp:15:
-In file included from stan/lib/stan_math/stan/math/prim/functor.hpp:16:
-In file included from stan/lib/stan_math/stan/math/prim/functor/integrate_ode_rk45.hpp:6:
-In file included from stan/lib/stan_math/stan/math/prim/functor/ode_rk45.hpp:9:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint.hpp:76:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint/integrate/observer_collection.hpp:23:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function.hpp:30:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/detail/prologue.hpp:17:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/function_base.hpp:21:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index.hpp:29:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index/stl_type_index.hpp:47:
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:132:33: warning: &#39;unary_function&lt;char, unsigned long&gt;&#39; is deprecated [-Wdeprecated-declarations]
-        struct hash_base : std::unary_function&lt;T, std::size_t&gt; {};
-                                ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:610:5: note: in instantiation of template class &#39;boost::hash_detail::hash_base&lt;char&gt;&#39; requested here
-    BOOST_HASH_SPECIALIZE(char)
-    ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:581:19: note: expanded from macro &#39;BOOST_HASH_SPECIALIZE&#39;
-         : public boost::hash_detail::hash_base&lt;type&gt; \
-                  ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/unary_function.h:23:29: note: &#39;unary_function&lt;char, unsigned long&gt;&#39; has been ex</code></pre>
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>plicitly marked deprecated here
-struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function
-                            ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:825:41: note: expanded from macro &#39;_LIBCPP_DEPRECATED_IN_CXX11&#39;
-#    define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
-                                        ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro &#39;_LIBCPP_DEPRECATED&#39;
-#      define _LIBCPP_DEPRECATED __attribute__((deprecated))
-                                                ^
-In file included from src/cmdstan/main.cpp:1:
-In file included from src/cmdstan/command.hpp:14:
-In file included from src/cmdstan/command_helper.hpp:20:
-In file included from stan/src/stan/io/dump.hpp:7:
-In file included from stan/lib/stan_math/stan/math/prim.hpp:15:
-In file included from stan/lib/stan_math/stan/math/prim/functor.hpp:16:
-In file included from stan/lib/stan_math/stan/math/prim/functor/integrate_ode_rk45.hpp:6:
-In file included from stan/lib/stan_math/stan/math/prim/functor/ode_rk45.hpp:9:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint.hpp:76:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint/integrate/observer_collection.hpp:23:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function.hpp:30:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/detail/prologue.hpp:17:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/function_base.hpp:21:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index.hpp:29:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index/stl_type_index.hpp:47:
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:132:33: warning: &#39;unary_function&lt;signed char, unsigned long&gt;&#39; is deprecated [-Wdeprecated-declarations]
-        struct hash_base : std::unary_</code></pre>
-</div>
-<div class="cell-output cell-output-stderr">
-<pre><code>function&lt;T, std::size_t&gt; {};
-                                ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:611:5: note: in instantiation of template class &#39;boost::hash_detail::hash_base&lt;signed char&gt;&#39; requested here
-    BOOST_HASH_SPECIALIZE(signed char)
-    ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:581:19: note: expanded from macro &#39;BOOST_HASH_SPECIALIZE&#39;
-         : public boost::hash_detail::hash_base&lt;type&gt; \
-                  ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/unary_function.h:23:29: note: &#39;unary_function&lt;signed char, unsigned long&gt;&#39; has been explicitly marked deprecated here
-struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function
-                            ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:825:41: note: expanded from macro &#39;_LIBCPP_DEPRECATED_IN_CXX11&#39;
-#    define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
-                                        ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro &#39;_LIBCPP_DEPRECATED&#39;
-#      define _LIBCPP_DEPRECATED __attribute__((deprecated))
-                                                ^
-In file included from src/cmdstan/main.cpp:1:
-In file included from src/cmdstan/command.hpp:14:
-In file included from src/cmdstan/command_helper.hpp:20:
-In file included from stan/src/stan/io/dump.hpp:7:
-In file included from stan/lib/stan_math/stan/math/prim.hpp:15:
-In file included from stan/lib/stan_math/stan/math/prim/functor.hpp:16:
-In file included from stan/lib/stan_math/stan/math/prim/functor/integrate_ode_rk45.hpp:6:
-In file included from stan/lib/stan_math/stan/math/prim/functor/ode_rk45.hpp:9:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint.hpp:76:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint/integrate/observer_collection.hpp:23:
-In file in</code></pre>
-</div>
-<div class="cell-output cell-output-stderr">
-<pre><code>cluded from stan/lib/stan_math/lib/boost_1.78.0/boost/function.hpp:30:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/detail/prologue.hpp:17:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/function_base.hpp:21:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index.hpp:29:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index/stl_type_index.hpp:47:
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:132:33: warning: &#39;unary_function&lt;unsigned char, unsigned long&gt;&#39; is deprecated [-Wdeprecated-declarations]
-        struct hash_base : std::unary_function&lt;T, std::size_t&gt; {};
-                                ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:612:5: note: in instantiation of template class &#39;boost::hash_detail::hash_base&lt;unsigned char&gt;&#39; requested here
-    BOOST_HASH_SPECIALIZE(unsigned char)
-    ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:581:19: note: expanded from macro &#39;BOOST_HASH_SPECIALIZE&#39;
-         : public boost::hash_detail::hash_base&lt;type&gt; \
-                  ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/unary_function.h:23:29: note: &#39;unary_function&lt;unsigned char, unsigned long&gt;&#39; has been explicitly marked deprecated here
-struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function
-                            ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:825:41: note: expanded from macro &#39;_LIBCPP_DEPRECATED_IN_CXX11&#39;
-#    define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
-                                        ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro &#39;_LIBCPP_DEPRECATED&#39;
-#      define _LIBCPP_DEPRECATED __attribute__((deprecated))
-                                                ^
-In file included from src/cmdstan/main.cpp:1:
-In file included f</code></pre>
-</div>
-<div class="cell-output cell-output-stderr">
-<pre><code>rom src/cmdstan/command.hpp:14:
-In file included from src/cmdstan/command_helper.hpp:20:
-In file included from stan/src/stan/io/dump.hpp:7:
-In file included from </code></pre>
-</div>
-<div class="cell-output cell-output-stderr">
-<pre><code>stan/lib/stan_math/stan/math/prim.hpp:15:
-In file included from stan/lib/stan_math/stan/math/prim/functor.hpp:16:
-In file included from stan/lib/stan_math/stan/math/prim/functor/integrate_ode_rk45.hpp:6:
-In file included from stan/lib/stan_math/stan/math/prim/functor/ode_rk45.hpp:9:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint.hpp:76:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint/integrate/observer_collection.hpp:23:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function.hpp:30:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/detail/prologue.hpp:17:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/function_base.hpp:21:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index.hpp:29:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index/stl_type_index.hpp:47:
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:132:33: warning: &#39;unary_function&lt;wchar_t, unsigned long&gt;&#39; is deprecated [-Wdeprecated-declarations]
-        struct hash_base : std::unary_function&lt;T, std::size_t&gt; {};
-                                ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:614:5: note: in instantiation of template class &#39;boost::hash_detail::hash_base&lt;wchar_t&gt;&#39; requested here
-    BOOST_HASH_SPECIALIZE(wchar_t)
-    ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:581:19: note: expanded from macro &#39;BOOST_HASH_SPECIALIZE&#39;
-         : public boost::hash_detail::hash_base&lt;type&gt; \
-                  ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/unary_function.h:23:29: note: &#39;unary_function&lt;wchar_t, unsigned long&gt;&#39; has been explicitly marked deprecated here
-struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function
-                            ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:8</code></pre>
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -4.78745e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>25:41: note: expanded from macro &#39;_LIBCPP_DEPRECATED_IN_CXX11&#39;
-#    define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
-                                        ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro &#39;_LIBCPP_DEPRECATED&#39;
-#      define _LIBCPP_DEPRECATED __attribute__((deprecated))
-                                                ^
-In file included from src/cmdstan/main.cpp:1:
-In file included from src/cmdstan/command.hpp:14:
-In file included from src/cmdstan/command_helper.hpp:20:
-In file included from stan/src/stan/io/dump.hpp:7:
-In file included from stan/lib/stan_math/stan/math/prim.hpp:15:
-In file included from stan/lib/stan_math/stan/math/prim/functor.hpp:16:
-In file included from stan/lib/stan_math/stan/math/prim/functor/integrate_ode_rk45.hpp:6:
-In file included from stan/lib/stan_math/stan/math/prim/functor/ode_rk45.hpp:9:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint.hpp:76:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint/integrate/observer_collection.hpp:23:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function.hpp:30:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/detail/prologue.hpp:17:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/function_base.hpp:21:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index.hpp:29:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index/stl_type_index.hpp:47:
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:132:33: warning: &#39;unary_function&lt;char16_t, unsigned long&gt;&#39; is deprecated [-Wdeprecated-declarations]
-        struct hash_base : std::unary_function&lt;T, std::size_t&gt; {};
-                                ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:617:5: note: in instantiation of template class &#39;boost::hash_detail::hash_base&lt;char16_t&gt;</code></pre>
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>&#39; requested here
-    BOOST_HASH_SPECIALIZE(char16_t)
-    ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:581:19: note: expanded from macro &#39;BOOST_HASH_SPECIALIZE&#39;
-         : public boost::hash_detail::hash_base&lt;type&gt; \
-                  ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/unary_function.h:23:29: note: &#39;unary_function&lt;char16_t, unsigned long&gt;&#39; has been explicitly marked deprecated here
-struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function
-                            ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:825:41: note: expanded from macro &#39;_LIBCPP_DEPRECATED_IN_CXX11&#39;
-#    define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
-                                        ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro &#39;_LIBCPP_DEPRECATED&#39;
-#      define _LIBCPP_DEPRECATED __attribute__((deprecated))
-                                                ^
-In file included from src/cmdstan/main.cpp:1:
-In file included from src/cmdstan/command.hpp:14:
-In file included from src/cmdstan/command_helper.hpp:20:
-In file included from stan/src/stan/io/dump.hpp:7:
-In file included from stan/lib/stan_math/stan/math/prim.hpp:15:
-In file included from stan/lib/stan_math/stan/math/prim/functor.hpp:16:
-In file included from stan/lib/stan_math/stan/math/prim/functor/integrate_ode_rk45.hpp:6:
-In file included from stan/lib/stan_math/stan/math/prim/functor/ode_rk45.hpp:9:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint.hpp:76:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint/integrate/observer_collection.hpp:23:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function.hpp:30:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/detail/prologue.hpp:17:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/</code></pre>
-</div>
-<div class="cell-output cell-output-stderr">
-<pre><code>boost/function/function_base.hpp:21:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index.hpp:29:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index/stl_type_index.hpp:47:
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:132:33: warning: &#39;unary_function&lt;char32_t, unsigned long&gt;&#39; is deprecated [-Wdeprecated-declarations]
-        struct hash_base : std::unary_function&lt;T, std::size_t&gt; {};
-                                ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:620:5: note: in instantiation of template class &#39;boost::hash_detail::hash_base&lt;char32_t&gt;&#39; requested here
-    BOOST_HASH_SPECIALIZE(char32_t)
-    ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:581:19: note: expanded from macro &#39;BOOST_HASH_SPECIALIZE&#39;
-         : public boost::hash_detail::hash_base&lt;type&gt; \
-                  ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/unary_function.h:23:29: note: &#39;unary_function&lt;char32_t, unsigned long&gt;&#39; has been explicitly marked deprecated here
-struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function
-                            ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:825:41: note: expanded from macro &#39;_LIBCPP_DEPRECATED_IN_CXX11&#39;
-#    define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
-                                        ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro &#39;_LIBCPP_DEPRECATED&#39;
-#      define _LIBCPP_DEPRECATED __attribute__((deprecated))
-                                                ^
-In file included from src/cmdstan/main.cpp:1:
-In file included from src/cmdstan/command.hpp:14:
-In file included from src/cmdstan/command_helper.hpp:20:
-In file included from stan/src/stan/io/dump.hpp:7:
-In file included from stan/lib/stan_math/stan/math/prim.hpp:15:
-In file included from stan/lib/stan_math/s</code></pre>
-</div>
-<div class="cell-output cell-output-stderr">
-<pre><code>tan/math/prim/functor.hpp:16:
-In file included from stan/lib/stan_math/stan/math/prim/functor/integrate_ode_rk45.hpp:6:
-In file included from </code></pre>
-</div>
-<div class="cell-output cell-output-stderr">
-<pre><code>stan/lib/stan_math/stan/math/prim/functor/ode_rk45.hpp:9:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint.hpp:76:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint/integrate/observer_collection.hpp:23:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function.hpp:30:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/detail/prologue.hpp:17:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/function_base.hpp:21:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index.hpp:29:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index/stl_type_index.hpp:47:
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:132:33: warning: &#39;unary_function&lt;short, unsigned long&gt;&#39; is deprecated [-Wdeprecated-declarations]
-        struct hash_base : std::unary_function&lt;T, std::size_t&gt; {};
-                                ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:622:5: note: in instantiation of template class &#39;boost::hash_detail::hash_base&lt;short&gt;&#39; requested here
-    BOOST_HASH_SPECIALIZE(short)
-    ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:581:19: note: expanded from macro &#39;BOOST_HASH_SPECIALIZE&#39;
-         : public boost::hash_detail::hash_base&lt;type&gt; \
-                  ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/unary_function.h:23:29: note: &#39;unary_function&lt;short, unsigned long&gt;&#39; has been explicitly marked deprecated here
-struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function
-                            ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:825:41: note: expanded from macro &#39;_LIBCPP_DEPRECATED_IN_CXX11&#39;
-#    define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
-                                        ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1</code></pre>
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>/__config:810:49: note: expanded from macro &#39;_LIBCPP_DEPRECATED&#39;
-#      define _LIBCPP_DEPRECATED __attribute__((deprecated))
-                                                ^
-In file included from src/cmdstan/main.cpp:1:
-In file included from src/cmdstan/command.hpp:14:
-In file included from src/cmdstan/command_helper.hpp:20:
-In file included from stan/src/stan/io/dump.hpp:7:
-In file included from stan/lib/stan_math/stan/math/prim.hpp:15:
-In file included from stan/lib/stan_math/stan/math/prim/functor.hpp:16:
-In file included from stan/lib/stan_math/stan/math/prim/functor/integrate_ode_rk45.hpp:6:
-In file included from stan/lib/stan_math/stan/math/prim/functor/ode_rk45.hpp:9:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint.hpp:76:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint/integrate/observer_collection.hpp:23:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function.hpp:30:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/detail/prologue.hpp:17:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/function_base.hpp:21:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index.hpp:29:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index/stl_type_index.hpp:47:
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:132:33: warning: &#39;unary_function&lt;unsigned short, unsigned long&gt;&#39; is deprecated [-Wdeprecated-declarations]
-        struct hash_base : std::unary_function&lt;T, std::size_t&gt; {};
-                                ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:623:5: note: in instantiation of template class &#39;boost::hash_detail::hash_base&lt;unsigned short&gt;&#39; requested here
-    BOOST_HASH_SPECIALIZE(unsigned short)
-    ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:581:19: note: expanded from macro &#39;BOOST_HASH_SPECIALIZE&#39;
-         : public boost::hash_det</code></pre>
+<pre><code>Chain 2 </code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>ail::hash_base&lt;type&gt; \
-                  ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/unary_function.h:23:29: note: &#39;unary_function&lt;unsigned short, unsigned long&gt;&#39; has been explicitly marked deprecated here
-struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function
-                            ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:825:41: note: expanded from macro &#39;_LIBCPP_DEPRECATED_IN_CXX11&#39;
-#    define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
-                                        ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro &#39;_LIBCPP_DEPRECATED&#39;
-#      define _LIBCPP_DEPRECATED __attribute__((deprecated))
-                                                ^
-In file included from src/cmdstan/main.cpp:1:
-In file included from src/cmdstan/command.hpp:14:
-In file included from src/cmdstan/command_helper.hpp:20:
-In file included from stan/src/stan/io/dump.hpp:7:
-In file included from stan/lib/stan_math/stan/math/prim.hpp:15:
-In file included from stan/lib/stan_math/stan/math/prim/functor.hpp:16:
-In file included from stan/lib/stan_math/stan/math/prim/functor/integrate_ode_rk45.hpp:6:
-In file included from stan/lib/stan_math/stan/math/prim/functor/ode_rk45.hpp:9:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint.hpp:76:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint/integrate/observer_collection.hpp:23:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function.hpp:30:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/detail/prologue.hpp:17:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/function_base.hpp:21:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index.hpp:29:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index/stl_type_index.</code></pre>
-</div>
-<div class="cell-output cell-output-stderr">
-<pre><code>hpp:47:
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:132:33: warning: &#39;unary_function&lt;int, unsigned long&gt;&#39; is deprecated [-Wdeprecated-declarations]
-        struct hash_base : std::unary_function&lt;T, std::size_t&gt; {};
-                                ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:624:5: note: in instantiation of template class &#39;boost::hash_detail::hash_base&lt;int&gt;&#39; requested here
-    BOOST_HASH_SPECIALIZE(int)
-    ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:581:19: note: expanded from macro &#39;BOOST_HASH_SPECIALIZE&#39;
-         : public boost::hash_detail::hash_base&lt;type&gt; \
-                  ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/unary_function.h:23:29: note: &#39;unary_function&lt;int, unsigned long&gt;&#39; has been explicitly marked deprecated here
-struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function
-                            ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:825:41: note: expanded from macro &#39;_LIBCPP_DEPRECATED_IN_CXX11&#39;
-#    define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
-                                        ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro &#39;_LIBCPP_DEPRECATED&#39;
-#      define _LIBCPP_DEPRECATED __attribute__((deprecated))
-                                                ^
-In file included from src/cmdstan/main.cpp:1:
-In file included from src/cmdstan/command.hpp:14:
-In file included from src/cmdstan/command_helper.hpp:20:
-In file included from stan/src/stan/io/dump.hpp:7:
-In file included from stan/lib/stan_math/stan/math/prim.hpp:15:
-In file included from stan/lib/stan_math/stan/math/prim/functor.hpp:16:
-In file included from stan/lib/stan_math/stan/math/prim/functor/integrate_ode_rk45.hpp:6:
-In file included from stan/lib/stan_math/stan/math/prim/functor/ode_rk45.hpp:9:
-In file included from stan/lib</code></pre>
-</div>
-<div class="cell-output cell-output-stderr">
-<pre><code>/stan_math/lib/boost_1.78.0/boost/numeric/odeint.hpp:76:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint/integrate/observer_collection.hpp:23:</code></pre>
-</div>
-<div class="cell-output cell-output-stderr">
-<pre><code>In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function.hpp:30:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/detail/prologue.hpp:17:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/function_base.hpp:21:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index.hpp:29:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index/stl_type_index.hpp:47:
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:132:33: warning: &#39;unary_function&lt;unsigned int, unsigned long&gt;&#39; is deprecated [-Wdeprecated-declarations]
-        struct hash_base : std::unary_function&lt;T, std::size_t&gt; {};
-                                ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:625:5: note: in instantiation of template class &#39;boost::hash_detail::hash_base&lt;unsigned int&gt;&#39; requested here
-    BOOST_HASH_SPECIALIZE(unsigned int)
-    ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:581:19: note: expanded from macro &#39;BOOST_HASH_SPECIALIZE&#39;
-         : public boost::hash_detail::hash_base&lt;type&gt; \
-                  ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/unary_function.h:23:29: note: &#39;unary_function&lt;unsigned int, unsigned long&gt;&#39; has been explicitly marked deprecated here
-struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function
-                            ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:825:41: note: expanded from macro &#39;_LIBCPP_DEPRECATED_IN_CXX11&#39;
-#    define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
-                                        ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro &#39;_LIBCPP_DEPRECATED&#39;
-#      define _LIBCPP_DEPRECATED __attribute__((deprecated))
-                                                ^
-In file included from src/cmdstan/main.cpp:1:
-In file incl</code></pre>
-</div>
-<div class="cell-output cell-output-stderr">
-<pre><code>uded from src/cmdstan/command.hpp:14:
-In file included from src/cmdstan/command_helper.hpp:20:
-In file included from stan/src/stan/io/dump.hpp:7:
-In file included from stan/lib/stan_math/stan/math/prim.hpp:15:
-In file included from stan/lib/stan_math/stan/math/prim/functor.hpp:16:
-In file included from stan/lib/stan_math/stan/math/prim/functor/integrate_ode_rk45.hpp:6:
-In file included from stan/lib/stan_math/stan/math/prim/functor/ode_rk45.hpp:9:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint.hpp:76:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint/integrate/observer_collection.hpp:23:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function.hpp:30:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/detail/prologue.hpp:17:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/function_base.hpp:21:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index.hpp:29:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index/stl_type_index.hpp:47:
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:132:33: warning: &#39;unary_function&lt;long, unsigned long&gt;&#39; is deprecated [-Wdeprecated-declarations]
-        struct hash_base : std::unary_function&lt;T, std::size_t&gt; {};
-                                ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:626:5: note: in instantiation of template class &#39;boost::hash_detail::hash_base&lt;long&gt;&#39; requested here
-    BOOST_HASH_SPECIALIZE(long)
-    ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:581:19: note: expanded from macro &#39;BOOST_HASH_SPECIALIZE&#39;
-         : public boost::hash_detail::hash_base&lt;type&gt; \
-                  ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/unary_function.h:23:29: note: &#39;unary_function&lt;long, unsigned long&gt;&#39; has been explicitly marked deprecated here
-struct _LIBCPP_TEMPLATE_VI</code></pre>
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>S _LIBCPP_DEPRECATED_IN_CXX11 unary_function
-                            ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:825:41: note: expanded from macro &#39;_LIBCPP_DEPRECATED_IN_CXX11&#39;
-#    define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
-                                        ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro &#39;_LIBCPP_DEPRECATED&#39;
-#      define _LIBCPP_DEPRECATED __attribute__((deprecated))
-                                                ^
-In file included from src/cmdstan/main.cpp:1:
-In file included from src/cmdstan/command.hpp:14:
-In file included from src/cmdstan/command_helper.hpp:20:
-In file included from stan/src/stan/io/dump.hpp:7:
-In file included from stan/lib/stan_math/stan/math/prim.hpp:15:
-In file included from stan/lib/stan_math/stan/math/prim/functor.hpp:16:
-In file included from stan/lib/stan_math/stan/math/prim/functor/integrate_ode_rk45.hpp:6:
-In file included from stan/lib/stan_math/stan/math/prim/functor/ode_rk45.hpp:9:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint.hpp:76:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint/integrate/observer_collection.hpp:23:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function.hpp:30:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/detail/prologue.hpp:17:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/function_base.hpp:21:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index.hpp:29:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index/stl_type_index.hpp:47:
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:132:33: warning: &#39;unary_function&lt;unsigned long, unsigned long&gt;&#39; is deprecated [-Wdeprecated-declarations]
-        struct hash_base : std::unary_function&lt;T, std::size_t&gt; {};
-                           </code></pre>
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -4.60644e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>     ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:627:5: note: in instantiation of template class &#39;boost::hash_detail::hash_base&lt;unsigned long&gt;&#39; requested here
-    BOOST_HASH_SPECIALIZE(unsigned long)
-    ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:581:19: note: expanded from macro &#39;BOOST_HASH_SPECIALIZE&#39;
-         : public boost::hash_detail::hash_base&lt;type&gt; \
-                  ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/unary_function.h:23:29: note: &#39;unary_function&lt;unsigned long, unsigned long&gt;&#39; has been explicitly marked deprecated here
-struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function
-                            ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:825:41: note: expanded from macro &#39;_LIBCPP_DEPRECATED_IN_CXX11&#39;
-#    define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
-                                        ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro &#39;_LIBCPP_DEPRECATED&#39;
-#      define _LIBCPP_DEPRECATED __attribute__((deprecated))
-                                                ^
-In file included from src/cmdstan/main.cpp:1:
-In file included from src/cmdstan/command.hpp:14:
-In file included from src/cmdstan/command_helper.hpp:20:
-In file included from stan/src/stan/io/dump.hpp:7:
-In file included from stan/lib/stan_math/stan/math/prim.hpp:15:
-In file included from stan/lib/stan_math/stan/math/prim/functor.hpp:16:
-In file included from stan/lib/stan_math/stan/math/prim/functor/integrate_ode_rk45.hpp:6:
-In file included from stan/lib/stan_math/stan/math/prim/functor/ode_rk45.hpp:9:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint.hpp:76:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint/integrate/observer_collection.hpp:23:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/bo</code></pre>
-</div>
-<div class="cell-output cell-output-stderr">
-<pre><code>ost/function.hpp:30:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/detail/prologue.hpp:17:
-In file included from </code></pre>
-</div>
-<div class="cell-output cell-output-stderr">
-<pre><code>stan/lib/stan_math/lib/boost_1.78.0/boost/function/function_base.hpp:21:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index.hpp:29:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index/stl_type_index.hpp:47:
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:132:33: warning: &#39;unary_function&lt;float, unsigned long&gt;&#39; is deprecated [-Wdeprecated-declarations]
-        struct hash_base : std::unary_function&lt;T, std::size_t&gt; {};
-                                ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:629:5: note: in instantiation of template class &#39;boost::hash_detail::hash_base&lt;float&gt;&#39; requested here
-    BOOST_HASH_SPECIALIZE(float)
-    ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:581:19: note: expanded from macro &#39;BOOST_HASH_SPECIALIZE&#39;
-         : public boost::hash_detail::hash_base&lt;type&gt; \
-                  ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/unary_function.h:23:29: note: &#39;unary_function&lt;float, unsigned long&gt;&#39; has been explicitly marked deprecated here
-struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function
-                            ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:825:41: note: expanded from macro &#39;_LIBCPP_DEPRECATED_IN_CXX11&#39;
-#    define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
-                                        ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro &#39;_LIBCPP_DEPRECATED&#39;
-#      define _LIBCPP_DEPRECATED __attribute__((deprecated))
-                                                ^
-In file included from src/cmdstan/main.cpp:1:
-In file included from src/cmdstan/command.hpp:14:
-In file included from src/cmdstan/command_helper.hpp:20:
-In file included from stan/src/stan/io/dump.hpp:7:
-In file included from stan/lib/stan_math/stan/math/prim.hpp:15:
-In file included f</code></pre>
-</div>
-<div class="cell-output cell-output-stderr">
-<pre><code>rom stan/lib/stan_math/stan/math/prim/functor.hpp:16:
-In file included from stan/lib/stan_math/stan/math/prim/functor/integrate_ode_rk45.hpp:6:
-In file included from stan/lib/stan_math/stan/math/prim/functor/ode_rk45.hpp:9:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint.hpp:76:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint/integrate/observer_collection.hpp:23:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function.hpp:30:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/detail/prologue.hpp:17:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/function_base.hpp:21:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index.hpp:29:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index/stl_type_index.hpp:47:
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:132:33: warning: &#39;unary_function&lt;double, unsigned long&gt;&#39; is deprecated [-Wdeprecated-declarations]
-        struct hash_base : std::unary_function&lt;T, std::size_t&gt; {};
-                                ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:630:5: note: in instantiation of template class &#39;boost::hash_detail::hash_base&lt;double&gt;&#39; requested here
-    BOOST_HASH_SPECIALIZE(double)
-    ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:581:19: note: expanded from macro &#39;BOOST_HASH_SPECIALIZE&#39;
-         : public boost::hash_detail::hash_base&lt;type&gt; \
-                  ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/unary_function.h:23:29: note: &#39;unary_function&lt;double, unsigned long&gt;&#39; has been explicitly marked deprecated here
-struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function
-                            ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:825:41: note: expanded from macro &#39;_LIBCPP_DEPRECATED_IN_CXX11&#39;
-#</code></pre>
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>    define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
-                                        ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro &#39;_LIBCPP_DEPRECATED&#39;
-#      define _LIBCPP_DEPRECATED __attribute__((deprecated))
-                                                ^
-In file included from src/cmdstan/main.cpp:1:
-In file included from src/cmdstan/command.hpp:14:
-In file included from src/cmdstan/command_helper.hpp:20:
-In file included from stan/src/stan/io/dump.hpp:7:
-In file included from stan/lib/stan_math/stan/math/prim.hpp:15:
-In file included from stan/lib/stan_math/stan/math/prim/functor.hpp:16:
-In file included from stan/lib/stan_math/stan/math/prim/functor/integrate_ode_rk45.hpp:6:
-In file included from stan/lib/stan_math/stan/math/prim/functor/ode_rk45.hpp:9:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint.hpp:76:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint/integrate/observer_collection.hpp:23:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function.hpp:30:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/detail/prologue.hpp:17:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/function_base.hpp:21:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index.hpp:29:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index/stl_type_index.hpp:47:
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:132:33: warning: &#39;unary_function&lt;long double, unsigned long&gt;&#39; is deprecated [-Wdeprecated-declarations]
-        struct hash_base : std::unary_function&lt;T, std::size_t&gt; {};
-                                ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:631:5: note: in instantiation of template class &#39;boost::hash_detail::hash_base&lt;long double&gt;&#39; requested here
-    BOOST_HASH_SPECIALIZE(long double)
-  </code></pre>
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>  ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:581:19: note: expanded from macro &#39;BOOST_HASH_SPECIALIZE&#39;
-         : public boost::hash_detail::hash_base&lt;type&gt; \
-                  ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/unary_function.h:23:29: note: &#39;unary_function&lt;long double, unsigned long&gt;&#39; has been explicitly marked deprecated here
-struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function
-                            ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:825:41: note: expanded from macro &#39;_LIBCPP_DEPRECATED_IN_CXX11&#39;
-#    define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
-                                        ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro &#39;_LIBCPP_DEPRECATED&#39;
-#      define _LIBCPP_DEPRECATED __attribute__((deprecated))
-                                                ^
-In file included from src/cmdstan/main.cpp:1:
-In file included from src/cmdstan/command.hpp:14:
-In file included from src/cmdstan/command_helper.hpp:20:
-In file included from stan/src/stan/io/dump.hpp:7:
-In file included from stan/lib/stan_math/stan/math/prim.hpp:15:
-In file included from stan/lib/stan_math/stan/math/prim/functor.hpp:16:
-In file included from stan/lib/stan_math/stan/math/prim/functor/integrate_ode_rk45.hpp:6:
-In file included from stan/lib/stan_math/stan/math/prim/functor/ode_rk45.hpp:9:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint.hpp:76:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint/integrate/observer_collection.hpp:23:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function.hpp:30:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/detail/prologue.hpp:17:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/function_base.hpp:21:
-In file include</code></pre>
-</div>
-<div class="cell-output cell-output-stderr">
-<pre><code>d from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index.hpp:29:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index/stl_type_index.hpp:47:</code></pre>
-</div>
-<div class="cell-output cell-output-stderr">
-<pre><code>stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:132:33: warning: &#39;unary_function&lt;std::string, unsigned long&gt;&#39; is deprecated [-Wdeprecated-declarations]
-        struct hash_base : std::unary_function&lt;T, std::size_t&gt; {};
-                                ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:633:5: note: in instantiation of template class &#39;boost::hash_detail::hash_base&lt;std::string&gt;&#39; requested here
-    BOOST_HASH_SPECIALIZE_REF(std::string)
-    ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:591:19: note: expanded from macro &#39;BOOST_HASH_SPECIALIZE_REF&#39;
-         : public boost::hash_detail::hash_base&lt;type&gt; \
-                  ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/unary_function.h:23:29: note: &#39;unary_function&lt;std::string, unsigned long&gt;&#39; has been explicitly marked deprecated here
-struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function
-                            ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:825:41: note: expanded from macro &#39;_LIBCPP_DEPRECATED_IN_CXX11&#39;
-#    define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
-                                        ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro &#39;_LIBCPP_DEPRECATED&#39;
-#      define _LIBCPP_DEPRECATED __attribute__((deprecated))
-                                                ^
-In file included from src/cmdstan/main.cpp:1:
-In file included from src/cmdstan/command.hpp:14:
-In file included from src/cmdstan/command_helper.hpp:20:
-In file included from stan/src/stan/io/dump.hpp:7:
-In file included from stan/lib/stan_math/stan/math/prim.hpp:15:
-In file included from stan/lib/stan_math/stan/math/prim/functor.hpp:16:
-In file included from stan/lib/stan_math/stan/math/prim/functor/integrate_ode_rk45.hpp:6:
-In file included from stan/lib/stan_math/stan/math/prim/functor/ode_rk45.hpp:9</code></pre>
-</div>
-<div class="cell-output cell-output-stderr">
-<pre><code>:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint.hpp:76:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint/integrate/observer_collection.hpp:23:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function.hpp:30:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/detail/prologue.hpp:17:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/function_base.hpp:21:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index.hpp:29:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index/stl_type_index.hpp:47:
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:132:33: warning: &#39;unary_function&lt;std::wstring, unsigned long&gt;&#39; is deprecated [-Wdeprecated-declarations]
-        struct hash_base : std::unary_function&lt;T, std::size_t&gt; {};
-                                ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:635:5: note: in instantiation of template class &#39;boost::hash_detail::hash_base&lt;std::wstring&gt;&#39; requested here
-    BOOST_HASH_SPECIALIZE_REF(std::wstring)
-    ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:591:19: note: expanded from macro &#39;BOOST_HASH_SPECIALIZE_REF&#39;
-         : public boost::hash_detail::hash_base&lt;type&gt; \
-                  ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/unary_function.h:23:29: note: &#39;unary_function&lt;std::wstring, unsigned long&gt;&#39; has been explicitly marked deprecated here
-struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function
-                            ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:825:41: note: expanded from macro &#39;_LIBCPP_DEPRECATED_IN_CXX11&#39;
-#    define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
-                                        ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:810:49: no</code></pre>
+<pre><code>Chain 2 </code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>te: expanded from macro &#39;_LIBCPP_DEPRECATED&#39;
-#      define _LIBCPP_DEPRECATED __attribute__((deprecated))
-                                                ^
-In file included from src/cmdstan/main.cpp:1:
-In file included from src/cmdstan/command.hpp:14:
-In file included from src/cmdstan/command_helper.hpp:20:
-In file included from stan/src/stan/io/dump.hpp:7:
-In file included from stan/lib/stan_math/stan/math/prim.hpp:15:
-In file included from stan/lib/stan_math/stan/math/prim/functor.hpp:16:
-In file included from stan/lib/stan_math/stan/math/prim/functor/integrate_ode_rk45.hpp:6:
-In file included from stan/lib/stan_math/stan/math/prim/functor/ode_rk45.hpp:9:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint.hpp:76:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint/integrate/observer_collection.hpp:23:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function.hpp:30:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/detail/prologue.hpp:17:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/function_base.hpp:21:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index.hpp:29:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index/stl_type_index.hpp:47:
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:132:33: warning: &#39;unary_function&lt;std::u16string, unsigned long&gt;&#39; is deprecated [-Wdeprecated-declarations]
-        struct hash_base : std::unary_function&lt;T, std::size_t&gt; {};
-                                ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:638:5: note: in instantiation of template class &#39;boost::hash_detail::hash_base&lt;std::u16string&gt;&#39; requested here
-    BOOST_HASH_SPECIALIZE_REF(std::basic_string&lt;char16_t&gt;)
-    ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:591:19: note: expanded from macro &#39;BOOST_HASH_SPECIALIZE_REF&#39;
-         : public boost::hash_de</code></pre>
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>tail::hash_base&lt;type&gt; \
-                  ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/unary_function.h:23:29: note: &#39;unary_function&lt;std::u16string, unsigned long&gt;&#39; has been explicitly marked deprecated here
-struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function
-                            ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:825:41: note: expanded from macro &#39;_LIBCPP_DEPRECATED_IN_CXX11&#39;
-#    define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
-                                        ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro &#39;_LIBCPP_DEPRECATED&#39;
-#      define _LIBCPP_DEPRECATED __attribute__((deprecated))
-                                                ^
-In file included from src/cmdstan/main.cpp:1:
-In file included from src/cmdstan/command.hpp:14:
-In file included from src/cmdstan/command_helper.hpp:20:
-In file included from stan/src/stan/io/dump.hpp:7:
-In file included from stan/lib/stan_math/stan/math/prim.hpp:15:
-In file included from stan/lib/stan_math/stan/math/prim/functor.hpp:16:
-In file included from stan/lib/stan_math/stan/math/prim/functor/integrate_ode_rk45.hpp:6:
-In file included from stan/lib/stan_math/stan/math/prim/functor/ode_rk45.hpp:9:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint.hpp:76:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint/integrate/observer_collection.hpp:23:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function.hpp:30:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/detail/prologue.hpp:17:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/function_base.hpp:21:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index.hpp:29:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index/stl_type_index</code></pre>
-</div>
-<div class="cell-output cell-output-stderr">
-<pre><code>.hpp:47:
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:132:33: warning: &#39;unary_function&lt;std::u32string, unsigned long&gt;&#39; is deprecated [-Wdeprecated-declarations]</code></pre>
-</div>
-<div class="cell-output cell-output-stderr">
-<pre><code>        struct hash_base : std::unary_function&lt;T, std::size_t&gt; {};
-                                ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:641:5: note: in instantiation of template class &#39;boost::hash_detail::hash_base&lt;std::u32string&gt;&#39; requested here
-    BOOST_HASH_SPECIALIZE_REF(std::basic_string&lt;char32_t&gt;)
-    ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:591:19: note: expanded from macro &#39;BOOST_HASH_SPECIALIZE_REF&#39;
-         : public boost::hash_detail::hash_base&lt;type&gt; \
-                  ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/unary_function.h:23:29: note: &#39;unary_function&lt;std::u32string, unsigned long&gt;&#39; has been explicitly marked deprecated here
-struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function
-                            ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:825:41: note: expanded from macro &#39;_LIBCPP_DEPRECATED_IN_CXX11&#39;
-#    define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
-                                        ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro &#39;_LIBCPP_DEPRECATED&#39;
-#      define _LIBCPP_DEPRECATED __attribute__((deprecated))
-                                                ^
-In file included from src/cmdstan/main.cpp:1:
-In file included from src/cmdstan/command.hpp:14:
-In file included from src/cmdstan/command_helper.hpp:20:
-In file included from stan/src/stan/io/dump.hpp:7:
-In file included from stan/lib/stan_math/stan/math/prim.hpp:15:
-In file included from stan/lib/stan_math/stan/math/prim/functor.hpp:16:
-In file included from stan/lib/stan_math/stan/math/prim/functor/integrate_ode_rk45.hpp:6:
-In file included from stan/lib/stan_math/stan/math/prim/functor/ode_rk45.hpp:9:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint.hpp:76:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/b</code></pre>
-</div>
-<div class="cell-output cell-output-stderr">
-<pre><code>oost/numeric/odeint/integrate/observer_collection.hpp:23:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function.hpp:30:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/detail/prologue.hpp:17:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/function_base.hpp:21:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index.hpp:29:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index/stl_type_index.hpp:47:
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:132:33: warning: &#39;unary_function&lt;long long, unsigned long&gt;&#39; is deprecated [-Wdeprecated-declarations]
-        struct hash_base : std::unary_function&lt;T, std::size_t&gt; {};
-                                ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:658:5: note: in instantiation of template class &#39;boost::hash_detail::hash_base&lt;long long&gt;&#39; requested here
-    BOOST_HASH_SPECIALIZE(boost::long_long_type)
-    ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:581:19: note: expanded from macro &#39;BOOST_HASH_SPECIALIZE&#39;
-         : public boost::hash_detail::hash_base&lt;type&gt; \
-                  ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/unary_function.h:23:29: note: &#39;unary_function&lt;long long, unsigned long&gt;&#39; has been explicitly marked deprecated here
-struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function
-                            ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:825:41: note: expanded from macro &#39;_LIBCPP_DEPRECATED_IN_CXX11&#39;
-#    define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
-                                        ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro &#39;_LIBCPP_DEPRECATED&#39;
-#      define _LIBCPP_DEPRECATED __attribute__((deprecated))
-                                                ^</code></pre>
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -8.55241e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>In file included from src/cmdstan/main.cpp:1:
-In file included from src/cmdstan/command.hpp:14:
-In file included from src/cmdstan/command_helper.hpp:20:
-In file included from stan/src/stan/io/dump.hpp:7:
-In file included from stan/lib/stan_math/stan/math/prim.hpp:15:
-In file included from stan/lib/stan_math/stan/math/prim/functor.hpp:16:
-In file included from stan/lib/stan_math/stan/math/prim/functor/integrate_ode_rk45.hpp:6:
-In file included from stan/lib/stan_math/stan/math/prim/functor/ode_rk45.hpp:9:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint.hpp:76:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint/integrate/observer_collection.hpp:23:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function.hpp:30:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/detail/prologue.hpp:17:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/function_base.hpp:21:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index.hpp:29:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index/stl_type_index.hpp:47:
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:132:33: warning: &#39;unary_function&lt;unsigned long long, unsigned long&gt;&#39; is deprecated [-Wdeprecated-declarations]
-        struct hash_base : std::unary_function&lt;T, std::size_t&gt; {};
-                                ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:659:5: note: in instantiation of template class &#39;boost::hash_detail::hash_base&lt;unsigned long long&gt;&#39; requested here
-    BOOST_HASH_SPECIALIZE(boost::ulong_long_type)
-    ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:581:19: note: expanded from macro &#39;BOOST_HASH_SPECIALIZE&#39;
-         : public boost::hash_detail::hash_base&lt;type&gt; \
-                  ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/unary_function.h:23:29: note: &#39;un</code></pre>
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>ary_function&lt;unsigned long long, unsigned long&gt;&#39; has been explicitly marked deprecated here
-struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function
-                            ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:825:41: note: expanded from macro &#39;_LIBCPP_DEPRECATED_IN_CXX11&#39;
-#    define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
-                                        ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro &#39;_LIBCPP_DEPRECATED&#39;
-#      define _LIBCPP_DEPRECATED __attribute__((deprecated))
-                                                ^
-In file included from src/cmdstan/main.cpp:1:
-In file included from src/cmdstan/command.hpp:14:
-In file included from src/cmdstan/command_helper.hpp:20:
-In file included from stan/src/stan/io/dump.hpp:7:
-In file included from stan/lib/stan_math/stan/math/prim.hpp:15:
-In file included from stan/lib/stan_math/stan/math/prim/functor.hpp:16:
-In file included from stan/lib/stan_math/stan/math/prim/functor/integrate_ode_rk45.hpp:6:
-In file included from stan/lib/stan_math/stan/math/prim/functor/ode_rk45.hpp:9:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint.hpp:76:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint/integrate/observer_collection.hpp:23:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function.hpp:30:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/detail/prologue.hpp:17:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/function_base.hpp:21:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index.hpp:29:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index/stl_type_index.hpp:47:
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:132:33: warning: &#39;unary_function&lt;__int128, unsigned long&gt;&#39; is deprecated [-Wdeprec</code></pre>
-</div>
-<div class="cell-output cell-output-stderr">
-<pre><code>ated-declarations]
-        struct hash_base : std::unary_function&lt;T, std::size_t&gt; {};
-                                ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:663:5:</code></pre>
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code> note: in instantiation of template class &#39;boost::hash_detail::hash_base&lt;__int128&gt;&#39; requested here
-    BOOST_HASH_SPECIALIZE(boost::int128_type)
-    ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:581:19: note: expanded from macro &#39;BOOST_HASH_SPECIALIZE&#39;
-         : public boost::hash_detail::hash_base&lt;type&gt; \
-                  ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/unary_function.h:23:29: note: &#39;unary_function&lt;__int128, unsigned long&gt;&#39; has been explicitly marked deprecated here
-struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function
-                            ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:825:41: note: expanded from macro &#39;_LIBCPP_DEPRECATED_IN_CXX11&#39;
-#    define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
-                                        ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro &#39;_LIBCPP_DEPRECATED&#39;
-#      define _LIBCPP_DEPRECATED __attribute__((deprecated))
-                                                ^
-In file included from src/cmdstan/main.cpp:1:
-In file included from src/cmdstan/command.hpp:14:
-In file included from src/cmdstan/command_helper.hpp:20:
-In file included from stan/src/stan/io/dump.hpp:7:
-In file included from stan/lib/stan_math/stan/math/prim.hpp:15:
-In file included from stan/lib/stan_math/stan/math/prim/functor.hpp:16:
-In file included from stan/lib/stan_math/stan/math/prim/functor/integrate_ode_rk45.hpp:6:
-In file included from stan/lib/stan_math/stan/math/prim/functor/ode_rk45.hpp:9:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint.hpp:76:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint/integrate/observer_collection.hpp:23:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function.hpp:30:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost</code></pre>
-</div>
-<div class="cell-output cell-output-stderr">
-<pre><code>/function/detail/prologue.hpp:17:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/function_base.hpp:21:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index.hpp:29:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index/stl_type_index.hpp:47:
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:132:33: warning: &#39;unary_function&lt;unsigned __int128, unsigned long&gt;&#39; is deprecated [-Wdeprecated-declarations]
-        struct hash_base : std::unary_function&lt;T, std::size_t&gt; {};
-                                ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:664:5: note: in instantiation of template class &#39;boost::hash_detail::hash_base&lt;unsigned __int128&gt;&#39; requested here
-    BOOST_HASH_SPECIALIZE(boost::uint128_type)
-    ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:581:19: note: expanded from macro &#39;BOOST_HASH_SPECIALIZE&#39;
-         : public boost::hash_detail::hash_base&lt;type&gt; \
-                  ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/unary_function.h:23:29: note: &#39;unary_function&lt;unsigned __int128, unsigned long&gt;&#39; has been explicitly marked deprecated here
-struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function
-                            ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:825:41: note: expanded from macro &#39;_LIBCPP_DEPRECATED_IN_CXX11&#39;
-#    define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
-                                        ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro &#39;_LIBCPP_DEPRECATED&#39;
-#      define _LIBCPP_DEPRECATED __attribute__((deprecated))
-                                                ^
-In file included from src/cmdstan/main.cpp:1:
-In file included from src/cmdstan/command.hpp:14:
-In file included from src/cmdstan/command_helper.hpp:20:
-In file included from stan/</code></pre>
-</div>
-<div class="cell-output cell-output-stderr">
-<pre><code>src/stan/io/dump.hpp:7:
-In file included from stan/lib/stan_math/stan/math/prim.hpp:15:
-In file included from stan/lib/stan_math/stan/math/prim/functor.hpp:16:
-In file included from stan/lib/stan_math/stan/math/prim/functor/integrate_ode_rk45.hpp:6:
-In file included from stan/lib/stan_math/stan/math/prim/functor/ode_rk45.hpp:9:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint.hpp:76:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint/integrate/observer_collection.hpp:23:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function.hpp:30:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/detail/prologue.hpp:17:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/function_base.hpp:21:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index.hpp:29:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index/stl_type_index.hpp:47:
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:132:33: warning: &#39;unary_function&lt;std::type_index, unsigned long&gt;&#39; is deprecated [-Wdeprecated-declarations]
-        struct hash_base : std::unary_function&lt;T, std::size_t&gt; {};
-                                ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:679:5: note: in instantiation of template class &#39;boost::hash_detail::hash_base&lt;std::type_index&gt;&#39; requested here
-    BOOST_HASH_SPECIALIZE(std::type_index)
-    ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:581:19: note: expanded from macro &#39;BOOST_HASH_SPECIALIZE&#39;
-         : public boost::hash_detail::hash_base&lt;type&gt; \
-                  ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/unary_function.h:23:29: note: &#39;unary_function&lt;std::type_index, unsigned long&gt;&#39; has been explicitly marked deprecated here
-struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function
-                            ^
-/Li</code></pre>
+<pre><code>Chain 2 </code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>brary/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:825:41: note: expanded from macro &#39;_LIBCPP_DEPRECATED_IN_CXX11&#39;
-#    define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
-                                        ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro &#39;_LIBCPP_DEPRECATED&#39;
-#      define _LIBCPP_DEPRECATED __attribute__((deprecated))
-                                                ^</code></pre>
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>In file included from src/cmdstan/main.cpp:1:
-In file included from src/cmdstan/command.hpp:14:
-In file included from src/cmdstan/command_helper.hpp:20:
-In file included from stan/src/stan/io/dump.hpp:7:
-In file included from stan/lib/stan_math/stan/math/prim.hpp:15:
-In file included from stan/lib/stan_math/stan/math/prim/functor.hpp:16:
-In file included from stan/lib/stan_math/stan/math/prim/functor/integrate_ode_rk45.hpp:6:
-In file included from stan/lib/stan_math/stan/math/prim/functor/ode_rk45.hpp:9:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint.hpp:76:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint/integrate/observer_collection.hpp:23:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function.hpp:30:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/detail/prologue.hpp:17:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/function_base.hpp:21:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index.hpp:29:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index/stl_type_index.hpp:47:
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:132:33: warning: &#39;unary_function&lt;const std::error_category *, unsigned long&gt;&#39; is deprecated [-Wdeprecated-declarations]
-        struct hash_base : std::unary_function&lt;T, std::size_t&gt; {};
-                                ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:692:18: note: in instantiation of template class &#39;boost::hash_detail::hash_base&lt;const std::error_category *&gt;&#39; requested here
-        : public boost::hash_detail::hash_base&lt;T*&gt;
-                 ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:420:24: note: in instantiation of template class &#39;boost::hash&lt;const std::error_category *&gt;&#39; requested here
-        boost::hash&lt;T&gt; hasher;
-                       ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_has</code></pre>
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -5.14659e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>h/hash.hpp:551:9: note: in instantiation of function template specialization &#39;boost::hash_combine&lt;const std::error_category *&gt;&#39; requested here
-        hash_combine(seed, &amp;v.category());
-        ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/unary_function.h:23:29: note: &#39;unary_function&lt;const std::error_category *, unsigned long&gt;&#39; has been explicitly marked deprecated here
-struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function
-                            ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:825:41: note: expanded from macro &#39;_LIBCPP_DEPRECATED_IN_CXX11&#39;
-#    define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
-                                        ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro &#39;_LIBCPP_DEPRECATED&#39;
-#      define _LIBCPP_DEPRECATED __attribute__((deprecated))
-                                                ^</code></pre>
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>33 warnings generated.</code></pre>
-</div>
-<div class="cell-output cell-output-stderr">
-<pre><code>In file included from stan/src/stan/model/model_header.hpp:4:
-In file included from stan/lib/stan_math/stan/math.hpp:19:
-In file included from stan/lib/stan_math/stan/math/rev.hpp:8:
-In file included from stan/lib/stan_math/stan/math/rev/core.hpp:10:
-In file included from stan/lib/stan_math/stan/math/rev/core/chainable_object.hpp:6:
-In file included from stan/lib/stan_math/stan/math/rev/core/typedefs.hpp:7:
-In file included from stan/lib/stan_math/stan/math/rev/core/Eigen_NumTraits.hpp:5:
-In file included from stan/lib/stan_math/stan/math/prim/core.hpp:4:
-In file included from stan/lib/stan_math/stan/math/prim/core/init_threadpool_tbb.hpp:6:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/lexical_cast.hpp:31:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/lexical_cast/bad_lexical_cast.hpp:28:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/throw_exception.hpp:24:
-stan/lib/stan_math/lib/boost_1.78.0/boost/assert/source_location.hpp:75:14: warning: &#39;sprintf&#39; is deprecated: This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
-        std::sprintf( buffer, &quot;:%ld&quot;, static_cast&lt;long&gt;( line() ) );
-             ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: &#39;sprintf&#39; has been explicitly marked deprecated here
-__deprecated_msg(&quot;This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.&quot;)
-^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro &#39;__deprecated_msg&#39;
-        #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
-                                                      ^
-In file included from stan/src/stan/model/model_header.hpp:4:
-In file</code></pre>
-</div>
-<div class="cell-output cell-output-stderr">
-<pre><code> included from stan/lib/stan_math/stan/math.hpp:19:
-In file included from stan/lib/stan_math/stan/math/rev.hpp:8:
-In file included from stan/lib/stan_math/stan/math/rev/core.hpp:10:
-In file included from stan/lib/stan_math/stan/math/rev/core/chainable_object.hpp:6:
-In file included from stan/lib/stan_math/stan/math/rev/core/typedefs.hpp:7:
-In file included from stan/lib/stan_math/stan/math/rev/core/Eigen_NumTraits.hpp:5:
-In file included from stan/lib/stan_math/stan/math/prim/core.hpp:4:
-In file included from stan/lib/stan_math/stan/math/prim/core/init_threadpool_tbb.hpp:6:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/lexical_cast.hpp:31:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/lexical_cast/bad_lexical_cast.hpp:28:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/throw_exception.hpp:24:
-stan/lib/stan_math/lib/boost_1.78.0/boost/assert/source_location.hpp:80:18: warning: &#39;sprintf&#39; is deprecated: This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
-            std::sprintf( buffer, &quot;:%ld&quot;, static_cast&lt;long&gt;( column() ) );
-                 ^</code></pre>
-</div>
-<div class="cell-output cell-output-stderr">
-<pre><code>/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: &#39;sprintf&#39; has been explicitly marked deprecated here
-__deprecated_msg(&quot;This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.&quot;)
-^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro &#39;__deprecated_msg&#39;
-        #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
-                                                      ^</code></pre>
-</div>
-<div class="cell-output cell-output-stderr">
-<pre><code>In file included from stan/src/stan/model/model_header.hpp:4:
-In file included from stan/lib/stan_math/stan/math.hpp:19:
-In file included from stan/lib/stan_math/stan/math/rev.hpp:8:
-In file included from stan/lib/stan_math/stan/math/rev/core.hpp:10:
-In file included from stan/lib/stan_math/stan/math/rev/core/chainable_object.hpp:6:
-In file included from stan/lib/stan_math/stan/math/rev/core/typedefs.hpp:7:
-In file included from stan/lib/stan_math/stan/math/rev/core/Eigen_NumTraits.hpp:5:
-In file included from stan/lib/stan_math/stan/math/prim/core.hpp:4:
-In file included from stan/lib/stan_math/stan/math/prim/core/init_threadpool_tbb.hpp:6:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/lexical_cast.hpp:32:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/lexical_cast/try_lexical_convert.hpp:44:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/lexical_cast/detail/converter_lexical.hpp:54:
-stan/lib/stan_math/lib/boost_1.78.0/boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: &#39;sprintf&#39; is deprecated: This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
-                    sprintf(begin,
-                    ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: &#39;sprintf&#39; has been explicitly marked deprecated here
-__deprecated_msg(&quot;This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.&quot;)
-^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro &#39;__deprecated_msg&#39;
-        #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
-                                                      ^
-In file included from stan/src/stan/model/model</code></pre>
-</div>
-<div class="cell-output cell-output-stderr">
-<pre><code>_header.hpp:4:
-In file included from stan/lib/stan_math/stan/math.hpp:19:
-In file included from stan/lib/stan_math/stan/math/rev.hpp:8:
-In file included from stan/lib/stan_math/stan/math/rev/core.hpp:10:
-In file included from stan/lib/stan_math/stan/math/rev/core/chainable_object.hpp:6:
-In file included from stan/lib/stan_math/stan/math/rev/core/typedefs.hpp:7:
-In file included from stan/lib/stan_math/stan/math/rev/core/Eigen_NumTraits.hpp:5:
-In file included from stan/lib/stan_math/stan/math/prim/core.hpp:4:
-In file included from stan/lib/stan_math/stan/math/prim/core/init_threadpool_tbb.hpp:6:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/lexical_cast.hpp:32:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/lexical_cast/try_lexical_convert.hpp:44:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/lexical_cast/detail/converter_lexical.hpp:54:
-stan/lib/stan_math/lib/boost_1.78.0/boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: &#39;sprintf&#39; is deprecated: This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
-                    sprintf(begin,
-                    ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: &#39;sprintf&#39; has been explicitly marked deprecated here
-__deprecated_msg(&quot;This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.&quot;)
-^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro &#39;__deprecated_msg&#39;
-        #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
-                                                      ^</code></pre>
-</div>
-<div class="cell-output cell-output-stderr">
-<pre><code>In file included from stan/src/stan/model/model_header.hpp:4:
-In file included from stan/lib/stan_math/stan/math.hpp:19:
-In file included from stan/lib/stan_math/stan/math/rev.hpp:8:
-In file included from stan/lib/stan_math/stan/math/rev/core.hpp:10:
-In file included from stan/lib/stan_math/stan/math/rev/core/chainable_object.hpp:6:
-In file included from stan/lib/stan_math/stan/math/rev/core/typedefs.hpp:7:
-In file included from stan/lib/stan_math/stan/math/rev/core/Eigen_NumTraits.hpp:5:
-In file included from stan/lib/stan_math/stan/math/prim/core.hpp:4:
-In file included from stan/lib/stan_math/stan/math/prim/core/init_threadpool_tbb.hpp:6:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/lexical_cast.hpp:32:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/lexical_cast/try_lexical_convert.hpp:44:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/lexical_cast/detail/converter_lexical.hpp:54:
-stan/lib/stan_math/lib/boost_1.78.0/boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: &#39;sprintf&#39; is deprecated: This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
-                    sprintf(begin,
-                    ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: &#39;sprintf&#39; has been explicitly marked deprecated here
-__deprecated_msg(&quot;This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.&quot;)
-^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro &#39;__deprecated_msg&#39;
-        #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
-                                                      ^</code></pre>
-</div>
-<div class="cell-output cell-output-stderr">
-<pre><code>In file included from stan/src/stan/model/model_header.hpp:4:
-In file included from stan/lib/stan_math/stan/math.hpp:19:
-In file included from stan/lib/stan_math/stan/math/rev.hpp:10:
-In file included from stan/lib/stan_math/stan/math/rev/fun.hpp:200:
-In file included from stan/lib/stan_math/stan/math/prim/functor.hpp:16:
-In file included from stan/lib/stan_math/stan/math/prim/functor/integrate_ode_rk45.hpp:6:
-In file included from stan/lib/stan_math/stan/math/prim/functor/ode_rk45.hpp:9:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint.hpp:37:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint/stepper/dense_output_runge_kutta.hpp:40:
-stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint/integrate/max_step_checker.hpp:72:18: warning: &#39;sprintf&#39; is deprecated: This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
-            std::sprintf(error_msg, &quot;Max number of iterations exceeded (%d).&quot;, m_max_steps);
-                 ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: &#39;sprintf&#39; has been explicitly marked deprecated here
-__deprecated_msg(&quot;This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.&quot;)
-^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro &#39;__deprecated_msg&#39;
-        #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
-                                                      ^</code></pre>
-</div>
-<div class="cell-output cell-output-stderr">
-<pre><code>In file included from stan/src/stan/model/model_header.hpp:4:
-In file included from stan/lib/stan_math/stan/math.hpp:19:
-In file included from stan/lib/stan_math/stan/math/rev.hpp:10:
-In file included from stan/lib/stan_math/stan/math/rev/fun.hpp:200:
-In file included from stan/lib/stan_math/stan/math/prim/functor.hpp:16:
-In file included from stan/lib/stan_math/stan/math/prim/functor/integrate_ode_rk45.hpp:6:
-In file included from stan/lib/stan_math/stan/math/prim/functor/ode_rk45.hpp:9:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint.hpp:37:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint/stepper/dense_output_runge_kutta.hpp:40:
-stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint/integrate/max_step_checker.hpp:104:18: warning: &#39;sprintf&#39; is deprecated: This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
-            std::sprintf(error_msg, &quot;Max number of iterations exceeded (%d). A new step size was not found.&quot;, m_max_steps);
-                 ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: &#39;sprintf&#39; has been explicitly marked deprecated here
-__deprecated_msg(&quot;This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.&quot;)
-^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro &#39;__deprecated_msg&#39;
-        #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
-                                                      ^</code></pre>
-</div>
-<div class="cell-output cell-output-stderr">
-<pre><code>In file included from stan/src/stan/model/model_header.hpp:4:
-In file included from stan/lib/stan_math/stan/math.hpp:19:
-In file included from stan/lib/stan_math/stan/math/rev.hpp:10:
-In file included from stan/lib/stan_math/stan/math/rev/fun.hpp:200:
-In file included from stan/lib/stan_math/stan/math/prim/functor.hpp:16:
-In file included from stan/lib/stan_math/stan/math/prim/functor/integrate_ode_rk45.hpp:6:
-In file included from stan/lib/stan_math/stan/math/prim/functor/ode_rk45.hpp:9:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint.hpp:76:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint/integrate/observer_collection.hpp:23:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function.hpp:30:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/detail/prologue.hpp:17:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/function_base.hpp:21:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index.hpp:29:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index/stl_type_index.hpp:47:
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:132:33: warning: &#39;unary_function&lt;bool, unsigned long&gt;&#39; is deprecated [-Wdeprecated-declarations]
-        struct hash_base : std::unary_function&lt;T, std::size_t&gt; {};
-                                ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:609:5: note: in instantiation of template class &#39;boost::hash_detail::hash_base&lt;bool&gt;&#39; requested here
-    BOOST_HASH_SPECIALIZE(bool)
-    ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:581:19: note: expanded from macro &#39;BOOST_HASH_SPECIALIZE&#39;
-         : public boost::hash_detail::hash_base&lt;type&gt; \
-                  ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/unary_function.h:23:29: note: &#39;unary_function&lt;bool, unsigned long&gt;&#39; has been explicitly marked </code></pre>
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>deprecated here
-struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function
-                            ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:825:41: note: expanded from macro &#39;_LIBCPP_DEPRECATED_IN_CXX11&#39;
-#    define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
-                                        ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro &#39;_LIBCPP_DEPRECATED&#39;
-#      define _LIBCPP_DEPRECATED __attribute__((deprecated))
-                                                ^</code></pre>
+<pre><code>Chain 2 </code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>In file included from stan/src/stan/model/model_header.hpp:4:
-In file included from stan/lib/stan_math/stan/math.hpp:19:
-In file included from stan/lib/stan_math/stan/math/rev.hpp:10:
-In file included from stan/lib/stan_math/stan/math/rev/fun.hpp:200:
-In file included from stan/lib/stan_math/stan/math/prim/functor.hpp:16:
-In file included from stan/lib/stan_math/stan/math/prim/functor/integrate_ode_rk45.hpp:6:
-In file included from stan/lib/stan_math/stan/math/prim/functor/ode_rk45.hpp:9:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint.hpp:76:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint/integrate/observer_collection.hpp:23:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function.hpp:30:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/detail/prologue.hpp:17:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/function_base.hpp:21:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index.hpp:29:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index/stl_type_index.hpp:47:
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:132:33: warning: &#39;unary_function&lt;char, unsigned long&gt;&#39; is deprecated [-Wdeprecated-declarations]
-        struct hash_base : std::unary_function&lt;T, std::size_t&gt; {};
-                                ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:610:5: note: in instantiation of template class &#39;boost::hash_detail::hash_base&lt;char&gt;&#39; requested here
-    BOOST_HASH_SPECIALIZE(char)
-    ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:581:19: note: expanded from macro &#39;BOOST_HASH_SPECIALIZE&#39;
-         : public boost::hash_detail::hash_base&lt;type&gt; \
-                  ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/unary_function.h:23:29: note: &#39;unary_function&lt;char, unsigned long&gt;&#39; has been explicitly marked </code></pre>
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>deprecated here
-struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function
-                            ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:825:41: note: expanded from macro &#39;_LIBCPP_DEPRECATED_IN_CXX11&#39;
-#    define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
-                                        ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro &#39;_LIBCPP_DEPRECATED&#39;
-#      define _LIBCPP_DEPRECATED __attribute__((deprecated))
-                                                ^
-In file included from stan/src/stan/model/model_header.hpp:4:
-In file included from stan/lib/stan_math/stan/math.hpp:19:
-In file included from stan/lib/stan_math/stan/math/rev.hpp:10:
-In file included from stan/lib/stan_math/stan/math/rev/fun.hpp:200:
-In file included from stan/lib/stan_math/stan/math/prim/functor.hpp:16:
-In file included from stan/lib/stan_math/stan/math/prim/functor/integrate_ode_rk45.hpp:6:
-In file included from stan/lib/stan_math/stan/math/prim/functor/ode_rk45.hpp:9:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint.hpp:76:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint/integrate/observer_collection.hpp:23:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function.hpp:30:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/detail/prologue.hpp:17:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/function_base.hpp:21:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index.hpp:29:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index/stl_type_index.hpp:47:
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:132:33: warning: &#39;unary_function&lt;signed char, unsigned long&gt;&#39; is deprecated [-Wdeprecated-declarations]
-        struct hash_base : std::unary_function&lt;T, std::size_t&gt; {};
-   </code></pre>
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -6.81513e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>                             ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:611:5: note: in instantiation of template class &#39;boost::hash_detail::hash_base&lt;signed char&gt;&#39; requested here
-    BOOST_HASH_SPECIALIZE(signed char)
-    ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:581:19: note: expanded from macro &#39;BOOST_HASH_SPECIALIZE&#39;
-         : public boost::hash_detail::hash_base&lt;type&gt; \
-                  ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/unary_function.h:23:29: note: &#39;unary_function&lt;signed char, unsigned long&gt;&#39; has been explicitly marked deprecated here
-struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function
-                            ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:825:41: note: expanded from macro &#39;_LIBCPP_DEPRECATED_IN_CXX11&#39;
-#    define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
-                                        ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro &#39;_LIBCPP_DEPRECATED&#39;
-#      define _LIBCPP_DEPRECATED __attribute__((deprecated))
-                                                ^
-In file included from stan/src/stan/model/model_header.hpp:4:
-In file included from stan/lib/stan_math/stan/math.hpp:19:
-In file included from stan/lib/stan_math/stan/math/rev.hpp:10:
-In file included from stan/lib/stan_math/stan/math/rev/fun.hpp:200:
-In file included from stan/lib/stan_math/stan/math/prim/functor.hpp:16:
-In file included from stan/lib/stan_math/stan/math/prim/functor/integrate_ode_rk45.hpp:6:
-In file included from stan/lib/stan_math/stan/math/prim/functor/ode_rk45.hpp:9:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint.hpp:76:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint/integrate/observer_collection.hpp:23:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/</code></pre>
-</div>
-<div class="cell-output cell-output-stderr">
-<pre><code>boost/function.hpp:30:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/detail/prologue.hpp:17:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/function_base.hpp:21:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index.hpp:29:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index/stl_type_index.hpp:47:
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:132:33: warning: &#39;unary_function&lt;unsigned char, unsigned long&gt;&#39; is deprecated [-Wdeprecated-declarations]
-        struct hash_base : std::unary_function&lt;T, std::size_t&gt; {};
-                                ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:612:5: note: in instantiation of template class &#39;boost::hash_detail::hash_base&lt;unsigned char&gt;&#39; requested here
-    BOOST_HASH_SPECIALIZE(unsigned char)
-    ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:581:19: note: expanded from macro &#39;BOOST_HASH_SPECIALIZE&#39;
-         : public boost::hash_detail::hash_base&lt;type&gt; \
-                  ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/unary_function.h:23:29: note: &#39;unary_function&lt;unsigned char, unsigned long&gt;&#39; has been explicitly marked deprecated here
-struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function
-                            ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:825:41: note: expanded from macro &#39;_LIBCPP_DEPRECATED_IN_CXX11&#39;
-#    define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
-                                        ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro &#39;_LIBCPP_DEPRECATED&#39;
-#      define _LIBCPP_DEPRECATED __attribute__((deprecated))
-                                                ^
-In file included from stan/src/stan/model/model_header.hpp:4:
-In file included from stan/lib/stan_math/stan/math</code></pre>
-</div>
-<div class="cell-output cell-output-stderr">
-<pre><code>.hpp:19:
-In file included from stan/lib/stan_math/stan/math/rev.hpp:10:
-In file included from stan/lib/stan_math/stan/math/rev/fun.hpp:200:
-In file included from </code></pre>
-</div>
-<div class="cell-output cell-output-stderr">
-<pre><code>stan/lib/stan_math/stan/math/prim/functor.hpp:16:
-In file included from stan/lib/stan_math/stan/math/prim/functor/integrate_ode_rk45.hpp:6:
-In file included from stan/lib/stan_math/stan/math/prim/functor/ode_rk45.hpp:9:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint.hpp:76:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint/integrate/observer_collection.hpp:23:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function.hpp:30:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/detail/prologue.hpp:17:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/function_base.hpp:21:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index.hpp:29:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index/stl_type_index.hpp:47:
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:132:33: warning: &#39;unary_function&lt;wchar_t, unsigned long&gt;&#39; is deprecated [-Wdeprecated-declarations]
-        struct hash_base : std::unary_function&lt;T, std::size_t&gt; {};
-                                ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:614:5: note: in instantiation of template class &#39;boost::hash_detail::hash_base&lt;wchar_t&gt;&#39; requested here
-    BOOST_HASH_SPECIALIZE(wchar_t)
-    ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:581:19: note: expanded from macro &#39;BOOST_HASH_SPECIALIZE&#39;
-         : public boost::hash_detail::hash_base&lt;type&gt; \
-                  ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/unary_function.h:23:29: note: &#39;unary_function&lt;wchar_t, unsigned long&gt;&#39; has been explicitly marked deprecated here
-struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function
-                            ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:825:41: note: expanded from macro &#39;_LIBCPP_DEPRECATED_IN_CXX11&#39;
-#</code></pre>
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>    define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
-                                        ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro &#39;_LIBCPP_DEPRECATED&#39;
-#      define _LIBCPP_DEPRECATED __attribute__((deprecated))
-                                                ^
-In file included from stan/src/stan/model/model_header.hpp:4:
-In file included from stan/lib/stan_math/stan/math.hpp:19:
-In file included from stan/lib/stan_math/stan/math/rev.hpp:10:
-In file included from stan/lib/stan_math/stan/math/rev/fun.hpp:200:
-In file included from stan/lib/stan_math/stan/math/prim/functor.hpp:16:
-In file included from stan/lib/stan_math/stan/math/prim/functor/integrate_ode_rk45.hpp:6:
-In file included from stan/lib/stan_math/stan/math/prim/functor/ode_rk45.hpp:9:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint.hpp:76:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint/integrate/observer_collection.hpp:23:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function.hpp:30:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/detail/prologue.hpp:17:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/function_base.hpp:21:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index.hpp:29:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index/stl_type_index.hpp:47:
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:132:33: warning: &#39;unary_function&lt;char16_t, unsigned long&gt;&#39; is deprecated [-Wdeprecated-declarations]
-        struct hash_base : std::unary_function&lt;T, std::size_t&gt; {};
-                                ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:617:5: note: in instantiation of template class &#39;boost::hash_detail::hash_base&lt;char16_t&gt;&#39; requested here
-    BOOST_HASH_SPECIALIZE(char16_t)
-    ^
-stan/lib/stan_math/li</code></pre>
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>b/boost_1.78.0/boost/container_hash/hash.hpp:581:19: note: expanded from macro &#39;BOOST_HASH_SPECIALIZE&#39;
-         : public boost::hash_detail::hash_base&lt;type&gt; \
-                  ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/unary_function.h:23:29: note: &#39;unary_function&lt;char16_t, unsigned long&gt;&#39; has been explicitly marked deprecated here
-struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function
-                            ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:825:41: note: expanded from macro &#39;_LIBCPP_DEPRECATED_IN_CXX11&#39;
-#    define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
-                                        ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro &#39;_LIBCPP_DEPRECATED&#39;
-#      define _LIBCPP_DEPRECATED __attribute__((deprecated))
-                                                ^
-In file included from stan/src/stan/model/model_header.hpp:4:
-In file included from stan/lib/stan_math/stan/math.hpp:19:
-In file included from stan/lib/stan_math/stan/math/rev.hpp:10:
-In file included from stan/lib/stan_math/stan/math/rev/fun.hpp:200:
-In file included from stan/lib/stan_math/stan/math/prim/functor.hpp:16:
-In file included from stan/lib/stan_math/stan/math/prim/functor/integrate_ode_rk45.hpp:6:
-In file included from stan/lib/stan_math/stan/math/prim/functor/ode_rk45.hpp:9:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint.hpp:76:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint/integrate/observer_collection.hpp:23:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function.hpp:30:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/detail/prologue.hpp:17:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/function_base.hpp:21:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/b</code></pre>
-</div>
-<div class="cell-output cell-output-stderr">
-<pre><code>oost/type_index.hpp:29:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index/stl_type_index.hpp:47:
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:132:33: warning: &#39;unary_function&lt;char32_t, unsigned long&gt;&#39; is deprecated [-Wdeprecated-declarations]
-        struct hash_base : std::unary_function&lt;T, std::size_t&gt; {};
-                                ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:620:5: note: in instantiation of template class &#39;boost::hash_detail::hash_base&lt;char32_t&gt;&#39; requested here
-    BOOST_HASH_SPECIALIZE(char32_t)
-    ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:581:19: note: expanded from macro &#39;BOOST_HASH_SPECIALIZE&#39;
-         : public boost::hash_detail::hash_base&lt;type&gt; \
-                  ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/unary_function.h:23:29: note: &#39;unary_function&lt;char32_t, unsigned long&gt;&#39; has been explicitly marked deprecated here
-struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function
-                            ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:825:41: note: expanded from macro &#39;_LIBCPP_DEPRECATED_IN_CXX11&#39;
-#    define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
-                                        ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro &#39;_LIBCPP_DEPRECATED&#39;
-#      define _LIBCPP_DEPRECATED __attribute__((deprecated))
-                                                ^
-In file included from stan/src/stan/model/model_header.hpp:4:
-In file included from stan/lib/stan_math/stan/math.hpp:19:
-In file included from stan/lib/stan_math/stan/math/rev.hpp:10:
-In file included from stan/lib/stan_math/stan/math/rev/fun.hpp:200:
-In file included from stan/lib/stan_math/stan/math/prim/functor.hpp:16:
-In file included from stan/lib/stan_math/stan/math/prim/functor/integrate_ode_rk45</code></pre>
-</div>
-<div class="cell-output cell-output-stderr">
-<pre><code>.hpp:6:
-In file included from stan/lib/stan_math/stan/math/prim/functor/ode_rk45.hpp:9:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint.hpp:76:</code></pre>
-</div>
-<div class="cell-output cell-output-stderr">
-<pre><code>In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint/integrate/observer_collection.hpp:23:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function.hpp:30:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/detail/prologue.hpp:17:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/function_base.hpp:21:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index.hpp:29:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index/stl_type_index.hpp:47:
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:132:33: warning: &#39;unary_function&lt;short, unsigned long&gt;&#39; is deprecated [-Wdeprecated-declarations]
-        struct hash_base : std::unary_function&lt;T, std::size_t&gt; {};
-                                ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:622:5: note: in instantiation of template class &#39;boost::hash_detail::hash_base&lt;short&gt;&#39; requested here
-    BOOST_HASH_SPECIALIZE(short)
-    ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:581:19: note: expanded from macro &#39;BOOST_HASH_SPECIALIZE&#39;
-         : public boost::hash_detail::hash_base&lt;type&gt; \
-                  ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/unary_function.h:23:29: note: &#39;unary_function&lt;short, unsigned long&gt;&#39; has been explicitly marked deprecated here
-struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function
-                            ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:825:41: note: expanded from macro &#39;_LIBCPP_DEPRECATED_IN_CXX11&#39;
-#    define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
-                                        ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro &#39;_LIBCPP_DEPRECATED&#39;
-#      define _LIBCPP_DEPRECATED __attribute__((deprecated))
-                   </code></pre>
-</div>
-<div class="cell-output cell-output-stderr">
-<pre><code>                             ^
-In file included from stan/src/stan/model/model_header.hpp:4:
-In file included from stan/lib/stan_math/stan/math.hpp:19:
-In file included from stan/lib/stan_math/stan/math/rev.hpp:10:
-In file included from stan/lib/stan_math/stan/math/rev/fun.hpp:200:
-In file included from stan/lib/stan_math/stan/math/prim/functor.hpp:16:
-In file included from stan/lib/stan_math/stan/math/prim/functor/integrate_ode_rk45.hpp:6:
-In file included from stan/lib/stan_math/stan/math/prim/functor/ode_rk45.hpp:9:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint.hpp:76:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint/integrate/observer_collection.hpp:23:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function.hpp:30:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/detail/prologue.hpp:17:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/function_base.hpp:21:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index.hpp:29:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index/stl_type_index.hpp:47:
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:132:33: warning: &#39;unary_function&lt;unsigned short, unsigned long&gt;&#39; is deprecated [-Wdeprecated-declarations]
-        struct hash_base : std::unary_function&lt;T, std::size_t&gt; {};
-                                ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:623:5: note: in instantiation of template class &#39;boost::hash_detail::hash_base&lt;unsigned short&gt;&#39; requested here
-    BOOST_HASH_SPECIALIZE(unsigned short)
-    ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:581:19: note: expanded from macro &#39;BOOST_HASH_SPECIALIZE&#39;
-         : public boost::hash_detail::hash_base&lt;type&gt; \
-                  ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/unary_function.h:23:29: note: &#39;una</code></pre>
+<pre><code>Chain 2 </code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>ry_function&lt;unsigned short, unsigned long&gt;&#39; has been explicitly marked deprecated here
-struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function
-                            ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:825:41: note: expanded from macro &#39;_LIBCPP_DEPRECATED_IN_CXX11&#39;
-#    define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
-                                        ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro &#39;_LIBCPP_DEPRECATED&#39;
-#      define _LIBCPP_DEPRECATED __attribute__((deprecated))
-                                                ^
-In file included from stan/src/stan/model/model_header.hpp:4:
-In file included from stan/lib/stan_math/stan/math.hpp:19:
-In file included from stan/lib/stan_math/stan/math/rev.hpp:10:
-In file included from stan/lib/stan_math/stan/math/rev/fun.hpp:200:
-In file included from stan/lib/stan_math/stan/math/prim/functor.hpp:16:
-In file included from stan/lib/stan_math/stan/math/prim/functor/integrate_ode_rk45.hpp:6:
-In file included from stan/lib/stan_math/stan/math/prim/functor/ode_rk45.hpp:9:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint.hpp:76:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint/integrate/observer_collection.hpp:23:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function.hpp:30:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/detail/prologue.hpp:17:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/function_base.hpp:21:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index.hpp:29:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index/stl_type_index.hpp:47:
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:132:33: warning: &#39;unary_function&lt;int, unsigned long&gt;&#39; is deprecated [-Wdeprecated-declarations]
-       </code></pre>
-</div>
-<div class="cell-output cell-output-stderr">
-<pre><code> struct hash_base : std::unary_function&lt;T, std::size_t&gt; {};
-                                ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:624:5: note: in instantiation of template class &#39;boost::hash_detail::hash_base&lt;int&gt;&#39; requested here
-    BOOST_HASH_SPECIALIZE(int)
-    ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:581:19: note: expanded from macro &#39;BOOST_HASH_SPECIALIZE&#39;
-         : public boost::hash_detail::hash_base&lt;type&gt; \
-                  ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/unary_function.h:23:29: note: &#39;unary_function&lt;int, unsigned long&gt;&#39; has been explicitly marked deprecated here
-struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function
-                            ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:825:41: note: expanded from macro &#39;_LIBCPP_DEPRECATED_IN_CXX11&#39;
-#    define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
-                                        ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro &#39;_LIBCPP_DEPRECATED&#39;
-#      define _LIBCPP_DEPRECATED __attribute__((deprecated))
-                                                ^
-In file included from stan/src/stan/model/model_header.hpp:4:
-In file included from stan/lib/stan_math/stan/math.hpp:19:
-In file included from stan/lib/stan_math/stan/math/rev.hpp:10:
-In file included from stan/lib/stan_math/stan/math/rev/fun.hpp:200:
-In file included from stan/lib/stan_math/stan/math/prim/functor.hpp:16:
-In file included from stan/lib/stan_math/stan/math/prim/functor/integrate_ode_rk45.hpp:6:
-In file included from stan/lib/stan_math/stan/math/prim/functor/ode_rk45.hpp:9:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint.hpp:76:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint/integrate/observer_collection.hpp:23:
-In file included fr</code></pre>
-</div>
-<div class="cell-output cell-output-stderr">
-<pre><code>om stan/lib/stan_math/lib/boost_1.78.0/boost/function.hpp:30:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/detail/prologue.hpp:17:
-In file included from </code></pre>
-</div>
-<div class="cell-output cell-output-stderr">
-<pre><code>stan/lib/stan_math/lib/boost_1.78.0/boost/function/function_base.hpp:21:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index.hpp:29:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index/stl_type_index.hpp:47:
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:132:33: warning: &#39;unary_function&lt;unsigned int, unsigned long&gt;&#39; is deprecated [-Wdeprecated-declarations]
-        struct hash_base : std::unary_function&lt;T, std::size_t&gt; {};
-                                ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:625:5: note: in instantiation of template class &#39;boost::hash_detail::hash_base&lt;unsigned int&gt;&#39; requested here
-    BOOST_HASH_SPECIALIZE(unsigned int)
-    ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:581:19: note: expanded from macro &#39;BOOST_HASH_SPECIALIZE&#39;
-         : public boost::hash_detail::hash_base&lt;type&gt; \
-                  ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/unary_function.h:23:29: note: &#39;unary_function&lt;unsigned int, unsigned long&gt;&#39; has been explicitly marked deprecated here
-struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function
-                            ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:825:41: note: expanded from macro &#39;_LIBCPP_DEPRECATED_IN_CXX11&#39;
-#    define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
-                                        ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro &#39;_LIBCPP_DEPRECATED&#39;
-#      define _LIBCPP_DEPRECATED __attribute__((deprecated))
-                                                ^
-In file included from stan/src/stan/model/model_header.hpp:4:
-In file included from stan/lib/stan_math/stan/math.hpp:19:
-In file included from stan/lib/stan_math/stan/math/rev.hpp:10:
-In file included from stan/lib/stan_math/stan/math/rev/fun.hpp:200:
-In fil</code></pre>
-</div>
-<div class="cell-output cell-output-stderr">
-<pre><code>e included from stan/lib/stan_math/stan/math/prim/functor.hpp:16:
-In file included from stan/lib/stan_math/stan/math/prim/functor/integrate_ode_rk45.hpp:6:
-In file included from stan/lib/stan_math/stan/math/prim/functor/ode_rk45.hpp:9:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint.hpp:76:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint/integrate/observer_collection.hpp:23:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function.hpp:30:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/detail/prologue.hpp:17:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/function_base.hpp:21:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index.hpp:29:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index/stl_type_index.hpp:47:
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:132:33: warning: &#39;unary_function&lt;long, unsigned long&gt;&#39; is deprecated [-Wdeprecated-declarations]
-        struct hash_base : std::unary_function&lt;T, std::size_t&gt; {};
-                                ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:626:5: note: in instantiation of template class &#39;boost::hash_detail::hash_base&lt;long&gt;&#39; requested here
-    BOOST_HASH_SPECIALIZE(long)
-    ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:581:19: note: expanded from macro &#39;BOOST_HASH_SPECIALIZE&#39;
-         : public boost::hash_detail::hash_base&lt;type&gt; \
-                  ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/unary_function.h:23:29: note: &#39;unary_function&lt;long, unsigned long&gt;&#39; has been explicitly marked deprecated here
-struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function
-                            ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:825:41: note: expanded from macro &#39;_LIBCPP_DEPRECATED_IN_CXX1</code></pre>
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>1&#39;
-#    define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
-                                        ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro &#39;_LIBCPP_DEPRECATED&#39;
-#      define _LIBCPP_DEPRECATED __attribute__((deprecated))
-                                                ^
-In file included from stan/src/stan/model/model_header.hpp:4:
-In file included from stan/lib/stan_math/stan/math.hpp:19:
-In file included from stan/lib/stan_math/stan/math/rev.hpp:10:
-In file included from stan/lib/stan_math/stan/math/rev/fun.hpp:200:
-In file included from stan/lib/stan_math/stan/math/prim/functor.hpp:16:
-In file included from stan/lib/stan_math/stan/math/prim/functor/integrate_ode_rk45.hpp:6:
-In file included from stan/lib/stan_math/stan/math/prim/functor/ode_rk45.hpp:9:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint.hpp:76:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint/integrate/observer_collection.hpp:23:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function.hpp:30:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/detail/prologue.hpp:17:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/function_base.hpp:21:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index.hpp:29:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index/stl_type_index.hpp:47:
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:132:33: warning: &#39;unary_function&lt;unsigned long, unsigned long&gt;&#39; is deprecated [-Wdeprecated-declarations]
-        struct hash_base : std::unary_function&lt;T, std::size_t&gt; {};
-                                ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:627:5: note: in instantiation of template class &#39;boost::hash_detail::hash_base&lt;unsigned long&gt;&#39; requested here
-    BOOST_HASH_SPECIALIZE(unsigned long)
-    ^
-st</code></pre>
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -6.81513e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>an/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:581:19: note: expanded from macro &#39;BOOST_HASH_SPECIALIZE&#39;
-         : public boost::hash_detail::hash_base&lt;type&gt; \
-                  ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/unary_function.h:23:29: note: &#39;unary_function&lt;unsigned long, unsigned long&gt;&#39; has been explicitly marked deprecated here
-struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function
-                            ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:825:41: note: expanded from macro &#39;_LIBCPP_DEPRECATED_IN_CXX11&#39;
-#    define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
-                                        ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro &#39;_LIBCPP_DEPRECATED&#39;
-#      define _LIBCPP_DEPRECATED __attribute__((deprecated))
-                                                ^
-In file included from stan/src/stan/model/model_header.hpp:4:
-In file included from stan/lib/stan_math/stan/math.hpp:19:
-In file included from stan/lib/stan_math/stan/math/rev.hpp:10:
-In file included from stan/lib/stan_math/stan/math/rev/fun.hpp:200:
-In file included from stan/lib/stan_math/stan/math/prim/functor.hpp:16:
-In file included from stan/lib/stan_math/stan/math/prim/functor/integrate_ode_rk45.hpp:6:
-In file included from stan/lib/stan_math/stan/math/prim/functor/ode_rk45.hpp:9:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint.hpp:76:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint/integrate/observer_collection.hpp:23:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function.hpp:30:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/detail/prologue.hpp:17:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/function_base.hpp:21:
-In file included from stan/lib/stan</code></pre>
-</div>
-<div class="cell-output cell-output-stderr">
-<pre><code>_math/lib/boost_1.78.0/boost/type_index.hpp:29:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index/stl_type_index.hpp:47:</code></pre>
-</div>
-<div class="cell-output cell-output-stderr">
-<pre><code>stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:132:33: warning: &#39;unary_function&lt;float, unsigned long&gt;&#39; is deprecated [-Wdeprecated-declarations]
-        struct hash_base : std::unary_function&lt;T, std::size_t&gt; {};
-                                ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:629:5: note: in instantiation of template class &#39;boost::hash_detail::hash_base&lt;float&gt;&#39; requested here
-    BOOST_HASH_SPECIALIZE(float)
-    ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:581:19: note: expanded from macro &#39;BOOST_HASH_SPECIALIZE&#39;
-         : public boost::hash_detail::hash_base&lt;type&gt; \
-                  ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/unary_function.h:23:29: note: &#39;unary_function&lt;float, unsigned long&gt;&#39; has been explicitly marked deprecated here
-struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function
-                            ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:825:41: note: expanded from macro &#39;_LIBCPP_DEPRECATED_IN_CXX11&#39;
-#    define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
-                                        ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro &#39;_LIBCPP_DEPRECATED&#39;
-#      define _LIBCPP_DEPRECATED __attribute__((deprecated))
-                                                ^
-In file included from stan/src/stan/model/model_header.hpp:4:
-In file included from stan/lib/stan_math/stan/math.hpp:19:
-In file included from stan/lib/stan_math/stan/math/rev.hpp:10:
-In file included from stan/lib/stan_math/stan/math/rev/fun.hpp:200:
-In file included from stan/lib/stan_math/stan/math/prim/functor.hpp:16:
-In file included from stan/lib/stan_math/stan/math/prim/functor/integrate_ode_rk45.hpp:6:
-In file included from stan/lib/stan_math/stan/math/prim/functor/ode_rk45.hpp:9:
-In file included from stan/lib/stan_math/lib/b</code></pre>
-</div>
-<div class="cell-output cell-output-stderr">
-<pre><code>oost_1.78.0/boost/numeric/odeint.hpp:76:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint/integrate/observer_collection.hpp:23:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function.hpp:30:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/detail/prologue.hpp:17:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/function_base.hpp:21:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index.hpp:29:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index/stl_type_index.hpp:47:
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:132:33: warning: &#39;unary_function&lt;double, unsigned long&gt;&#39; is deprecated [-Wdeprecated-declarations]
-        struct hash_base : std::unary_function&lt;T, std::size_t&gt; {};
-                                ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:630:5: note: in instantiation of template class &#39;boost::hash_detail::hash_base&lt;double&gt;&#39; requested here
-    BOOST_HASH_SPECIALIZE(double)
-    ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:581:19: note: expanded from macro &#39;BOOST_HASH_SPECIALIZE&#39;
-         : public boost::hash_detail::hash_base&lt;type&gt; \
-                  ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/unary_function.h:23:29: note: &#39;unary_function&lt;double, unsigned long&gt;&#39; has been explicitly marked deprecated here
-struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function
-                            ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:825:41: note: expanded from macro &#39;_LIBCPP_DEPRECATED_IN_CXX11&#39;
-#    define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
-                                        ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro &#39;_LIBCPP_DEPRECATED&#39;
-#      define _LIBCPP_DEPRECATED __</code></pre>
-</div>
-<div class="cell-output cell-output-stderr">
-<pre><code>attribute__((deprecated))
-                                                ^
-In file included from stan/src/stan/model/model_header.hpp:4:
-In file included from stan/lib/stan_math/stan/math.hpp:19:
-In file included from stan/lib/stan_math/stan/math/rev.hpp:10:
-In file included from stan/lib/stan_math/stan/math/rev/fun.hpp:200:
-In file included from stan/lib/stan_math/stan/math/prim/functor.hpp:16:
-In file included from stan/lib/stan_math/stan/math/prim/functor/integrate_ode_rk45.hpp:6:
-In file included from stan/lib/stan_math/stan/math/prim/functor/ode_rk45.hpp:9:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint.hpp:76:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint/integrate/observer_collection.hpp:23:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function.hpp:30:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/detail/prologue.hpp:17:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/function_base.hpp:21:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index.hpp:29:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index/stl_type_index.hpp:47:
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:132:33: warning: &#39;unary_function&lt;long double, unsigned long&gt;&#39; is deprecated [-Wdeprecated-declarations]
-        struct hash_base : std::unary_function&lt;T, std::size_t&gt; {};
-                                ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:631:5: note: in instantiation of template class &#39;boost::hash_detail::hash_base&lt;long double&gt;&#39; requested here
-    BOOST_HASH_SPECIALIZE(long double)
-    ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:581:19: note: expanded from macro &#39;BOOST_HASH_SPECIALIZE&#39;
-         : public boost::hash_detail::hash_base&lt;type&gt; \
-                  ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__functiona</code></pre>
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>l/unary_function.h:23:29: note: &#39;unary_function&lt;long double, unsigned long&gt;&#39; has been explicitly marked deprecated here
-struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function
-                            ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:825:41: note: expanded from macro &#39;_LIBCPP_DEPRECATED_IN_CXX11&#39;
-#    define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
-                                        ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro &#39;_LIBCPP_DEPRECATED&#39;
-#      define _LIBCPP_DEPRECATED __attribute__((deprecated))
-                                                ^
-In file included from stan/src/stan/model/model_header.hpp:4:
-In file included from stan/lib/stan_math/stan/math.hpp:19:
-In file included from stan/lib/stan_math/stan/math/rev.hpp:10:
-In file included from stan/lib/stan_math/stan/math/rev/fun.hpp:200:
-In file included from stan/lib/stan_math/stan/math/prim/functor.hpp:16:
-In file included from stan/lib/stan_math/stan/math/prim/functor/integrate_ode_rk45.hpp:6:
-In file included from stan/lib/stan_math/stan/math/prim/functor/ode_rk45.hpp:9:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint.hpp:76:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint/integrate/observer_collection.hpp:23:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function.hpp:30:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/detail/prologue.hpp:17:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/function_base.hpp:21:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index.hpp:29:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index/stl_type_index.hpp:47:
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:132:33: warning: &#39;unary_function&lt;std::string, unsigned long&gt;&#39; is depre</code></pre>
-</div>
-<div class="cell-output cell-output-stderr">
-<pre><code>cated [-Wdeprecated-declarations]
-        struct hash_base : std::unary_function&lt;T, std::size_t&gt; {};
-                                ^</code></pre>
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:633:5: note: in instantiation of template class &#39;boost::hash_detail::hash_base&lt;std::string&gt;&#39; requested here
-    BOOST_HASH_SPECIALIZE_REF(std::string)
-    ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:591:19: note: expanded from macro &#39;BOOST_HASH_SPECIALIZE_REF&#39;
-         : public boost::hash_detail::hash_base&lt;type&gt; \
-                  ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/unary_function.h:23:29: note: &#39;unary_function&lt;std::string, unsigned long&gt;&#39; has been explicitly marked deprecated here
-struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function
-                            ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:825:41: note: expanded from macro &#39;_LIBCPP_DEPRECATED_IN_CXX11&#39;
-#    define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
-                                        ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro &#39;_LIBCPP_DEPRECATED&#39;
-#      define _LIBCPP_DEPRECATED __attribute__((deprecated))
-                                                ^
-In file included from stan/src/stan/model/model_header.hpp:4:
-In file included from stan/lib/stan_math/stan/math.hpp:19:
-In file included from stan/lib/stan_math/stan/math/rev.hpp:10:
-In file included from stan/lib/stan_math/stan/math/rev/fun.hpp:200:
-In file included from stan/lib/stan_math/stan/math/prim/functor.hpp:16:
-In file included from stan/lib/stan_math/stan/math/prim/functor/integrate_ode_rk45.hpp:6:
-In file included from stan/lib/stan_math/stan/math/prim/functor/ode_rk45.hpp:9:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint.hpp:76:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint/integrate/observer_collection.hpp:23:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function.hpp:30:</code></pre>
-</div>
-<div class="cell-output cell-output-stderr">
-<pre><code>In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/detail/prologue.hpp:17:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/function_base.hpp:21:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index.hpp:29:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index/stl_type_index.hpp:47:
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:132:33: warning: &#39;unary_function&lt;std::wstring, unsigned long&gt;&#39; is deprecated [-Wdeprecated-declarations]
-        struct hash_base : std::unary_function&lt;T, std::size_t&gt; {};
-                                ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:635:5: note: in instantiation of template class &#39;boost::hash_detail::hash_base&lt;std::wstring&gt;&#39; requested here
-    BOOST_HASH_SPECIALIZE_REF(std::wstring)
-    ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:591:19: note: expanded from macro &#39;BOOST_HASH_SPECIALIZE_REF&#39;
-         : public boost::hash_detail::hash_base&lt;type&gt; \
-                  ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/unary_function.h:23:29: note: &#39;unary_function&lt;std::wstring, unsigned long&gt;&#39; has been explicitly marked deprecated here
-struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function
-                            ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:825:41: note: expanded from macro &#39;_LIBCPP_DEPRECATED_IN_CXX11&#39;
-#    define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
-                                        ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro &#39;_LIBCPP_DEPRECATED&#39;
-#      define _LIBCPP_DEPRECATED __attribute__((deprecated))
-                                                ^
-In file included from stan/src/stan/model/model_header.hpp:4:
-In file included from stan/lib/stan_math/stan/math.hpp:19:
-In file in</code></pre>
-</div>
-<div class="cell-output cell-output-stderr">
-<pre><code>cluded from stan/lib/stan_math/stan/math/rev.hpp:10:
-In file included from stan/lib/stan_math/stan/math/rev/fun.hpp:200:
-In file included from stan/lib/stan_math/stan/math/prim/functor.hpp:16:
-In file included from stan/lib/stan_math/stan/math/prim/functor/integrate_ode_rk45.hpp:6:
-In file included from stan/lib/stan_math/stan/math/prim/functor/ode_rk45.hpp:9:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint.hpp:76:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint/integrate/observer_collection.hpp:23:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function.hpp:30:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/detail/prologue.hpp:17:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/function_base.hpp:21:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index.hpp:29:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index/stl_type_index.hpp:47:
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:132:33: warning: &#39;unary_function&lt;std::u16string, unsigned long&gt;&#39; is deprecated [-Wdeprecated-declarations]
-        struct hash_base : std::unary_function&lt;T, std::size_t&gt; {};
-                                ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:638:5: note: in instantiation of template class &#39;boost::hash_detail::hash_base&lt;std::u16string&gt;&#39; requested here
-    BOOST_HASH_SPECIALIZE_REF(std::basic_string&lt;char16_t&gt;)
-    ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:591:19: note: expanded from macro &#39;BOOST_HASH_SPECIALIZE_REF&#39;
-         : public boost::hash_detail::hash_base&lt;type&gt; \
-                  ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/unary_function.h:23:29: note: &#39;unary_function&lt;std::u16string, unsigned long&gt;&#39; has been explicitly marked deprecated here
-struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX1</code></pre>
+<pre><code>Chain 2 </code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>1 unary_function
-                            ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:825:41: note: expanded from macro &#39;_LIBCPP_DEPRECATED_IN_CXX11&#39;
-#    define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
-                                        ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro &#39;_LIBCPP_DEPRECATED&#39;
-#      define _LIBCPP_DEPRECATED __attribute__((deprecated))
-                                                ^
-In file included from stan/src/stan/model/model_header.hpp:4:
-In file included from stan/lib/stan_math/stan/math.hpp:19:
-In file included from stan/lib/stan_math/stan/math/rev.hpp:10:
-In file included from stan/lib/stan_math/stan/math/rev/fun.hpp:200:
-In file included from stan/lib/stan_math/stan/math/prim/functor.hpp:16:
-In file included from stan/lib/stan_math/stan/math/prim/functor/integrate_ode_rk45.hpp:6:
-In file included from stan/lib/stan_math/stan/math/prim/functor/ode_rk45.hpp:9:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint.hpp:76:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint/integrate/observer_collection.hpp:23:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function.hpp:30:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/detail/prologue.hpp:17:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/function_base.hpp:21:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index.hpp:29:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index/stl_type_index.hpp:47:
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:132:33: warning: &#39;unary_function&lt;std::u32string, unsigned long&gt;&#39; is deprecated [-Wdeprecated-declarations]
-        struct hash_base : std::unary_function&lt;T, std::size_t&gt; {};
-                                ^
-stan/lib/stan_math/lib/boost_1.78.0/</code></pre>
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>boost/container_hash/hash.hpp:641:5: note: in instantiation of template class &#39;boost::hash_detail::hash_base&lt;std::u32string&gt;&#39; requested here</code></pre>
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -5.14659e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>    BOOST_HASH_SPECIALIZE_REF(std::basic_string&lt;char32_t&gt;)
-    ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:591:19: note: expanded from macro &#39;BOOST_HASH_SPECIALIZE_REF&#39;
-         : public boost::hash_detail::hash_base&lt;type&gt; \
-                  ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/unary_function.h:23:29: note: &#39;unary_function&lt;std::u32string, unsigned long&gt;&#39; has been explicitly marked deprecated here
-struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function
-                            ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:825:41: note: expanded from macro &#39;_LIBCPP_DEPRECATED_IN_CXX11&#39;
-#    define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
-                                        ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro &#39;_LIBCPP_DEPRECATED&#39;
-#      define _LIBCPP_DEPRECATED __attribute__((deprecated))
-                                                ^
-In file included from stan/src/stan/model/model_header.hpp:4:
-In file included from stan/lib/stan_math/stan/math.hpp:19:
-In file included from stan/lib/stan_math/stan/math/rev.hpp:10:
-In file included from stan/lib/stan_math/stan/math/rev/fun.hpp:200:
-In file included from stan/lib/stan_math/stan/math/prim/functor.hpp:16:
-In file included from stan/lib/stan_math/stan/math/prim/functor/integrate_ode_rk45.hpp:6:
-In file included from stan/lib/stan_math/stan/math/prim/functor/ode_rk45.hpp:9:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint.hpp:76:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint/integrate/observer_collection.hpp:23:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function.hpp:30:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/detail/prologue.hpp:17:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/</code></pre>
-</div>
-<div class="cell-output cell-output-stderr">
-<pre><code>boost/function/function_base.hpp:21:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index.hpp:29:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index/stl_type_index.hpp:47:
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:132:33: warning: &#39;unary_function&lt;long long, unsigned long&gt;&#39; is deprecated [-Wdeprecated-declarations]
-        struct hash_base : std::unary_function&lt;T, std::size_t&gt; {};
-                                ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:658:5: note: in instantiation of template class &#39;boost::hash_detail::hash_base&lt;long long&gt;&#39; requested here
-    BOOST_HASH_SPECIALIZE(boost::long_long_type)
-    ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:581:19: note: expanded from macro &#39;BOOST_HASH_SPECIALIZE&#39;
-         : public boost::hash_detail::hash_base&lt;type&gt; \
-                  ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/unary_function.h:23:29: note: &#39;unary_function&lt;long long, unsigned long&gt;&#39; has been explicitly marked deprecated here
-struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function
-                            ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:825:41: note: expanded from macro &#39;_LIBCPP_DEPRECATED_IN_CXX11&#39;
-#    define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
-                                        ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro &#39;_LIBCPP_DEPRECATED&#39;
-#      define _LIBCPP_DEPRECATED __attribute__((deprecated))
-                                                ^
-In file included from stan/src/stan/model/model_header.hpp:4:
-In file included from stan/lib/stan_math/stan/math.hpp:19:
-In file included from stan/lib/stan_math/stan/math/rev.hpp:10:
-In file included from stan/lib/stan_math/stan/math/rev/fun.hpp:200:
-In file included from stan/lib/stan_math/s</code></pre>
-</div>
-<div class="cell-output cell-output-stderr">
-<pre><code>tan/math/prim/functor.hpp:16:
-In file included from stan/lib/stan_math/stan/math/prim/functor/integrate_ode_rk45.hpp:6:
-In file included from stan/lib/stan_math/stan/math/prim/functor/ode_rk45.hpp:9:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint.hpp:76:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint/integrate/observer_collection.hpp:23:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function.hpp:30:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/detail/prologue.hpp:17:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/function_base.hpp:21:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index.hpp:29:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index/stl_type_index.hpp:47:
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:132:33: warning: &#39;unary_function&lt;unsigned long long, unsigned long&gt;&#39; is deprecated [-Wdeprecated-declarations]
-        struct hash_base : std::unary_function&lt;T, std::size_t&gt; {};
-                                ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:659:5: note: in instantiation of template class &#39;boost::hash_detail::hash_base&lt;unsigned long long&gt;&#39; requested here
-    BOOST_HASH_SPECIALIZE(boost::ulong_long_type)
-    ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:581:19: note: expanded from macro &#39;BOOST_HASH_SPECIALIZE&#39;
-         : public boost::hash_detail::hash_base&lt;type&gt; \
-                  ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/unary_function.h:23:29: note: &#39;unary_function&lt;unsigned long long, unsigned long&gt;&#39; has been explicitly marked deprecated here
-struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function
-                            ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:825:41: note: expanded from macro &#39;_L</code></pre>
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -4.60644e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -1.38587e-12, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -4.60644e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -4.60644e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.74077e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -5.14659e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -5.14659e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -5.14659e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -5.14659e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -5.14659e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -6.81736e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -5.14659e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -2.19468e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -5.14659e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -6.81513e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -6.81513e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.38163e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -6.81513e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -2.19468e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -6.81513e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -2.19468e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -2.19468e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -5.71078e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -2.19468e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -2.19468e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -6.81513e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -6.81513e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -2.19468e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -2.19468e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -2.19468e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -5.14659e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.57232e-12, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -8.55241e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -8.55241e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.57232e-12, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -8.75872e-14, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -4.50602e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -2.19468e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -5.71078e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.38163e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.38163e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -5.14659e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -5.14659e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -5.14659e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -5.14659e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -4.50602e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -8.75872e-14, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -5.14659e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -5.14659e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -8.75872e-14, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -8.75872e-14, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -4.60644e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.38163e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.38163e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -6.81513e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.74077e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -7.91948e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -7.91948e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -7.62201e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -5.14659e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -5.14659e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -7.62201e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -5.14659e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -4.60644e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stdout">
+<pre><code>Chain 2 Iteration: 100 / 400 [ 25%]  (Warmup) </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.74077e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.38163e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -4.50602e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -5.14659e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -8.55241e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.38163e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.38163e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.74077e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -2.19468e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -5.71078e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -5.71078e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -5.14659e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -2.19468e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.74077e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -5.14659e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -5.71078e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -6.81736e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -8.75872e-14, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.74077e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -6.81513e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.74077e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -6.81736e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -2.19468e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -6.81513e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -2.19468e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -2.19468e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -2.19468e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -2.19468e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -2.19468e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -2.19468e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -6.81513e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -5.14659e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -5.14659e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -2.19468e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -2.19468e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -2.19468e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -2.19468e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -5.14659e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -2.19468e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -2.19468e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -5.14659e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -2.19468e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -2.19468e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -5.14659e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.38163e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.38163e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.38163e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -6.81513e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -6.81513e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.38163e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -4.60644e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -6.81513e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.38163e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.38163e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -1.22447e-12, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.74077e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.38163e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -5.14659e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.38163e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -7.91948e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -2.19468e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -4.60644e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -5.71078e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -5.71078e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -5.71078e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.19582e-12, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -2.19468e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -2.19468e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -1.22447e-12, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -1.22447e-12, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -4.60644e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -4.50602e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -4.60644e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -5.71078e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -4.50602e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -2.19468e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.38163e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -5.71078e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -5.71078e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -5.71078e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -5.14659e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -2.19468e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.38163e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -2.19468e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -2.19468e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -2.19468e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -4.60644e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -5.14659e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -4.60644e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -2.19468e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -4.60644e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -2.19468e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -9.93335e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -1.22447e-12, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -9.93335e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -8.55241e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -4.60644e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -5.14659e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -5.71078e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.23174e-12, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.38163e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stdout">
+<pre><code>Chain 2 Iteration: 200 / 400 [ 50%]  (Warmup) </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -2.19468e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.38163e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -4.60644e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.38163e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -4.60644e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -4.50602e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.74077e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -1.22447e-12, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -5.14659e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -2.19468e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -2.19468e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -2.19468e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -5.71078e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -2.19468e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -8.55241e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -2.19468e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -2.19468e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -6.81736e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -8.55241e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -5.14659e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -1.22447e-12, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -7.91948e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -5.71078e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -1.22447e-12, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -2.19468e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -7.91948e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -9.02382e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -1.22447e-12, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -9.02382e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -2.19468e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -9.02382e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -9.02382e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -9.02382e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -9.02382e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -8.75872e-14, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -9.02382e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -9.02382e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -9.02382e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -5.71078e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -9.02382e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -9.02382e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -9.02382e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -9.02382e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -5.14659e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -5.14659e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -9.02382e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -9.02382e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.38163e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -9.02382e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -2.19468e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -5.14659e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -7.91948e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -1.38587e-12, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -9.93335e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -6.81736e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -8.55241e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -8.55241e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.74077e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -5.71078e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -5.14659e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -5.14659e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.38163e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.74077e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -5.14659e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -5.14659e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -5.14659e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -5.14659e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -5.14659e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -6.81513e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.38163e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -8.55241e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -6.81513e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.9129e-12, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.38163e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -8.55241e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -2.19468e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -9.93335e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -6.81513e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.9129e-12, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.9129e-12, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -5.71078e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -5.71078e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -5.71078e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.57232e-12, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -5.71078e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.57232e-12, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -4.60644e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -4.60644e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -4.60644e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -4.60644e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -6.81513e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -6.81513e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.74077e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -6.81513e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -6.81513e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -6.81513e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.38163e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.38163e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -4.50602e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.38163e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.38163e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -8.55241e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stdout">
+<pre><code>Chain 2 Iteration: 300 / 400 [ 75%]  (Warmup) </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -4.50602e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stdout">
+<pre><code>Chain 2 Iteration: 301 / 400 [ 75%]  (Sampling) </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -5.14659e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -5.71078e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -2.19468e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -5.14659e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.57232e-12, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -4.50602e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -4.50602e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -4.50602e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -2.19468e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -2.19468e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -2.19468e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -2.19468e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -2.19468e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.57232e-12, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.57232e-12, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -4.50602e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -4.50602e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -4.50602e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.57232e-12, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stdout">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 108] is -6.46654e-14, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32) </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 108] is -6.46654e-14, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -2.19468e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -5.14659e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.57232e-12, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -8.55241e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.57232e-12, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -4.50602e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.57232e-12, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -4.50602e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -4.50602e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.57232e-12, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.57232e-12, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.57232e-12, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -2.19468e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.57232e-12, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.57232e-12, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.57232e-12, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.57232e-12, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.38163e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -8.55241e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.57232e-12, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.57232e-12, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -8.55241e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -8.55241e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -8.55241e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.9129e-12, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.38163e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.38163e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -8.55241e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.38163e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.38163e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -6.81513e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.38163e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.38163e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stdout">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 432] is -4.14212e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32) </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 432] is -4.14212e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.38163e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -8.55241e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stdout">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 432] is -6.66447e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32) </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 432] is -6.66447e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stdout">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 432] is -6.66447e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32) </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 432] is -6.66447e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -2.19468e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -4.50602e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -8.55241e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.38163e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -7.91948e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stdout">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 324] is -4.27768e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32) </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 324] is -4.27768e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.38163e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -8.55241e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -6.81513e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stdout">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 324] is -4.27768e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32) </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 324] is -4.27768e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stdout">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 324] is -4.27768e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32) </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 324] is -4.27768e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -6.81513e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -6.81513e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stdout">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 324] is -4.27768e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32) </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 324] is -4.27768e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stdout">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 324] is -4.27768e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32) </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 324] is -4.27768e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stdout">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 324] is -4.27768e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32) </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 324] is -4.27768e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -8.55241e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -6.81513e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -6.81513e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stdout">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 324] is -4.27768e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32) </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 324] is -4.27768e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stdout">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 324] is -4.27768e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32) </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 324] is -4.27768e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -8.55241e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.38163e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stdout">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 324] is -6.74474e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32) </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 324] is -6.74474e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stdout">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 324] is -6.74474e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32) </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 324] is -6.74474e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -6.81513e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -6.81513e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stdout">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 324] is -6.74474e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32) </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 324] is -6.74474e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stdout">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 324] is -6.74474e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32) </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 324] is -6.74474e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -6.81513e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -6.81513e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stdout">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 324] is -7.16493e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32) </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 324] is -7.16493e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stdout">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 324] is -7.16493e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32) </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 324] is -7.16493e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.38163e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 432] is -4.50602e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stdout">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 324] is -7.16493e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32) </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 324] is -7.16493e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -6.81513e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stdout">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 324] is -7.16493e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32) </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 324] is -7.16493e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -8.55241e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stdout">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 324] is -7.16493e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32) </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 324] is -7.16493e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -8.55241e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stdout">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 324] is -7.16493e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32) </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 324] is -7.16493e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stdout">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 324] is -7.16493e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32) </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 324] is -7.16493e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stdout">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 324] is -7.16493e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32) </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 324] is -7.16493e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.19582e-12, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -8.55241e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -8.55241e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -6.81513e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stdout">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 432] is -3.7201e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32) </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 432] is -3.7201e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stdout">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 432] is -3.7201e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32) </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 432] is -3.7201e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.19582e-12, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.38163e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stdout">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 432] is -3.7201e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32) </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 432] is -3.7201e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stdout">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 324] is -6.87698e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32) </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 324] is -6.87698e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.38163e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -6.81513e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stdout">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 432] is -3.7201e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32) </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 432] is -3.7201e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stdout">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 432] is -3.7201e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32) </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 432] is -3.7201e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.19582e-12, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -8.55241e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stdout">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 432] is -3.7201e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32) </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 432] is -3.7201e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.38163e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stdout">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 324] is -6.87698e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32) </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 324] is -6.87698e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stdout">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 324] is -6.87698e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32) </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 324] is -6.87698e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -5.71078e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.38163e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stdout">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 324] is -6.87698e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32) </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 324] is -6.87698e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stdout">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 324] is -6.87698e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32) </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 324] is -6.87698e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -5.71078e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -1.57232e-12, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stdout">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 324] is -6.87698e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32) </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 324] is -6.87698e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stdout">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 324] is -6.87698e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32) </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 324] is -6.87698e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -6.81513e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -5.14659e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stdout">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 324] is -6.87698e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32) </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 324] is -6.87698e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stdout">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 432] is -3.7201e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32) </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 432] is -3.7201e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stdout">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 432] is -3.7201e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32) </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 432] is -3.7201e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -8.55241e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -6.81513e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -8.55241e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stdout">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 432] is -3.7201e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32) </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 432] is -3.7201e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stdout">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 432] is -3.7201e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32) </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 432] is -3.7201e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stdout">
+<pre><code>Chain 2 Iteration: 400 / 400 [100%]  (Sampling) </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::write_array: x[1, 432] is -6.24245e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 108] is -5.14659e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -6.81513e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: poppk2cpt_model_namespace::log_prob: x[1, 324] is -5.71078e-13, but must be greater than or equal to 0.000000 (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 83, column 2 to column 32)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stdout">
+<pre><code>Chain 2 finished in 43.5 seconds.
+Chain 4 Iteration: 100 / 400 [ 25%]  (Warmup) 
+Chain 1 Iteration: 100 / 400 [ 25%]  (Warmup) 
+Chain 4 Iteration: 200 / 400 [ 50%]  (Warmup) 
+Chain 3 Iteration: 100 / 400 [ 25%]  (Warmup) 
+Chain 1 Iteration: 200 / 400 [ 50%]  (Warmup) 
+Chain 4 Iteration: 300 / 400 [ 75%]  (Warmup) 
+Chain 4 Iteration: 301 / 400 [ 75%]  (Sampling) 
+Chain 3 Iteration: 200 / 400 [ 50%]  (Warmup) 
+Chain 1 Iteration: 300 / 400 [ 75%]  (Warmup) 
+Chain 1 Iteration: 301 / 400 [ 75%]  (Sampling) 
+Chain 4 Iteration: 400 / 400 [100%]  (Sampling) 
+Chain 4 finished in 261.1 seconds.
+Chain 1 Iteration: 400 / 400 [100%]  (Sampling) 
+Chain 1 finished in 268.1 seconds.
+Chain 3 Iteration: 300 / 400 [ 75%]  (Warmup) 
+Chain 3 Iteration: 301 / 400 [ 75%]  (Sampling) 
+Chain 3 Iteration: 400 / 400 [100%]  (Sampling) 
+Chain 3 finished in 278.9 seconds.
+
+All 4 chains finished successfully.
+Mean chain execution time: 212.9 seconds.
+Total execution time: 279.2 seconds.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Warning: 100 of 400 (25.0%) transitions ended with a divergence.
+See https://mc-stan.org/misc/warnings for details.</code></pre>
+</div>
+</div>
+</div>
+<!-- This one doesn't work. -->
+</section>
+<section id="general-ode-solution" class="level3" data-number="2.3.3">
+<h3 data-number="2.3.3" class="anchored" data-anchor-id="general-ode-solution"><span class="header-section-number">2.3.3</span> General ODE Solution</h3>
+<div class="scrolling_500">
+<div class="cell" data-hash="torsten_test_cache/html/unnamed-chunk-14_a612bf12bf9223eb5c0a9462682f3242">
+<details>
+<summary>Code</summary>
+<div class="sourceCode cell-code" id="cb2406"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb2406-1"><a href="#cb2406-1" aria-hidden="true" tabindex="-1"></a>stan_data<span class="sc">$</span>solver <span class="ot">&lt;-</span> <span class="dv">3</span></span>
+<span id="cb2406-2"><a href="#cb2406-2" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2406-3"><a href="#cb2406-3" aria-hidden="true" tabindex="-1"></a>fit_rk45 <span class="ot">&lt;-</span> model<span class="sc">$</span><span class="fu">sample</span>(</span>
+<span id="cb2406-4"><a href="#cb2406-4" aria-hidden="true" tabindex="-1"></a>  <span class="at">data =</span> stan_data, </span>
+<span id="cb2406-5"><a href="#cb2406-5" aria-hidden="true" tabindex="-1"></a>  <span class="at">init =</span> here<span class="sc">::</span><span class="fu">here</span>(<span class="st">&quot;M3/example_models_metrum/poppk2cpt/poppk2cpt.init.R&quot;</span>), </span>
+<span id="cb2406-6"><a href="#cb2406-6" aria-hidden="true" tabindex="-1"></a>  <span class="at">seed =</span> <span class="dv">3191951</span>,</span>
+<span id="cb2406-7"><a href="#cb2406-7" aria-hidden="true" tabindex="-1"></a>  <span class="at">chains =</span> <span class="dv">4</span>,</span>
+<span id="cb2406-8"><a href="#cb2406-8" aria-hidden="true" tabindex="-1"></a>  <span class="at">parallel_chains =</span> <span class="dv">4</span>,</span>
+<span id="cb2406-9"><a href="#cb2406-9" aria-hidden="true" tabindex="-1"></a>  <span class="at">iter_warmup =</span> <span class="dv">300</span>,</span>
+<span id="cb2406-10"><a href="#cb2406-10" aria-hidden="true" tabindex="-1"></a>  <span class="at">iter_sampling =</span> <span class="dv">100</span>,</span>
+<span id="cb2406-11"><a href="#cb2406-11" aria-hidden="true" tabindex="-1"></a>  <span class="at">adapt_delta =</span> <span class="fl">0.80</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+</details>
+<div class="cell-output cell-output-stdout">
+<pre><code>Running MCMC with 4 parallel chains...</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 1 Warning: file &#39;/Users/Arya/R-Projects/torsten_test/M3/example_models_metrum/poppk2cpt/poppk2cpt.init.R&#39; is being read as an &#39;RDump&#39; file.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 1     This format is deprecated and will not receive new features.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 1     Consider saving your data in JSON format instead.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Warning: file &#39;/Users/Arya/R-Projects/torsten_test/M3/example_models_metrum/poppk2cpt/poppk2cpt.init.R&#39; is being read as an &#39;RDump&#39; file.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2     This format is deprecated and will not receive new features.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2     Consider saving your data in JSON format instead.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 3 Warning: file &#39;/Users/Arya/R-Projects/torsten_test/M3/example_models_metrum/poppk2cpt/poppk2cpt.init.R&#39; is being read as an &#39;RDump&#39; file.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 3     This format is deprecated and will not receive new features.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 3     Consider saving your data in JSON format instead.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 4 Warning: file &#39;/Users/Arya/R-Projects/torsten_test/M3/example_models_metrum/poppk2cpt/poppk2cpt.init.R&#39; is being read as an &#39;RDump&#39; file.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 4     This format is deprecated and will not receive new features.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 4     Consider saving your data in JSON format instead.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 1 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 1 Exception: Max number of iterations exceeded (1000000). (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 140, column 6 to line 151, column 46)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 1 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 1 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 1 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: Max number of iterations exceeded (1000000). (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 140, column 6 to line 151, column 46)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 3 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 3 Exception: Max number of iterations exceeded (1000000). (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 140, column 6 to line 151, column 46)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 3 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 3 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 3 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 4 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 4 Exception: Max number of iterations exceeded (1000000). (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 140, column 6 to line 151, column 46)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 4 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 4 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 4 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 1 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 1 Exception: Max number of iterations exceeded (1000000). (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 140, column 6 to line 151, column 46)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 1 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 1 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 1 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: Max number of iterations exceeded (1000000). (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 140, column 6 to line 151, column 46)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 3 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 3 Exception: Max number of iterations exceeded (1000000). (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 140, column 6 to line 151, column 46)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 3 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 3 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 3 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 4 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 4 Exception: Max number of iterations exceeded (1000000). (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 140, column 6 to line 151, column 46)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 4 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 4 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 4 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 3 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 3 Exception: Max number of iterations exceeded (1000000). (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 140, column 6 to line 151, column 46)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 3 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 3 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 3 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>IBCPP_DEPRECATED_IN_CXX11&#39;
-#    define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
-                                        ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro &#39;_LIBCPP_DEPRECATED&#39;
-#      define _LIBCPP_DEPRECATED __attribute__((deprecated))
-                                                ^
-In file included from stan/src/stan/model/model_header.hpp:4:
-In file included from stan/lib/stan_math/stan/math.hpp:19:
-In file included from stan/lib/stan_math/stan/math/rev.hpp:10:
-In file included from stan/lib/stan_math/stan/math/rev/fun.hpp:200:
-In file included from stan/lib/stan_math/stan/math/prim/functor.hpp:16:
-In file included from stan/lib/stan_math/stan/math/prim/functor/integrate_ode_rk45.hpp:6:
-In file included from stan/lib/stan_math/stan/math/prim/functor/ode_rk45.hpp:9:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint.hpp:76:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint/integrate/observer_collection.hpp:23:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function.hpp:30:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/detail/prologue.hpp:17:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/function_base.hpp:21:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index.hpp:29:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index/stl_type_index.hpp:47:
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:132:33: warning: &#39;unary_function&lt;__int128, unsigned long&gt;&#39; is deprecated [-Wdeprecated-declarations]
-        struct hash_base : std::unary_function&lt;T, std::size_t&gt; {};
-                                ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:663:5: note: in instantiation of template class &#39;boost::hash_detail::hash_base&lt;__int128&gt;&#39; requested here
-    BOOST_HASH_SPECIALIZE(boost::in</code></pre>
+<pre><code>Chain 2 Exception: Max number of iterations exceeded (1000000). (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 140, column 6 to line 151, column 46)</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>t128_type)
-    ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:581:19: note: expanded from macro &#39;BOOST_HASH_SPECIALIZE&#39;</code></pre>
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>         : public boost::hash_detail::hash_base&lt;type&gt; \
-                  ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/unary_function.h:23:29: note: &#39;unary_function&lt;__int128, unsigned long&gt;&#39; has been explicitly marked deprecated here
-struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function
-                            ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:825:41: note: expanded from macro &#39;_LIBCPP_DEPRECATED_IN_CXX11&#39;
-#    define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
-                                        ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro &#39;_LIBCPP_DEPRECATED&#39;
-#      define _LIBCPP_DEPRECATED __attribute__((deprecated))
-                                                ^
-In file included from stan/src/stan/model/model_header.hpp:4:
-In file included from stan/lib/stan_math/stan/math.hpp:19:
-In file included from stan/lib/stan_math/stan/math/rev.hpp:10:
-In file included from stan/lib/stan_math/stan/math/rev/fun.hpp:200:
-In file included from stan/lib/stan_math/stan/math/prim/functor.hpp:16:
-In file included from stan/lib/stan_math/stan/math/prim/functor/integrate_ode_rk45.hpp:6:
-In file included from stan/lib/stan_math/stan/math/prim/functor/ode_rk45.hpp:9:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint.hpp:76:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint/integrate/observer_collection.hpp:23:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function.hpp:30:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/detail/prologue.hpp:17:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/function_base.hpp:21:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index.hpp:29:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index/stl_</code></pre>
-</div>
-<div class="cell-output cell-output-stderr">
-<pre><code>type_index.hpp:47:
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:132:33: warning: &#39;unary_function&lt;unsigned __int128, unsigned long&gt;&#39; is deprecated [-Wdeprecated-declarations]
-        struct hash_base : std::unary_function&lt;T, std::size_t&gt; {};
-                                ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:664:5: note: in instantiation of template class &#39;boost::hash_detail::hash_base&lt;unsigned __int128&gt;&#39; requested here
-    BOOST_HASH_SPECIALIZE(boost::uint128_type)
-    ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:581:19: note: expanded from macro &#39;BOOST_HASH_SPECIALIZE&#39;
-         : public boost::hash_detail::hash_base&lt;type&gt; \
-                  ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/unary_function.h:23:29: note: &#39;unary_function&lt;unsigned __int128, unsigned long&gt;&#39; has been explicitly marked deprecated here
-struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function
-                            ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:825:41: note: expanded from macro &#39;_LIBCPP_DEPRECATED_IN_CXX11&#39;
-#    define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
-                                        ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro &#39;_LIBCPP_DEPRECATED&#39;
-#      define _LIBCPP_DEPRECATED __attribute__((deprecated))
-                                                ^
-In file included from stan/src/stan/model/model_header.hpp:4:
-In file included from stan/lib/stan_math/stan/math.hpp:19:
-In file included from stan/lib/stan_math/stan/math/rev.hpp:10:
-In file included from stan/lib/stan_math/stan/math/rev/fun.hpp:200:
-In file included from stan/lib/stan_math/stan/math/prim/functor.hpp:16:
-In file included from stan/lib/stan_math/stan/math/prim/functor/integrate_ode_rk45.hpp:6:
-In file included from stan/lib/stan_math/stan/math/prim/f</code></pre>
-</div>
-<div class="cell-output cell-output-stderr">
-<pre><code>unctor/ode_rk45.hpp:9:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint.hpp:76:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint/integrate/observer_collection.hpp:23:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function.hpp:30:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/detail/prologue.hpp:17:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/function/function_base.hpp:21:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index.hpp:29:
-In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/type_index/stl_type_index.hpp:47:
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:132:33: warning: &#39;unary_function&lt;std::type_index, unsigned long&gt;&#39; is deprecated [-Wdeprecated-declarations]
-        struct hash_base : std::unary_function&lt;T, std::size_t&gt; {};
-                                ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:679:5: note: in instantiation of template class &#39;boost::hash_detail::hash_base&lt;std::type_index&gt;&#39; requested here
-    BOOST_HASH_SPECIALIZE(std::type_index)
-    ^
-stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:581:19: note: expanded from macro &#39;BOOST_HASH_SPECIALIZE&#39;
-         : public boost::hash_detail::hash_base&lt;type&gt; \
-                  ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/unary_function.h:23:29: note: &#39;unary_function&lt;std::type_index, unsigned long&gt;&#39; has been explicitly marked deprecated here
-struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function
-                            ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:825:41: note: expanded from macro &#39;_LIBCPP_DEPRECATED_IN_CXX11&#39;
-#    define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
-                                        ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c</code></pre>
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>++/v1/__config:810:49: note: expanded from macro &#39;_LIBCPP_DEPRECATED&#39;
-#      define _LIBCPP_DEPRECATED __attribute__((deprecated))
-                                                ^</code></pre>
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stdout">
+<pre><code>Chain 3 Iteration:   1 / 400 [  0%]  (Warmup) 
+Chain 2 Iteration:   1 / 400 [  0%]  (Warmup) </code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>32 warnings generated.</code></pre>
+<pre><code>Chain 3 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>In file included from /var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79275e5757b.hpp:1:
-In file included from /Users/Arya/Torsten/cmdstan/stan/src/stan/model/model_header.hpp:4:
-In file included from /Users/Arya/Torsten/cmdstan/stan/lib/stan_math/stan/math.hpp:19:
-In file included from /Users/Arya/Torsten/cmdstan/stan/lib/stan_math/stan/math/rev.hpp:10:
-In file included from /Users/Arya/Torsten/cmdstan/stan/lib/stan_math/stan/math/rev/fun.hpp:200:
-In file included from /Users/Arya/Torsten/cmdstan/stan/lib/stan_math/stan/math/prim/functor.hpp:16:
-In file included from /Users/Arya/Torsten/cmdstan/stan/lib/stan_math/stan/math/prim/functor/integrate_ode_rk45.hpp:6:
-In file included from /Users/Arya/Torsten/cmdstan/stan/lib/stan_math/stan/math/prim/functor/ode_rk45.hpp:9:
-In file included from /Users/Arya/Torsten/cmdstan/stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint.hpp:76:
-In file included from /Users/Arya/Torsten/cmdstan/stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint/integrate/observer_collection.hpp:23:
-In file included from /Users/Arya/Torsten/cmdstan/stan/lib/stan_math/lib/boost_1.78.0/boost/function.hpp:30:
-In file included from /Users/Arya/Torsten/cmdstan/stan/lib/stan_math/lib/boost_1.78.0/boost/function/detail/prologue.hpp:17:
-In file included from /Users/Arya/Torsten/cmdstan/stan/lib/stan_math/lib/boost_1.78.0/boost/function/function_base.hpp:21:
-In file included from /Users/Arya/Torsten/cmdstan/stan/lib/stan_math/lib/boost_1.78.0/boost/type_index.hpp:29:
-In file included from /Users/Arya/Torsten/cmdstan/stan/lib/stan_math/lib/boost_1.78.0/boost/type_index/stl_type_index.hpp:47:
-/Users/Arya/Torsten/cmdstan/stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:132:33: warning: &#39;unary_function&lt;const std::error_category *, unsigned long&gt;&#39; is deprecated [-Wdeprecated-declarations]
-        struct hash_base : std::unary_function&lt;T, std::size_t&gt; {};
-                                ^
-/Users/Arya/Torsten/cmdstan/stan/l</code></pre>
+<pre><code>Chain 3 Exception: PMX Variadic ODE System: initial state[2] is nan, but must be finite! (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 140, column 6 to line 151, column 46)</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>ib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:692:18: note: in instantiation of template class &#39;boost::hash_detail::hash_base&lt;const std::error_category *&gt;&#39; requested here
-        : public boost::hash_detail::hash_base&lt;T*&gt;
-                 ^
-/Users/Arya/Torsten/cmdstan/stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:420:24: note: in instantiation of template class &#39;boost::hash&lt;const std::error_category *&gt;&#39; requested here
-        boost::hash&lt;T&gt; hasher;
-                       ^
-/Users/Arya/Torsten/cmdstan/stan/lib/stan_math/lib/boost_1.78.0/boost/container_hash/hash.hpp:551:9: note: in instantiation of function template specialization &#39;boost::hash_combine&lt;const std::error_category *&gt;&#39; requested here
-        hash_combine(seed, &amp;v.category());
-        ^</code></pre>
+<pre><code>Chain 3 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/unary_function.h:23:29: note: &#39;unary_function&lt;const std::error_category *, unsigned long&gt;&#39; has been explicitly marked deprecated here
-struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function
-                            ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:825:41: note: expanded from macro &#39;_LIBCPP_DEPRECATED_IN_CXX11&#39;
-#    define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
-                                        ^
-/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro &#39;_LIBCPP_DEPRECATED&#39;
-#      define _LIBCPP_DEPRECATED __attribute__((deprecated))
-                                                ^</code></pre>
+<pre><code>Chain 3 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
 </div>
 <div class="cell-output cell-output-stderr">
-<pre><code>1 warning generated.</code></pre>
+<pre><code>Chain 3 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 1 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 1 Exception: Max number of iterations exceeded (1000000). (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 140, column 6 to line 151, column 46)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 1 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 1 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 1 </code></pre>
+</div>
+<div class="cell-output cell-output-stdout">
+<pre><code>Chain 1 Iteration:   1 / 400 [  0%]  (Warmup) </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 1 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 1 Exception: PMX Variadic ODE System: initial state[2] is nan, but must be finite! (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 140, column 6 to line 151, column 46)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 1 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 1 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 1 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 3 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 3 Exception: Max number of iterations exceeded (1000000). (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 140, column 6 to line 151, column 46)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 3 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 3 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 3 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 Exception: Max number of iterations exceeded (1000000). (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 140, column 6 to line 151, column 46)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 2 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 1 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 1 Exception: Max number of iterations exceeded (1000000). (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 140, column 6 to line 151, column 46)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 1 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 1 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 1 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 4 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 4 Exception: Max number of iterations exceeded (1000000). (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 140, column 6 to line 151, column 46)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 4 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 4 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 4 </code></pre>
+</div>
+<div class="cell-output cell-output-stdout">
+<pre><code>Chain 4 Iteration:   1 / 400 [  0%]  (Warmup) </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 4 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 4 Exception: PMX Variadic ODE System: initial state[2] is nan, but must be finite! (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 140, column 6 to line 151, column 46)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 4 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 4 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 4 </code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 4 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 4 Exception: PMX Variadic ODE System: initial state[2] is nan, but must be finite! (in &#39;/var/folders/c5/z01xp4bd02j_glk11wknb5jr0000gp/T/Rtmp8pkl24/model-79276bf128.stan&#39;, line 140, column 6 to line 151, column 46)</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 4 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 4 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Chain 4 </code></pre>
+</div>
+<div class="cell-output cell-output-stdout">
+<pre><code>Chain 1 Iteration: 100 / 400 [ 25%]  (Warmup) 
+Chain 3 Iteration: 100 / 400 [ 25%]  (Warmup) 
+Chain 2 Iteration: 100 / 400 [ 25%]  (Warmup) 
+Chain 1 Iteration: 200 / 400 [ 50%]  (Warmup) 
+Chain 4 Iteration: 100 / 400 [ 25%]  (Warmup) 
+Chain 2 Iteration: 200 / 400 [ 50%]  (Warmup) 
+Chain 1 Iteration: 300 / 400 [ 75%]  (Warmup) 
+Chain 1 Iteration: 301 / 400 [ 75%]  (Sampling) 
+Chain 4 Iteration: 200 / 400 [ 50%]  (Warmup) 
+Chain 3 Iteration: 200 / 400 [ 50%]  (Warmup) 
+Chain 2 Iteration: 300 / 400 [ 75%]  (Warmup) 
+Chain 2 Iteration: 301 / 400 [ 75%]  (Sampling) 
+Chain 1 Iteration: 400 / 400 [100%]  (Sampling) 
+Chain 1 finished in 3834.0 seconds.
+Chain 4 Iteration: 300 / 400 [ 75%]  (Warmup) 
+Chain 4 Iteration: 301 / 400 [ 75%]  (Sampling) 
+Chain 3 Iteration: 300 / 400 [ 75%]  (Warmup) 
+Chain 3 Iteration: 301 / 400 [ 75%]  (Sampling) 
+Chain 2 Iteration: 400 / 400 [100%]  (Sampling) 
+Chain 2 finished in 3922.8 seconds.
+Chain 4 Iteration: 400 / 400 [100%]  (Sampling) 
+Chain 4 finished in 3916.5 seconds.
+Chain 3 Iteration: 400 / 400 [100%]  (Sampling) 
+Chain 3 finished in 3996.8 seconds.
+
+All 4 chains finished successfully.
+Mean chain execution time: 3917.5 seconds.
+Total execution time: 4013.2 seconds.</code></pre>
+</div>
+</div>
+</div>
+<p>This one works.</p>
+</section>
+</section>
+<section id="fitting-poppk2cpt-from-example-models-with-my-own-models" class="level2" data-number="2.4">
+<h2 data-number="2.4" class="anchored" data-anchor-id="fitting-poppk2cpt-from-example-models-with-my-own-models"><span class="header-section-number">2.4</span> Fitting <code>poppk2cpt</code> from <code>example-models/</code> With My Own Models</h2>
+<p>I’ve previously written this model to fit with the analytical, linear ODE, and general ODE solutions with proportional error, so I’m just going to use that, but it shouldn’t make a difference.</p>
+<section id="data-wrangling" class="level3" data-number="2.4.1">
+<h3 data-number="2.4.1" class="anchored" data-anchor-id="data-wrangling"><span class="header-section-number">2.4.1</span> Data Wrangling</h3>
+<p>My models should work from a NONMEM dataset in .csv format, so I’ll wrangle the data into something like that first.</p>
+<div class="scrolling_500">
+<div class="cell">
+<details>
+<summary>Code</summary>
+<div class="sourceCode cell-code" id="cb2519"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb2519-1"><a href="#cb2519-1" aria-hidden="true" tabindex="-1"></a>dv <span class="ot">&lt;-</span> <span class="fu">rep</span>(<span class="cn">NA</span>, stan_data<span class="sc">$</span>nt)</span>
+<span id="cb2519-2"><a href="#cb2519-2" aria-hidden="true" tabindex="-1"></a>dv[stan_data<span class="sc">$</span>iObs] <span class="ot">&lt;-</span> stan_data<span class="sc">$</span>cObs</span>
+<span id="cb2519-3"><a href="#cb2519-3" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2519-4"><a href="#cb2519-4" aria-hidden="true" tabindex="-1"></a>nonmem_data <span class="ot">&lt;-</span> <span class="fu">with</span>(stan_data, </span>
+<span id="cb2519-5"><a href="#cb2519-5" aria-hidden="true" tabindex="-1"></a>                    <span class="fu">tibble</span>(<span class="at">ID =</span> <span class="fu">rep</span>(<span class="dv">1</span><span class="sc">:</span>stan_data<span class="sc">$</span>nSubj, <span class="at">each =</span> <span class="dv">54</span>),</span>
+<span id="cb2519-6"><a href="#cb2519-6" aria-hidden="true" tabindex="-1"></a>                           <span class="at">amt =</span> amt, </span>
+<span id="cb2519-7"><a href="#cb2519-7" aria-hidden="true" tabindex="-1"></a>                           <span class="at">ii =</span> ii,</span>
+<span id="cb2519-8"><a href="#cb2519-8" aria-hidden="true" tabindex="-1"></a>                           <span class="at">addl =</span> addl,</span>
+<span id="cb2519-9"><a href="#cb2519-9" aria-hidden="true" tabindex="-1"></a>                           <span class="at">rate =</span> rate,</span>
+<span id="cb2519-10"><a href="#cb2519-10" aria-hidden="true" tabindex="-1"></a>                           <span class="at">cmt =</span> cmt,</span>
+<span id="cb2519-11"><a href="#cb2519-11" aria-hidden="true" tabindex="-1"></a>                           <span class="at">evid =</span> evid, </span>
+<span id="cb2519-12"><a href="#cb2519-12" aria-hidden="true" tabindex="-1"></a>                           <span class="at">ss =</span> ss,</span>
+<span id="cb2519-13"><a href="#cb2519-13" aria-hidden="true" tabindex="-1"></a>                           <span class="at">lloq =</span> <span class="dv">0</span>,</span>
+<span id="cb2519-14"><a href="#cb2519-14" aria-hidden="true" tabindex="-1"></a>                           <span class="at">bloq =</span> <span class="dv">0</span>,</span>
+<span id="cb2519-15"><a href="#cb2519-15" aria-hidden="true" tabindex="-1"></a>                           <span class="at">time =</span> time,</span>
+<span id="cb2519-16"><a href="#cb2519-16" aria-hidden="true" tabindex="-1"></a>                           <span class="at">DV =</span> dv)) <span class="sc">%&gt;%</span> </span>
+<span id="cb2519-17"><a href="#cb2519-17" aria-hidden="true" tabindex="-1"></a>  <span class="fu">mutate</span>(<span class="at">DV =</span> <span class="fu">if_else</span>(<span class="fu">is.na</span>(DV), <span class="dv">5555555</span>, DV),    <span class="co"># This value can be anything except NA. It&#39;ll be indexed away </span></span>
+<span id="cb2519-18"><a href="#cb2519-18" aria-hidden="true" tabindex="-1"></a>         <span class="at">bloq =</span> <span class="fu">if_else</span>(<span class="fu">is.na</span>(bloq), <span class="sc">-</span><span class="dv">999</span>, bloq)) <span class="co"># This value can be anything except NA. It&#39;ll be indexed away </span></span>
+<span id="cb2519-19"><a href="#cb2519-19" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2519-20"><a href="#cb2519-20" aria-hidden="true" tabindex="-1"></a>n_subjects <span class="ot">&lt;-</span> nonmem_data <span class="sc">%&gt;%</span>  <span class="co"># number of individuals</span></span>
+<span id="cb2519-21"><a href="#cb2519-21" aria-hidden="true" tabindex="-1"></a>  <span class="fu">distinct</span>(ID) <span class="sc">%&gt;%</span></span>
+<span id="cb2519-22"><a href="#cb2519-22" aria-hidden="true" tabindex="-1"></a>  <span class="fu">count</span>() <span class="sc">%&gt;%</span></span>
+<span id="cb2519-23"><a href="#cb2519-23" aria-hidden="true" tabindex="-1"></a>  <span class="fu">deframe</span>()</span>
+<span id="cb2519-24"><a href="#cb2519-24" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2519-25"><a href="#cb2519-25" aria-hidden="true" tabindex="-1"></a>n_total <span class="ot">&lt;-</span> <span class="fu">nrow</span>(nonmem_data)   <span class="co"># total number of records</span></span>
+<span id="cb2519-26"><a href="#cb2519-26" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2519-27"><a href="#cb2519-27" aria-hidden="true" tabindex="-1"></a>i_obs <span class="ot">&lt;-</span> nonmem_data <span class="sc">%&gt;%</span></span>
+<span id="cb2519-28"><a href="#cb2519-28" aria-hidden="true" tabindex="-1"></a>  <span class="fu">mutate</span>(<span class="at">row_num =</span> <span class="dv">1</span><span class="sc">:</span><span class="fu">n</span>()) <span class="sc">%&gt;%</span></span>
+<span id="cb2519-29"><a href="#cb2519-29" aria-hidden="true" tabindex="-1"></a>  <span class="fu">filter</span>(evid <span class="sc">==</span> <span class="dv">0</span>) <span class="sc">%&gt;%</span></span>
+<span id="cb2519-30"><a href="#cb2519-30" aria-hidden="true" tabindex="-1"></a>  <span class="fu">select</span>(row_num) <span class="sc">%&gt;%</span></span>
+<span id="cb2519-31"><a href="#cb2519-31" aria-hidden="true" tabindex="-1"></a>  <span class="fu">deframe</span>()</span>
+<span id="cb2519-32"><a href="#cb2519-32" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2519-33"><a href="#cb2519-33" aria-hidden="true" tabindex="-1"></a>n_obs <span class="ot">&lt;-</span> <span class="fu">length</span>(i_obs)</span>
+<span id="cb2519-34"><a href="#cb2519-34" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2519-35"><a href="#cb2519-35" aria-hidden="true" tabindex="-1"></a>subj_start <span class="ot">&lt;-</span> nonmem_data <span class="sc">%&gt;%</span></span>
+<span id="cb2519-36"><a href="#cb2519-36" aria-hidden="true" tabindex="-1"></a>  <span class="fu">mutate</span>(<span class="at">row_num =</span> <span class="dv">1</span><span class="sc">:</span><span class="fu">n</span>()) <span class="sc">%&gt;%</span></span>
+<span id="cb2519-37"><a href="#cb2519-37" aria-hidden="true" tabindex="-1"></a>  <span class="fu">group_by</span>(ID) <span class="sc">%&gt;%</span></span>
+<span id="cb2519-38"><a href="#cb2519-38" aria-hidden="true" tabindex="-1"></a>  <span class="fu">slice_head</span>(<span class="at">n =</span> <span class="dv">1</span>) <span class="sc">%&gt;%</span></span>
+<span id="cb2519-39"><a href="#cb2519-39" aria-hidden="true" tabindex="-1"></a>  <span class="fu">ungroup</span>() <span class="sc">%&gt;%</span></span>
+<span id="cb2519-40"><a href="#cb2519-40" aria-hidden="true" tabindex="-1"></a>  <span class="fu">select</span>(row_num) <span class="sc">%&gt;%</span></span>
+<span id="cb2519-41"><a href="#cb2519-41" aria-hidden="true" tabindex="-1"></a>  <span class="fu">deframe</span>()</span>
+<span id="cb2519-42"><a href="#cb2519-42" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2519-43"><a href="#cb2519-43" aria-hidden="true" tabindex="-1"></a>subj_end <span class="ot">&lt;-</span> <span class="fu">c</span>(subj_start[<span class="sc">-</span><span class="dv">1</span>] <span class="sc">-</span> <span class="dv">1</span>, n_total)</span>
+<span id="cb2519-44"><a href="#cb2519-44" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2519-45"><a href="#cb2519-45" aria-hidden="true" tabindex="-1"></a>stan_data <span class="ot">&lt;-</span> <span class="fu">list</span>(<span class="at">n_subjects =</span> n_subjects,</span>
+<span id="cb2519-46"><a href="#cb2519-46" aria-hidden="true" tabindex="-1"></a>                  <span class="at">n_total =</span> n_total,</span>
+<span id="cb2519-47"><a href="#cb2519-47" aria-hidden="true" tabindex="-1"></a>                  <span class="at">n_obs =</span> n_obs,</span>
+<span id="cb2519-48"><a href="#cb2519-48" aria-hidden="true" tabindex="-1"></a>                  <span class="at">i_obs =</span> i_obs,</span>
+<span id="cb2519-49"><a href="#cb2519-49" aria-hidden="true" tabindex="-1"></a>                  <span class="at">ID =</span> nonmem_data<span class="sc">$</span>ID,</span>
+<span id="cb2519-50"><a href="#cb2519-50" aria-hidden="true" tabindex="-1"></a>                  <span class="at">amt =</span> nonmem_data<span class="sc">$</span>amt,</span>
+<span id="cb2519-51"><a href="#cb2519-51" aria-hidden="true" tabindex="-1"></a>                  <span class="at">cmt =</span> nonmem_data<span class="sc">$</span>cmt,</span>
+<span id="cb2519-52"><a href="#cb2519-52" aria-hidden="true" tabindex="-1"></a>                  <span class="at">evid =</span> nonmem_data<span class="sc">$</span>evid,</span>
+<span id="cb2519-53"><a href="#cb2519-53" aria-hidden="true" tabindex="-1"></a>                  <span class="at">rate =</span> nonmem_data<span class="sc">$</span>rate,</span>
+<span id="cb2519-54"><a href="#cb2519-54" aria-hidden="true" tabindex="-1"></a>                  <span class="at">ii =</span> nonmem_data<span class="sc">$</span>ii,</span>
+<span id="cb2519-55"><a href="#cb2519-55" aria-hidden="true" tabindex="-1"></a>                  <span class="at">addl =</span> nonmem_data<span class="sc">$</span>addl,</span>
+<span id="cb2519-56"><a href="#cb2519-56" aria-hidden="true" tabindex="-1"></a>                  <span class="at">ss =</span> nonmem_data<span class="sc">$</span>ss,</span>
+<span id="cb2519-57"><a href="#cb2519-57" aria-hidden="true" tabindex="-1"></a>                  <span class="at">time =</span> nonmem_data<span class="sc">$</span>time,</span>
+<span id="cb2519-58"><a href="#cb2519-58" aria-hidden="true" tabindex="-1"></a>                  <span class="at">dv =</span> nonmem_data<span class="sc">$</span>DV,</span>
+<span id="cb2519-59"><a href="#cb2519-59" aria-hidden="true" tabindex="-1"></a>                  <span class="at">subj_start =</span> subj_start,</span>
+<span id="cb2519-60"><a href="#cb2519-60" aria-hidden="true" tabindex="-1"></a>                  <span class="at">subj_end =</span> subj_end,</span>
+<span id="cb2519-61"><a href="#cb2519-61" aria-hidden="true" tabindex="-1"></a>                  <span class="at">lloq =</span> nonmem_data<span class="sc">$</span>lloq,</span>
+<span id="cb2519-62"><a href="#cb2519-62" aria-hidden="true" tabindex="-1"></a>                  <span class="at">bloq =</span> nonmem_data<span class="sc">$</span>bloq,</span>
+<span id="cb2519-63"><a href="#cb2519-63" aria-hidden="true" tabindex="-1"></a>                  <span class="at">location_tvcl =</span> <span class="fl">0.75</span>,</span>
+<span id="cb2519-64"><a href="#cb2519-64" aria-hidden="true" tabindex="-1"></a>                  <span class="at">location_tvvc =</span> <span class="dv">18</span>,</span>
+<span id="cb2519-65"><a href="#cb2519-65" aria-hidden="true" tabindex="-1"></a>                  <span class="at">location_tvq =</span> <span class="dv">3</span>,</span>
+<span id="cb2519-66"><a href="#cb2519-66" aria-hidden="true" tabindex="-1"></a>                  <span class="at">location_tvvp =</span> <span class="dv">35</span>,</span>
+<span id="cb2519-67"><a href="#cb2519-67" aria-hidden="true" tabindex="-1"></a>                  <span class="at">location_tvka =</span> <span class="fl">0.8</span>,</span>
+<span id="cb2519-68"><a href="#cb2519-68" aria-hidden="true" tabindex="-1"></a>                  <span class="at">scale_tvcl =</span> <span class="dv">1</span>,</span>
+<span id="cb2519-69"><a href="#cb2519-69" aria-hidden="true" tabindex="-1"></a>                  <span class="at">scale_tvvc =</span> <span class="dv">1</span>,</span>
+<span id="cb2519-70"><a href="#cb2519-70" aria-hidden="true" tabindex="-1"></a>                  <span class="at">scale_tvq =</span> <span class="dv">1</span>,</span>
+<span id="cb2519-71"><a href="#cb2519-71" aria-hidden="true" tabindex="-1"></a>                  <span class="at">scale_tvvp =</span> <span class="dv">1</span>,</span>
+<span id="cb2519-72"><a href="#cb2519-72" aria-hidden="true" tabindex="-1"></a>                  <span class="at">scale_tvka =</span> <span class="dv">1</span>,</span>
+<span id="cb2519-73"><a href="#cb2519-73" aria-hidden="true" tabindex="-1"></a>                  <span class="at">scale_omega_cl =</span> <span class="fl">0.4</span>,</span>
+<span id="cb2519-74"><a href="#cb2519-74" aria-hidden="true" tabindex="-1"></a>                  <span class="at">scale_omega_vc =</span> <span class="fl">0.4</span>,</span>
+<span id="cb2519-75"><a href="#cb2519-75" aria-hidden="true" tabindex="-1"></a>                  <span class="at">scale_omega_q =</span> <span class="fl">0.4</span>,</span>
+<span id="cb2519-76"><a href="#cb2519-76" aria-hidden="true" tabindex="-1"></a>                  <span class="at">scale_omega_vp =</span> <span class="fl">0.4</span>,</span>
+<span id="cb2519-77"><a href="#cb2519-77" aria-hidden="true" tabindex="-1"></a>                  <span class="at">scale_omega_ka =</span> <span class="fl">0.4</span>,</span>
+<span id="cb2519-78"><a href="#cb2519-78" aria-hidden="true" tabindex="-1"></a>                  <span class="at">lkj_df_omega =</span> <span class="dv">2</span>,</span>
+<span id="cb2519-79"><a href="#cb2519-79" aria-hidden="true" tabindex="-1"></a>                  <span class="at">scale_sigma_p =</span> <span class="fl">0.5</span>,</span>
+<span id="cb2519-80"><a href="#cb2519-80" aria-hidden="true" tabindex="-1"></a>                  <span class="at">prior_only =</span> <span class="dv">0</span>)</span>
+<span id="cb2519-81"><a href="#cb2519-81" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2519-82"><a href="#cb2519-82" aria-hidden="true" tabindex="-1"></a>model <span class="ot">&lt;-</span> <span class="fu">cmdstan_model</span>(</span>
+<span id="cb2519-83"><a href="#cb2519-83" aria-hidden="true" tabindex="-1"></a>  here<span class="sc">::</span><span class="fu">here</span>(<span class="st">&quot;M3/depot_2cmt_linear/Stan/Fit/depot_2cmt_prop_all_solvers.stan&quot;</span>),</span>
+<span id="cb2519-84"><a href="#cb2519-84" aria-hidden="true" tabindex="-1"></a>  <span class="at">cpp_options =</span> <span class="fu">list</span>(<span class="at">stan_threads =</span> <span class="cn">TRUE</span>))</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+</details>
 </div>
 </div>
 </section>
@@ -8122,25 +12092,25 @@ <h3 data-number="2.4.2" class="anchored" data-anchor-id="analytical-solution-1">
 <div class="cell" data-hash="torsten_test_cache/html/unnamed-chunk-16_98a7afb43885e4001b8274ed439ecd3f">
 <details>
 <summary>Code</summary>
-<div class="sourceCode cell-code" id="cb547"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb547-1"><a href="#cb547-1" aria-hidden="true" tabindex="-1"></a>stan_data<span class="sc">$</span>solver <span class="ot">&lt;-</span> <span class="dv">1</span></span>
-<span id="cb547-2"><a href="#cb547-2" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb547-3"><a href="#cb547-3" aria-hidden="true" tabindex="-1"></a>fit <span class="ot">&lt;-</span> model<span class="sc">$</span><span class="fu">sample</span>(<span class="at">data =</span> stan_data,</span>
-<span id="cb547-4"><a href="#cb547-4" aria-hidden="true" tabindex="-1"></a>                    <span class="at">seed =</span> <span class="dv">11235</span>,</span>
-<span id="cb547-5"><a href="#cb547-5" aria-hidden="true" tabindex="-1"></a>                    <span class="at">chains =</span> <span class="dv">4</span>,</span>
-<span id="cb547-6"><a href="#cb547-6" aria-hidden="true" tabindex="-1"></a>                    <span class="at">parallel_chains =</span> <span class="dv">4</span>,</span>
-<span id="cb547-7"><a href="#cb547-7" aria-hidden="true" tabindex="-1"></a>                    <span class="at">threads_per_chain =</span> parallel<span class="sc">::</span><span class="fu">detectCores</span>()<span class="sc">/</span><span class="dv">4</span>,</span>
-<span id="cb547-8"><a href="#cb547-8" aria-hidden="true" tabindex="-1"></a>                    <span class="at">iter_warmup =</span> <span class="dv">500</span>,</span>
-<span id="cb547-9"><a href="#cb547-9" aria-hidden="true" tabindex="-1"></a>                    <span class="at">iter_sampling =</span> <span class="dv">1000</span>,</span>
-<span id="cb547-10"><a href="#cb547-10" aria-hidden="true" tabindex="-1"></a>                    <span class="at">adapt_delta =</span> <span class="fl">0.8</span>,</span>
-<span id="cb547-11"><a href="#cb547-11" aria-hidden="true" tabindex="-1"></a>                    <span class="at">refresh =</span> <span class="dv">500</span>,</span>
-<span id="cb547-12"><a href="#cb547-12" aria-hidden="true" tabindex="-1"></a>                    <span class="at">max_treedepth =</span> <span class="dv">10</span>,</span>
-<span id="cb547-13"><a href="#cb547-13" aria-hidden="true" tabindex="-1"></a>                    <span class="at">init =</span> <span class="cf">function</span>() <span class="fu">list</span>(<span class="at">TVCL =</span> <span class="fu">rlnorm</span>(<span class="dv">1</span>, <span class="fu">log</span>(<span class="dv">5</span>), <span class="fl">0.1</span>),</span>
-<span id="cb547-14"><a href="#cb547-14" aria-hidden="true" tabindex="-1"></a>                                           <span class="at">TVVC =</span> <span class="fu">rlnorm</span>(<span class="dv">1</span>, <span class="fu">log</span>(<span class="dv">20</span>), <span class="fl">0.1</span>),</span>
-<span id="cb547-15"><a href="#cb547-15" aria-hidden="true" tabindex="-1"></a>                                           <span class="at">TVQ =</span> <span class="fu">rlnorm</span>(<span class="dv">1</span>, <span class="fu">log</span>(<span class="dv">7</span>), <span class="fl">0.1</span>),</span>
-<span id="cb547-16"><a href="#cb547-16" aria-hidden="true" tabindex="-1"></a>                                           <span class="at">TVVP =</span> <span class="fu">rlnorm</span>(<span class="dv">1</span>, <span class="fu">log</span>(<span class="dv">70</span>), <span class="fl">0.1</span>),</span>
-<span id="cb547-17"><a href="#cb547-17" aria-hidden="true" tabindex="-1"></a>                                           <span class="at">TVKA =</span> <span class="fu">rlnorm</span>(<span class="dv">1</span>, <span class="fu">log</span>(<span class="fl">1.2</span>), <span class="fl">0.1</span>),</span>
-<span id="cb547-18"><a href="#cb547-18" aria-hidden="true" tabindex="-1"></a>                                           <span class="at">omega =</span> <span class="fu">rlnorm</span>(<span class="dv">5</span>, <span class="fu">log</span>(<span class="fl">0.1</span>), <span class="fl">0.1</span>),</span>
-<span id="cb547-19"><a href="#cb547-19" aria-hidden="true" tabindex="-1"></a>                                           <span class="at">sigma_p =</span> <span class="fu">rlnorm</span>(<span class="dv">1</span>, <span class="fu">log</span>(<span class="fl">0.1</span>), <span class="fl">0.1</span>)))</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<div class="sourceCode cell-code" id="cb2520"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb2520-1"><a href="#cb2520-1" aria-hidden="true" tabindex="-1"></a>stan_data<span class="sc">$</span>solver <span class="ot">&lt;-</span> <span class="dv">1</span></span>
+<span id="cb2520-2"><a href="#cb2520-2" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2520-3"><a href="#cb2520-3" aria-hidden="true" tabindex="-1"></a>fit <span class="ot">&lt;-</span> model<span class="sc">$</span><span class="fu">sample</span>(<span class="at">data =</span> stan_data,</span>
+<span id="cb2520-4"><a href="#cb2520-4" aria-hidden="true" tabindex="-1"></a>                    <span class="at">seed =</span> <span class="dv">11235</span>,</span>
+<span id="cb2520-5"><a href="#cb2520-5" aria-hidden="true" tabindex="-1"></a>                    <span class="at">chains =</span> <span class="dv">4</span>,</span>
+<span id="cb2520-6"><a href="#cb2520-6" aria-hidden="true" tabindex="-1"></a>                    <span class="at">parallel_chains =</span> <span class="dv">4</span>,</span>
+<span id="cb2520-7"><a href="#cb2520-7" aria-hidden="true" tabindex="-1"></a>                    <span class="at">threads_per_chain =</span> parallel<span class="sc">::</span><span class="fu">detectCores</span>()<span class="sc">/</span><span class="dv">4</span>,</span>
+<span id="cb2520-8"><a href="#cb2520-8" aria-hidden="true" tabindex="-1"></a>                    <span class="at">iter_warmup =</span> <span class="dv">500</span>,</span>
+<span id="cb2520-9"><a href="#cb2520-9" aria-hidden="true" tabindex="-1"></a>                    <span class="at">iter_sampling =</span> <span class="dv">1000</span>,</span>
+<span id="cb2520-10"><a href="#cb2520-10" aria-hidden="true" tabindex="-1"></a>                    <span class="at">adapt_delta =</span> <span class="fl">0.8</span>,</span>
+<span id="cb2520-11"><a href="#cb2520-11" aria-hidden="true" tabindex="-1"></a>                    <span class="at">refresh =</span> <span class="dv">500</span>,</span>
+<span id="cb2520-12"><a href="#cb2520-12" aria-hidden="true" tabindex="-1"></a>                    <span class="at">max_treedepth =</span> <span class="dv">10</span>,</span>
+<span id="cb2520-13"><a href="#cb2520-13" aria-hidden="true" tabindex="-1"></a>                    <span class="at">init =</span> <span class="cf">function</span>() <span class="fu">list</span>(<span class="at">TVCL =</span> <span class="fu">rlnorm</span>(<span class="dv">1</span>, <span class="fu">log</span>(<span class="dv">5</span>), <span class="fl">0.1</span>),</span>
+<span id="cb2520-14"><a href="#cb2520-14" aria-hidden="true" tabindex="-1"></a>                                           <span class="at">TVVC =</span> <span class="fu">rlnorm</span>(<span class="dv">1</span>, <span class="fu">log</span>(<span class="dv">20</span>), <span class="fl">0.1</span>),</span>
+<span id="cb2520-15"><a href="#cb2520-15" aria-hidden="true" tabindex="-1"></a>                                           <span class="at">TVQ =</span> <span class="fu">rlnorm</span>(<span class="dv">1</span>, <span class="fu">log</span>(<span class="dv">7</span>), <span class="fl">0.1</span>),</span>
+<span id="cb2520-16"><a href="#cb2520-16" aria-hidden="true" tabindex="-1"></a>                                           <span class="at">TVVP =</span> <span class="fu">rlnorm</span>(<span class="dv">1</span>, <span class="fu">log</span>(<span class="dv">70</span>), <span class="fl">0.1</span>),</span>
+<span id="cb2520-17"><a href="#cb2520-17" aria-hidden="true" tabindex="-1"></a>                                           <span class="at">TVKA =</span> <span class="fu">rlnorm</span>(<span class="dv">1</span>, <span class="fu">log</span>(<span class="fl">1.2</span>), <span class="fl">0.1</span>),</span>
+<span id="cb2520-18"><a href="#cb2520-18" aria-hidden="true" tabindex="-1"></a>                                           <span class="at">omega =</span> <span class="fu">rlnorm</span>(<span class="dv">5</span>, <span class="fu">log</span>(<span class="fl">0.1</span>), <span class="fl">0.1</span>),</span>
+<span id="cb2520-19"><a href="#cb2520-19" aria-hidden="true" tabindex="-1"></a>                                           <span class="at">sigma_p =</span> <span class="fu">rlnorm</span>(<span class="dv">1</span>, <span class="fu">log</span>(<span class="fl">0.1</span>), <span class="fl">0.1</span>)))</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 </details>
 <div class="cell-output cell-output-stderr">
 <pre><code>Init values were only set for a subset of parameters. 
@@ -8612,7 +12582,7 @@ <h3 data-number="2.4.2" class="anchored" data-anchor-id="analytical-solution-1">
 </div>
 </div>
 </div>
-<p>Doesn’t work.</p>
+<p>Seems to work fine.</p>
 </section>
 <section id="linear-ode" class="level3" data-number="2.4.3">
 <h3 data-number="2.4.3" class="anchored" data-anchor-id="linear-ode"><span class="header-section-number">2.4.3</span> Linear ODE</h3>
@@ -8620,26 +12590,26 @@ <h3 data-number="2.4.3" class="anchored" data-anchor-id="linear-ode"><span class
 <div class="cell" data-hash="torsten_test_cache/html/unnamed-chunk-17_a2b3547cd0ebe558965607f724c16599">
 <details>
 <summary>Code</summary>
-<div class="sourceCode cell-code" id="cb694"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb694-1"><a href="#cb694-1" aria-hidden="true" tabindex="-1"></a>stan_data<span class="sc">$</span>solver <span class="ot">&lt;-</span> <span class="dv">2</span></span>
-<span id="cb694-2"><a href="#cb694-2" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb694-3"><a href="#cb694-3" aria-hidden="true" tabindex="-1"></a>fit_mat_exp_cd <span class="ot">&lt;-</span> model<span class="sc">$</span><span class="fu">sample</span>(</span>
-<span id="cb694-4"><a href="#cb694-4" aria-hidden="true" tabindex="-1"></a>  <span class="at">data =</span> stan_data,</span>
-<span id="cb694-5"><a href="#cb694-5" aria-hidden="true" tabindex="-1"></a>  <span class="at">seed =</span> <span class="dv">11235</span>,</span>
-<span id="cb694-6"><a href="#cb694-6" aria-hidden="true" tabindex="-1"></a>  <span class="at">chains =</span> <span class="dv">4</span>,</span>
-<span id="cb694-7"><a href="#cb694-7" aria-hidden="true" tabindex="-1"></a>  <span class="at">parallel_chains =</span> <span class="dv">4</span>,</span>
-<span id="cb694-8"><a href="#cb694-8" aria-hidden="true" tabindex="-1"></a>  <span class="at">threads_per_chain =</span> parallel<span class="sc">::</span><span class="fu">detectCores</span>()<span class="sc">/</span><span class="dv">4</span>,</span>
-<span id="cb694-9"><a href="#cb694-9" aria-hidden="true" tabindex="-1"></a>  <span class="at">iter_warmup =</span> <span class="dv">500</span>,</span>
-<span id="cb694-10"><a href="#cb694-10" aria-hidden="true" tabindex="-1"></a>  <span class="at">iter_sampling =</span> <span class="dv">1000</span>,</span>
-<span id="cb694-11"><a href="#cb694-11" aria-hidden="true" tabindex="-1"></a>  <span class="at">adapt_delta =</span> <span class="fl">0.8</span>,</span>
-<span id="cb694-12"><a href="#cb694-12" aria-hidden="true" tabindex="-1"></a>  <span class="at">refresh =</span> <span class="dv">500</span>,</span>
-<span id="cb694-13"><a href="#cb694-13" aria-hidden="true" tabindex="-1"></a>  <span class="at">max_treedepth =</span> <span class="dv">10</span>,</span>
-<span id="cb694-14"><a href="#cb694-14" aria-hidden="true" tabindex="-1"></a>  <span class="at">init =</span> <span class="cf">function</span>() <span class="fu">list</span>(<span class="at">TVCL =</span> <span class="fu">rlnorm</span>(<span class="dv">1</span>, <span class="fu">log</span>(<span class="dv">5</span>), <span class="fl">0.1</span>),</span>
-<span id="cb694-15"><a href="#cb694-15" aria-hidden="true" tabindex="-1"></a>                         <span class="at">TVVC =</span> <span class="fu">rlnorm</span>(<span class="dv">1</span>, <span class="fu">log</span>(<span class="dv">20</span>), <span class="fl">0.1</span>),</span>
-<span id="cb694-16"><a href="#cb694-16" aria-hidden="true" tabindex="-1"></a>                         <span class="at">TVQ =</span> <span class="fu">rlnorm</span>(<span class="dv">1</span>, <span class="fu">log</span>(<span class="dv">7</span>), <span class="fl">0.1</span>),</span>
-<span id="cb694-17"><a href="#cb694-17" aria-hidden="true" tabindex="-1"></a>                         <span class="at">TVVP =</span> <span class="fu">rlnorm</span>(<span class="dv">1</span>, <span class="fu">log</span>(<span class="dv">70</span>), <span class="fl">0.1</span>),</span>
-<span id="cb694-18"><a href="#cb694-18" aria-hidden="true" tabindex="-1"></a>                         <span class="at">TVKA =</span> <span class="fu">rlnorm</span>(<span class="dv">1</span>, <span class="fu">log</span>(<span class="fl">1.2</span>), <span class="fl">0.1</span>),</span>
-<span id="cb694-19"><a href="#cb694-19" aria-hidden="true" tabindex="-1"></a>                         <span class="at">omega =</span> <span class="fu">rlnorm</span>(<span class="dv">5</span>, <span class="fu">log</span>(<span class="fl">0.1</span>), <span class="fl">0.1</span>),</span>
-<span id="cb694-20"><a href="#cb694-20" aria-hidden="true" tabindex="-1"></a>                         <span class="at">sigma_p =</span> <span class="fu">rlnorm</span>(<span class="dv">1</span>, <span class="fu">log</span>(<span class="fl">0.1</span>), <span class="fl">0.1</span>)))</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<div class="sourceCode cell-code" id="cb2667"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb2667-1"><a href="#cb2667-1" aria-hidden="true" tabindex="-1"></a>stan_data<span class="sc">$</span>solver <span class="ot">&lt;-</span> <span class="dv">2</span></span>
+<span id="cb2667-2"><a href="#cb2667-2" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2667-3"><a href="#cb2667-3" aria-hidden="true" tabindex="-1"></a>fit_mat_exp_cd <span class="ot">&lt;-</span> model<span class="sc">$</span><span class="fu">sample</span>(</span>
+<span id="cb2667-4"><a href="#cb2667-4" aria-hidden="true" tabindex="-1"></a>  <span class="at">data =</span> stan_data,</span>
+<span id="cb2667-5"><a href="#cb2667-5" aria-hidden="true" tabindex="-1"></a>  <span class="at">seed =</span> <span class="dv">11235</span>,</span>
+<span id="cb2667-6"><a href="#cb2667-6" aria-hidden="true" tabindex="-1"></a>  <span class="at">chains =</span> <span class="dv">4</span>,</span>
+<span id="cb2667-7"><a href="#cb2667-7" aria-hidden="true" tabindex="-1"></a>  <span class="at">parallel_chains =</span> <span class="dv">4</span>,</span>
+<span id="cb2667-8"><a href="#cb2667-8" aria-hidden="true" tabindex="-1"></a>  <span class="at">threads_per_chain =</span> parallel<span class="sc">::</span><span class="fu">detectCores</span>()<span class="sc">/</span><span class="dv">4</span>,</span>
+<span id="cb2667-9"><a href="#cb2667-9" aria-hidden="true" tabindex="-1"></a>  <span class="at">iter_warmup =</span> <span class="dv">500</span>,</span>
+<span id="cb2667-10"><a href="#cb2667-10" aria-hidden="true" tabindex="-1"></a>  <span class="at">iter_sampling =</span> <span class="dv">1000</span>,</span>
+<span id="cb2667-11"><a href="#cb2667-11" aria-hidden="true" tabindex="-1"></a>  <span class="at">adapt_delta =</span> <span class="fl">0.8</span>,</span>
+<span id="cb2667-12"><a href="#cb2667-12" aria-hidden="true" tabindex="-1"></a>  <span class="at">refresh =</span> <span class="dv">500</span>,</span>
+<span id="cb2667-13"><a href="#cb2667-13" aria-hidden="true" tabindex="-1"></a>  <span class="at">max_treedepth =</span> <span class="dv">10</span>,</span>
+<span id="cb2667-14"><a href="#cb2667-14" aria-hidden="true" tabindex="-1"></a>  <span class="at">init =</span> <span class="cf">function</span>() <span class="fu">list</span>(<span class="at">TVCL =</span> <span class="fu">rlnorm</span>(<span class="dv">1</span>, <span class="fu">log</span>(<span class="dv">5</span>), <span class="fl">0.1</span>),</span>
+<span id="cb2667-15"><a href="#cb2667-15" aria-hidden="true" tabindex="-1"></a>                         <span class="at">TVVC =</span> <span class="fu">rlnorm</span>(<span class="dv">1</span>, <span class="fu">log</span>(<span class="dv">20</span>), <span class="fl">0.1</span>),</span>
+<span id="cb2667-16"><a href="#cb2667-16" aria-hidden="true" tabindex="-1"></a>                         <span class="at">TVQ =</span> <span class="fu">rlnorm</span>(<span class="dv">1</span>, <span class="fu">log</span>(<span class="dv">7</span>), <span class="fl">0.1</span>),</span>
+<span id="cb2667-17"><a href="#cb2667-17" aria-hidden="true" tabindex="-1"></a>                         <span class="at">TVVP =</span> <span class="fu">rlnorm</span>(<span class="dv">1</span>, <span class="fu">log</span>(<span class="dv">70</span>), <span class="fl">0.1</span>),</span>
+<span id="cb2667-18"><a href="#cb2667-18" aria-hidden="true" tabindex="-1"></a>                         <span class="at">TVKA =</span> <span class="fu">rlnorm</span>(<span class="dv">1</span>, <span class="fu">log</span>(<span class="fl">1.2</span>), <span class="fl">0.1</span>),</span>
+<span id="cb2667-19"><a href="#cb2667-19" aria-hidden="true" tabindex="-1"></a>                         <span class="at">omega =</span> <span class="fu">rlnorm</span>(<span class="dv">5</span>, <span class="fu">log</span>(<span class="fl">0.1</span>), <span class="fl">0.1</span>),</span>
+<span id="cb2667-20"><a href="#cb2667-20" aria-hidden="true" tabindex="-1"></a>                         <span class="at">sigma_p =</span> <span class="fu">rlnorm</span>(<span class="dv">1</span>, <span class="fu">log</span>(<span class="fl">0.1</span>), <span class="fl">0.1</span>)))</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 </details>
 <div class="cell-output cell-output-stderr">
 <pre><code>Init values were only set for a subset of parameters. 
@@ -9074,26 +13044,26 @@ <h3 data-number="2.4.4" class="anchored" data-anchor-id="general-ode"><span clas
 <div class="cell" data-hash="torsten_test_cache/html/unnamed-chunk-18_2dde6cdb6084b0c5e19ad861e07aca4d">
 <details>
 <summary>Code</summary>
-<div class="sourceCode cell-code" id="cb826"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb826-1"><a href="#cb826-1" aria-hidden="true" tabindex="-1"></a>stan_data<span class="sc">$</span>solver <span class="ot">&lt;-</span> <span class="dv">3</span></span>
-<span id="cb826-2"><a href="#cb826-2" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb826-3"><a href="#cb826-3" aria-hidden="true" tabindex="-1"></a>fit_rk45_cd <span class="ot">&lt;-</span> model<span class="sc">$</span><span class="fu">sample</span>(</span>
-<span id="cb826-4"><a href="#cb826-4" aria-hidden="true" tabindex="-1"></a>  <span class="at">data =</span> stan_data,</span>
-<span id="cb826-5"><a href="#cb826-5" aria-hidden="true" tabindex="-1"></a>  <span class="at">seed =</span> <span class="dv">11235</span>,</span>
-<span id="cb826-6"><a href="#cb826-6" aria-hidden="true" tabindex="-1"></a>  <span class="at">chains =</span> <span class="dv">4</span>,</span>
-<span id="cb826-7"><a href="#cb826-7" aria-hidden="true" tabindex="-1"></a>  <span class="at">parallel_chains =</span> <span class="dv">4</span>,</span>
-<span id="cb826-8"><a href="#cb826-8" aria-hidden="true" tabindex="-1"></a>  <span class="at">threads_per_chain =</span> parallel<span class="sc">::</span><span class="fu">detectCores</span>()<span class="sc">/</span><span class="dv">4</span>,</span>
-<span id="cb826-9"><a href="#cb826-9" aria-hidden="true" tabindex="-1"></a>  <span class="at">iter_warmup =</span> <span class="dv">300</span>,</span>
-<span id="cb826-10"><a href="#cb826-10" aria-hidden="true" tabindex="-1"></a>  <span class="at">iter_sampling =</span> <span class="dv">100</span>,</span>
-<span id="cb826-11"><a href="#cb826-11" aria-hidden="true" tabindex="-1"></a>  <span class="at">adapt_delta =</span> <span class="fl">0.8</span>,</span>
-<span id="cb826-12"><a href="#cb826-12" aria-hidden="true" tabindex="-1"></a>  <span class="at">refresh =</span> <span class="dv">0</span>,</span>
-<span id="cb826-13"><a href="#cb826-13" aria-hidden="true" tabindex="-1"></a>  <span class="at">max_treedepth =</span> <span class="dv">10</span>,</span>
-<span id="cb826-14"><a href="#cb826-14" aria-hidden="true" tabindex="-1"></a>  <span class="at">init =</span> <span class="cf">function</span>() <span class="fu">list</span>(<span class="at">TVCL =</span> <span class="fu">rlnorm</span>(<span class="dv">1</span>, <span class="fu">log</span>(<span class="dv">5</span>), <span class="fl">0.1</span>),</span>
-<span id="cb826-15"><a href="#cb826-15" aria-hidden="true" tabindex="-1"></a>                         <span class="at">TVVC =</span> <span class="fu">rlnorm</span>(<span class="dv">1</span>, <span class="fu">log</span>(<span class="dv">20</span>), <span class="fl">0.1</span>),</span>
-<span id="cb826-16"><a href="#cb826-16" aria-hidden="true" tabindex="-1"></a>                         <span class="at">TVQ =</span> <span class="fu">rlnorm</span>(<span class="dv">1</span>, <span class="fu">log</span>(<span class="dv">7</span>), <span class="fl">0.1</span>),</span>
-<span id="cb826-17"><a href="#cb826-17" aria-hidden="true" tabindex="-1"></a>                         <span class="at">TVVP =</span> <span class="fu">rlnorm</span>(<span class="dv">1</span>, <span class="fu">log</span>(<span class="dv">70</span>), <span class="fl">0.1</span>),</span>
-<span id="cb826-18"><a href="#cb826-18" aria-hidden="true" tabindex="-1"></a>                         <span class="at">TVKA =</span> <span class="fu">rlnorm</span>(<span class="dv">1</span>, <span class="fu">log</span>(<span class="fl">1.2</span>), <span class="fl">0.1</span>),</span>
-<span id="cb826-19"><a href="#cb826-19" aria-hidden="true" tabindex="-1"></a>                         <span class="at">omega =</span> <span class="fu">rlnorm</span>(<span class="dv">5</span>, <span class="fu">log</span>(<span class="fl">0.1</span>), <span class="fl">0.1</span>),</span>
-<span id="cb826-20"><a href="#cb826-20" aria-hidden="true" tabindex="-1"></a>                         <span class="at">sigma_p =</span> <span class="fu">rlnorm</span>(<span class="dv">1</span>, <span class="fu">log</span>(<span class="fl">0.1</span>), <span class="fl">0.1</span>)))</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<div class="sourceCode cell-code" id="cb2799"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb2799-1"><a href="#cb2799-1" aria-hidden="true" tabindex="-1"></a>stan_data<span class="sc">$</span>solver <span class="ot">&lt;-</span> <span class="dv">3</span></span>
+<span id="cb2799-2"><a href="#cb2799-2" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2799-3"><a href="#cb2799-3" aria-hidden="true" tabindex="-1"></a>fit_rk45_cd <span class="ot">&lt;-</span> model<span class="sc">$</span><span class="fu">sample</span>(</span>
+<span id="cb2799-4"><a href="#cb2799-4" aria-hidden="true" tabindex="-1"></a>  <span class="at">data =</span> stan_data,</span>
+<span id="cb2799-5"><a href="#cb2799-5" aria-hidden="true" tabindex="-1"></a>  <span class="at">seed =</span> <span class="dv">11235</span>,</span>
+<span id="cb2799-6"><a href="#cb2799-6" aria-hidden="true" tabindex="-1"></a>  <span class="at">chains =</span> <span class="dv">4</span>,</span>
+<span id="cb2799-7"><a href="#cb2799-7" aria-hidden="true" tabindex="-1"></a>  <span class="at">parallel_chains =</span> <span class="dv">4</span>,</span>
+<span id="cb2799-8"><a href="#cb2799-8" aria-hidden="true" tabindex="-1"></a>  <span class="at">threads_per_chain =</span> parallel<span class="sc">::</span><span class="fu">detectCores</span>()<span class="sc">/</span><span class="dv">4</span>,</span>
+<span id="cb2799-9"><a href="#cb2799-9" aria-hidden="true" tabindex="-1"></a>  <span class="at">iter_warmup =</span> <span class="dv">300</span>,</span>
+<span id="cb2799-10"><a href="#cb2799-10" aria-hidden="true" tabindex="-1"></a>  <span class="at">iter_sampling =</span> <span class="dv">100</span>,</span>
+<span id="cb2799-11"><a href="#cb2799-11" aria-hidden="true" tabindex="-1"></a>  <span class="at">adapt_delta =</span> <span class="fl">0.8</span>,</span>
+<span id="cb2799-12"><a href="#cb2799-12" aria-hidden="true" tabindex="-1"></a>  <span class="at">refresh =</span> <span class="dv">0</span>,</span>
+<span id="cb2799-13"><a href="#cb2799-13" aria-hidden="true" tabindex="-1"></a>  <span class="at">max_treedepth =</span> <span class="dv">10</span>,</span>
+<span id="cb2799-14"><a href="#cb2799-14" aria-hidden="true" tabindex="-1"></a>  <span class="at">init =</span> <span class="cf">function</span>() <span class="fu">list</span>(<span class="at">TVCL =</span> <span class="fu">rlnorm</span>(<span class="dv">1</span>, <span class="fu">log</span>(<span class="dv">5</span>), <span class="fl">0.1</span>),</span>
+<span id="cb2799-15"><a href="#cb2799-15" aria-hidden="true" tabindex="-1"></a>                         <span class="at">TVVC =</span> <span class="fu">rlnorm</span>(<span class="dv">1</span>, <span class="fu">log</span>(<span class="dv">20</span>), <span class="fl">0.1</span>),</span>
+<span id="cb2799-16"><a href="#cb2799-16" aria-hidden="true" tabindex="-1"></a>                         <span class="at">TVQ =</span> <span class="fu">rlnorm</span>(<span class="dv">1</span>, <span class="fu">log</span>(<span class="dv">7</span>), <span class="fl">0.1</span>),</span>
+<span id="cb2799-17"><a href="#cb2799-17" aria-hidden="true" tabindex="-1"></a>                         <span class="at">TVVP =</span> <span class="fu">rlnorm</span>(<span class="dv">1</span>, <span class="fu">log</span>(<span class="dv">70</span>), <span class="fl">0.1</span>),</span>
+<span id="cb2799-18"><a href="#cb2799-18" aria-hidden="true" tabindex="-1"></a>                         <span class="at">TVKA =</span> <span class="fu">rlnorm</span>(<span class="dv">1</span>, <span class="fu">log</span>(<span class="fl">1.2</span>), <span class="fl">0.1</span>),</span>
+<span id="cb2799-19"><a href="#cb2799-19" aria-hidden="true" tabindex="-1"></a>                         <span class="at">omega =</span> <span class="fu">rlnorm</span>(<span class="dv">5</span>, <span class="fu">log</span>(<span class="fl">0.1</span>), <span class="fl">0.1</span>),</span>
+<span id="cb2799-20"><a href="#cb2799-20" aria-hidden="true" tabindex="-1"></a>                         <span class="at">sigma_p =</span> <span class="fu">rlnorm</span>(<span class="dv">1</span>, <span class="fu">log</span>(<span class="fl">0.1</span>), <span class="fl">0.1</span>)))</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 </details>
 <div class="cell-output cell-output-stderr">
 <pre><code>Init values were only set for a subset of parameters. 
@@ -9544,14 +13514,15 @@ <h3 data-number="2.4.4" class="anchored" data-anchor-id="general-ode"><span clas
 </section>
 <section id="summary" class="level1" data-number="3">
 <h1 data-number="3"><span class="header-section-number">3</span> Summary</h1>
-<p>Basically, I haven’t figured out if there’s any rhyme or reason to when the analytical, linear ODE, or general ODE solution works or not.</p>
+<!-- Basically, I haven't figured out if there's any rhyme or reason to when the  -->
+<!-- analytical, linear ODE, or general ODE solution works or not.  -->
 </section>
 <section id="session-info" class="level1" data-number="4">
 <h1 data-number="4"><span class="header-section-number">4</span> Session Info</h1>
 <div class="cell">
 <details>
 <summary>Code</summary>
-<div class="sourceCode cell-code" id="cb970"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb970-1"><a href="#cb970-1" aria-hidden="true" tabindex="-1"></a><span class="fu">sessionInfo</span>()</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<div class="sourceCode cell-code" id="cb2943"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb2943-1"><a href="#cb2943-1" aria-hidden="true" tabindex="-1"></a><span class="fu">sessionInfo</span>()</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 </details>
 <div class="cell-output cell-output-stdout">
 <pre><code>R version 4.2.2 (2022-10-31)
@@ -9574,35 +13545,31 @@ <h1 data-number="4"><span class="header-section-number">4</span> Session Info</h
 [13] mrgsolve_1.3.0 
 
 loaded via a namespace (and not attached):
- [1] matrixStats_1.0.0    fs_1.6.0             lubridate_1.9.2     
- [4] httr_1.4.6           rprojroot_2.0.3      rstan_2.32.5        
- [7] tensorA_0.36.2       tools_4.2.2          backports_1.4.1     
-[10] utf8_1.2.3           R6_2.5.1             DBI_1.1.3           
-[13] colorspace_2.1-0     ggdist_3.3.1         withr_2.5.0         
-[16] gridExtra_2.3        prettyunits_1.1.1    tidyselect_1.2.0    
-[19] processx_3.8.1       compiler_4.2.2       cli_3.6.1           
-[22] rvest_1.0.3          arrayhelpers_1.1-0   xml2_1.3.5          
-[25] labeling_0.4.2       scales_1.2.1         checkmate_2.2.0     
-[28] callr_3.7.3          QuickJSR_1.0.9       StanHeaders_2.32.5  
-[31] digest_0.6.33        rmarkdown_2.20       pkgconfig_2.0.3     
-[34] htmltools_0.5.4      dbplyr_2.3.0         fastmap_1.1.1       
-[37] htmlwidgets_1.6.1    rlang_1.1.1          readxl_1.4.1        
-[40] rstudioapi_0.15.0    farver_2.1.1         generics_0.1.3      
-[43] svUnit_1.0.6         jsonlite_1.8.7       googlesheets4_1.0.1 
-[46] distributional_0.3.2 inline_0.3.19        magrittr_2.0.3      
-[49] loo_2.6.0            Rcpp_1.0.10          munsell_0.5.0       
-[52] fansi_1.0.4          abind_1.4-5          lifecycle_1.0.3     
-[55] stringi_1.7.12       yaml_2.3.7           pkgbuild_1.4.0      
-[58] grid_4.2.2           parallel_4.2.2       crayon_1.5.2        
-[61] lattice_0.20-45      haven_2.5.1          hms_1.1.3           
-[64] knitr_1.41           ps_1.7.5             pillar_1.9.0        
-[67] codetools_0.2-18     stats4_4.2.2         reprex_2.0.2        
-[70] glue_1.6.2           evaluate_0.20        RcppParallel_5.1.7  
-[73] data.table_1.14.8    modelr_0.1.10        vctrs_0.6.3         
-[76] tzdb_0.4.0           cellranger_1.1.0     gtable_0.3.3        
-[79] assertthat_0.2.1     xfun_0.41            broom_1.0.2         
-[82] coda_0.19-4          googledrive_2.0.0    gargle_1.2.1        
-[85] timechange_0.2.0     here_1.0.1          </code></pre>
+ [1] httr_1.4.6           jsonlite_1.8.7       here_1.0.1          
+ [4] modelr_0.1.10        assertthat_0.2.1     distributional_0.3.2
+ [7] ggdist_3.3.1         tensorA_0.36.2       googlesheets4_1.0.1 
+[10] cellranger_1.1.0     yaml_2.3.7           pillar_1.9.0        
+[13] backports_1.4.1      lattice_0.20-45      glue_1.6.2          
+[16] arrayhelpers_1.1-0   digest_0.6.33        checkmate_2.2.0     
+[19] rvest_1.0.3          colorspace_2.1-0     htmltools_0.5.4     
+[22] pkgconfig_2.0.3      broom_1.0.2          svUnit_1.0.6        
+[25] haven_2.5.1          scales_1.2.1         processx_3.8.1      
+[28] tzdb_0.4.0           timechange_0.2.0     googledrive_2.0.0   
+[31] generics_0.1.3       farver_2.1.1         withr_2.5.0         
+[34] cli_3.6.1            crayon_1.5.2         magrittr_2.0.3      
+[37] readxl_1.4.1         evaluate_0.20        ps_1.7.5            
+[40] fs_1.6.0             fansi_1.0.4          xml2_1.3.5          
+[43] data.table_1.14.8    tools_4.2.2          hms_1.1.3           
+[46] gargle_1.2.1         lifecycle_1.0.3      munsell_0.5.0       
+[49] reprex_2.0.2         compiler_4.2.2       rlang_1.1.1         
+[52] grid_4.2.2           rstudioapi_0.15.0    htmlwidgets_1.6.1   
+[55] labeling_0.4.2       rmarkdown_2.20       codetools_0.2-18    
+[58] gtable_0.3.3         abind_1.4-5          DBI_1.1.3           
+[61] R6_2.5.1             lubridate_1.9.2      knitr_1.41          
+[64] fastmap_1.1.1        utf8_1.2.3           rprojroot_2.0.3     
+[67] stringi_1.7.12       Rcpp_1.0.10          vctrs_0.6.3         
+[70] dbplyr_2.3.0         tidyselect_1.2.0     xfun_0.41           
+[73] coda_0.19-4         </code></pre>
 </div>
 </div>
 <!-- -->
@@ -9895,961 +13862,966 @@ <h1 data-number="4"><span class="header-section-number">4</span> Session Info</h
   }
 });
 </script><div class="modal fade" id="quarto-embedded-source-code-modal" tabindex="-1" aria-labelledby="quarto-embedded-source-code-modal-label" aria-hidden="true"><div class="modal-dialog modal-dialog-scrollable"><div class="modal-content"><div class="modal-header"><h5 class="modal-title" id="quarto-embedded-source-code-modal-label">Source Code</h5><button class="btn-close" data-bs-dismiss="modal"></button></div><div class="modal-body"><div class>
-<div class="sourceCode" id="cb972" data-shortcodes="false"><pre class="sourceCode markdown code-with-copy"><code class="sourceCode markdown"><span id="cb972-1"><a href="#cb972-1" aria-hidden="true" tabindex="-1"></a><span class="co">---</span></span>
-<span id="cb972-2"><a href="#cb972-2" aria-hidden="true" tabindex="-1"></a><span class="an">title:</span><span class="co"> &quot;Torsten Issues&quot;</span></span>
-<span id="cb972-3"><a href="#cb972-3" aria-hidden="true" tabindex="-1"></a><span class="an">author:</span><span class="co"> &quot;Casey Davis&quot;</span></span>
-<span id="cb972-4"><a href="#cb972-4" aria-hidden="true" tabindex="-1"></a><span class="an">date:</span><span class="co"> &quot;`r format(Sys.time(), &#39;%B %d, %Y&#39;)`&quot;</span></span>
-<span id="cb972-5"><a href="#cb972-5" aria-hidden="true" tabindex="-1"></a><span class="an">format:</span></span>
-<span id="cb972-6"><a href="#cb972-6" aria-hidden="true" tabindex="-1"></a><span class="co">  html:</span></span>
-<span id="cb972-7"><a href="#cb972-7" aria-hidden="true" tabindex="-1"></a><span class="co">    code-fold: true  </span></span>
-<span id="cb972-8"><a href="#cb972-8" aria-hidden="true" tabindex="-1"></a><span class="co">    code-summary: &quot;Code&quot;</span></span>
-<span id="cb972-9"><a href="#cb972-9" aria-hidden="true" tabindex="-1"></a><span class="co">    code-tools: true</span></span>
-<span id="cb972-10"><a href="#cb972-10" aria-hidden="true" tabindex="-1"></a><span class="co">    number-sections: true</span></span>
-<span id="cb972-11"><a href="#cb972-11" aria-hidden="true" tabindex="-1"></a><span class="co">    toc: true</span></span>
-<span id="cb972-12"><a href="#cb972-12" aria-hidden="true" tabindex="-1"></a><span class="co">    toc-depth: 5</span></span>
-<span id="cb972-13"><a href="#cb972-13" aria-hidden="true" tabindex="-1"></a><span class="co">    embed-resources: true  </span></span>
-<span id="cb972-14"><a href="#cb972-14" aria-hidden="true" tabindex="-1"></a><span class="an">editor_options:</span><span class="co"> </span></span>
-<span id="cb972-15"><a href="#cb972-15" aria-hidden="true" tabindex="-1"></a><span class="co">  chunk_output_type: console</span></span>
-<span id="cb972-16"><a href="#cb972-16" aria-hidden="true" tabindex="-1"></a><span class="co">---</span></span>
-<span id="cb972-17"><a href="#cb972-17" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-18"><a href="#cb972-18" aria-hidden="true" tabindex="-1"></a><span class="in">```{css, echo = FALSE}</span></span>
-<span id="cb972-19"><a href="#cb972-19" aria-hidden="true" tabindex="-1"></a><span class="op">.</span><span class="fu">scrolling_500</span> <span class="op">{</span></span>
-<span id="cb972-20"><a href="#cb972-20" aria-hidden="true" tabindex="-1"></a>  max<span class="op">-</span>height<span class="op">:</span> 500px<span class="op">;</span></span>
-<span id="cb972-21"><a href="#cb972-21" aria-hidden="true" tabindex="-1"></a>  overflow<span class="op">-</span>y<span class="op">:</span> auto<span class="op">;</span></span>
-<span id="cb972-22"><a href="#cb972-22" aria-hidden="true" tabindex="-1"></a><span class="op">}</span></span>
-<span id="cb972-23"><a href="#cb972-23" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-24"><a href="#cb972-24" aria-hidden="true" tabindex="-1"></a><span class="op">.</span><span class="fu">scrolling_700</span> <span class="op">{</span></span>
-<span id="cb972-25"><a href="#cb972-25" aria-hidden="true" tabindex="-1"></a>  max<span class="op">-</span>height<span class="op">:</span> 700px<span class="op">;</span></span>
-<span id="cb972-26"><a href="#cb972-26" aria-hidden="true" tabindex="-1"></a>  overflow<span class="op">-</span>y<span class="op">:</span> auto<span class="op">;</span></span>
-<span id="cb972-27"><a href="#cb972-27" aria-hidden="true" tabindex="-1"></a><span class="op">}</span></span>
-<span id="cb972-28"><a href="#cb972-28" aria-hidden="true" tabindex="-1"></a><span class="in">```</span></span>
-<span id="cb972-29"><a href="#cb972-29" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-32"><a href="#cb972-32" aria-hidden="true" tabindex="-1"></a><span class="in">```{r}</span></span>
-<span id="cb972-33"><a href="#cb972-33" aria-hidden="true" tabindex="-1"></a><span class="co">#| label: package-load</span></span>
-<span id="cb972-34"><a href="#cb972-34" aria-hidden="true" tabindex="-1"></a><span class="co">#| include: true</span></span>
-<span id="cb972-35"><a href="#cb972-35" aria-hidden="true" tabindex="-1"></a><span class="co">#| message: false</span></span>
-<span id="cb972-36"><a href="#cb972-36" aria-hidden="true" tabindex="-1"></a><span class="co">#| warning: false</span></span>
-<span id="cb972-37"><a href="#cb972-37" aria-hidden="true" tabindex="-1"></a><span class="co">#| echo: false</span></span>
-<span id="cb972-38"><a href="#cb972-38" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-39"><a href="#cb972-39" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(mrgsolve)</span>
-<span id="cb972-40"><a href="#cb972-40" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(tidybayes)</span>
-<span id="cb972-41"><a href="#cb972-41" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(posterior)</span>
-<span id="cb972-42"><a href="#cb972-42" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(cmdstanr)</span>
-<span id="cb972-43"><a href="#cb972-43" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(tidyverse)</span>
-<span id="cb972-44"><a href="#cb972-44" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-45"><a href="#cb972-45" aria-hidden="true" tabindex="-1"></a><span class="fu">set_cmdstan_path</span>(here<span class="sc">::</span><span class="fu">here</span>(<span class="st">&quot;~/Torsten/cmdstan&quot;</span>))</span>
-<span id="cb972-46"><a href="#cb972-46" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-47"><a href="#cb972-47" aria-hidden="true" tabindex="-1"></a><span class="in">```</span></span>
-<span id="cb972-48"><a href="#cb972-48" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-49"><a href="#cb972-49" aria-hidden="true" tabindex="-1"></a><span class="fu"># Introduction</span></span>
-<span id="cb972-50"><a href="#cb972-50" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-51"><a href="#cb972-51" aria-hidden="true" tabindex="-1"></a>I&#39;ve been doing some testing with the new Torsten release (v0.91.0) on an M3 </span>
-<span id="cb972-52"><a href="#cb972-52" aria-hidden="true" tabindex="-1"></a>Macbook Pro. I brought up an issue with M3 compatibility</span>
-<span id="cb972-53"><a href="#cb972-53" aria-hidden="true" tabindex="-1"></a><span class="co">[</span><span class="ot">here</span><span class="co">](https://discourse.mc-stan.org/t/problem-installing-torsten-0-90/27585/12)</span>.</span>
-<span id="cb972-54"><a href="#cb972-54" aria-hidden="true" tabindex="-1"></a>Thank you for fixing that issue. Now I&#39;m doing some more testing, and I&#39;m </span>
-<span id="cb972-55"><a href="#cb972-55" aria-hidden="true" tabindex="-1"></a>finding some issues with the Torsten solvers.</span>
-<span id="cb972-56"><a href="#cb972-56" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-57"><a href="#cb972-57" aria-hidden="true" tabindex="-1"></a>I&#39;ve mostly done testing on my own models, but I&#39;ve also worked on the </span>
-<span id="cb972-58"><a href="#cb972-58" aria-hidden="true" tabindex="-1"></a>```pk2cpt<span class="in">```, ```</span>pk2cpt_linode<span class="in">```, ```</span>pk2cpt_ode```, and ```poppk2cpt``` models,</span>
-<span id="cb972-59"><a href="#cb972-59" aria-hidden="true" tabindex="-1"></a>For the single subject models, the analytical solution didn&#39;t work, the linear </span>
-<span id="cb972-60"><a href="#cb972-60" aria-hidden="true" tabindex="-1"></a>ODE solution worked, and the ODE solution didn&#39;t work (although I&#39;m not exactly </span>
-<span id="cb972-61"><a href="#cb972-61" aria-hidden="true" tabindex="-1"></a>sure why the ODE solution didn&#39;t work. Still needs worked on, I guess.) For the </span>
-<span id="cb972-62"><a href="#cb972-62" aria-hidden="true" tabindex="-1"></a>population model, the analytical solution and the ODE solution worked with the</span>
-<span id="cb972-63"><a href="#cb972-63" aria-hidden="true" tabindex="-1"></a>model that you&#39;ve written, but the linear ODE soolution didn&#39;t work. So I then</span>
-<span id="cb972-64"><a href="#cb972-64" aria-hidden="true" tabindex="-1"></a>used the data in ```poppk2cpt``` and fit it with a model I&#39;ve written, and the</span>
-<span id="cb972-65"><a href="#cb972-65" aria-hidden="true" tabindex="-1"></a>linear ODE and general ODE solutions worked, but the analytical solution didn&#39;t.</span>
-<span id="cb972-66"><a href="#cb972-66" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-67"><a href="#cb972-67" aria-hidden="true" tabindex="-1"></a><span class="fu"># Some Examples</span></span>
-<span id="cb972-68"><a href="#cb972-68" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-69"><a href="#cb972-69" aria-hidden="true" tabindex="-1"></a><span class="fu">## Simulate from My Models</span></span>
-<span id="cb972-70"><a href="#cb972-70" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-71"><a href="#cb972-71" aria-hidden="true" tabindex="-1"></a>I&#39;m starting out with simulations, mainly because it&#39;s simpler and faster.</span>
-<span id="cb972-72"><a href="#cb972-72" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-73"><a href="#cb972-73" aria-hidden="true" tabindex="-1"></a><span class="fu">### One-Compartment Oral with Lognormal Error</span></span>
-<span id="cb972-74"><a href="#cb972-74" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-75"><a href="#cb972-75" aria-hidden="true" tabindex="-1"></a>The following code simulates with Stan + Torsten with an analytical solution, </span>
-<span id="cb972-76"><a href="#cb972-76" aria-hidden="true" tabindex="-1"></a>linear ODE solution, and general ODE solution using code I&#39;ve written in the </span>
-<span id="cb972-77"><a href="#cb972-77" aria-hidden="true" tabindex="-1"></a>past, and then also a simulation with mrgsolve as a comparison.</span>
-<span id="cb972-78"><a href="#cb972-78" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-79"><a href="#cb972-79" aria-hidden="true" tabindex="-1"></a>:::{.scrolling_500}</span>
-<span id="cb972-80"><a href="#cb972-80" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-83"><a href="#cb972-83" aria-hidden="true" tabindex="-1"></a><span class="in">```{r}</span></span>
-<span id="cb972-84"><a href="#cb972-84" aria-hidden="true" tabindex="-1"></a><span class="co">#| cache: true</span></span>
-<span id="cb972-85"><a href="#cb972-85" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-86"><a href="#cb972-86" aria-hidden="true" tabindex="-1"></a>TVCL <span class="ot">&lt;-</span> <span class="fl">0.5</span></span>
-<span id="cb972-87"><a href="#cb972-87" aria-hidden="true" tabindex="-1"></a>TVVC <span class="ot">&lt;-</span> <span class="dv">12</span></span>
-<span id="cb972-88"><a href="#cb972-88" aria-hidden="true" tabindex="-1"></a>TVKA <span class="ot">&lt;-</span> <span class="dv">1</span></span>
-<span id="cb972-89"><a href="#cb972-89" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-90"><a href="#cb972-90" aria-hidden="true" tabindex="-1"></a>omega_cl <span class="ot">&lt;-</span> <span class="dv">0</span></span>
-<span id="cb972-91"><a href="#cb972-91" aria-hidden="true" tabindex="-1"></a>omega_vc <span class="ot">&lt;-</span> <span class="dv">0</span></span>
-<span id="cb972-92"><a href="#cb972-92" aria-hidden="true" tabindex="-1"></a>omega_ka <span class="ot">&lt;-</span> <span class="dv">0</span></span>
-<span id="cb972-93"><a href="#cb972-93" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-94"><a href="#cb972-94" aria-hidden="true" tabindex="-1"></a>R <span class="ot">&lt;-</span> <span class="fu">diag</span>(<span class="fu">rep</span>(<span class="dv">1</span>, <span class="at">times =</span> <span class="dv">3</span>))</span>
-<span id="cb972-95"><a href="#cb972-95" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-96"><a href="#cb972-96" aria-hidden="true" tabindex="-1"></a>sigma <span class="ot">&lt;-</span> <span class="fl">0.2</span></span>
-<span id="cb972-97"><a href="#cb972-97" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-98"><a href="#cb972-98" aria-hidden="true" tabindex="-1"></a>dosing_data <span class="ot">&lt;-</span> <span class="fu">expand.ev</span>(<span class="at">ID =</span> <span class="dv">1</span>, <span class="at">addl =</span> <span class="dv">6</span>, <span class="at">ii =</span> <span class="dv">24</span>, </span>
-<span id="cb972-99"><a href="#cb972-99" aria-hidden="true" tabindex="-1"></a>                         <span class="at">cmt =</span> <span class="dv">1</span>, <span class="at">amt =</span> <span class="dv">200</span>, <span class="at">ss =</span> <span class="dv">0</span>, <span class="at">tinf =</span> <span class="dv">0</span>, </span>
-<span id="cb972-100"><a href="#cb972-100" aria-hidden="true" tabindex="-1"></a>                         <span class="at">evid =</span> <span class="dv">1</span>) <span class="sc">%&gt;%</span></span>
-<span id="cb972-101"><a href="#cb972-101" aria-hidden="true" tabindex="-1"></a>  <span class="fu">as_tibble</span>() <span class="sc">%&gt;%</span> </span>
-<span id="cb972-102"><a href="#cb972-102" aria-hidden="true" tabindex="-1"></a>  <span class="fu">rename_all</span>(toupper) <span class="sc">%&gt;%</span></span>
-<span id="cb972-103"><a href="#cb972-103" aria-hidden="true" tabindex="-1"></a>  <span class="fu">select</span>(ID, TIME, <span class="fu">everything</span>()) </span>
-<span id="cb972-104"><a href="#cb972-104" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-105"><a href="#cb972-105" aria-hidden="true" tabindex="-1"></a>times_to_simulate <span class="ot">&lt;-</span> <span class="fu">c</span>(<span class="fl">0.25</span>, <span class="fu">seq</span>(<span class="fl">0.5</span>, <span class="dv">24</span><span class="sc">*</span><span class="dv">7</span>, <span class="at">by =</span> <span class="fl">0.5</span>))</span>
-<span id="cb972-106"><a href="#cb972-106" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-107"><a href="#cb972-107" aria-hidden="true" tabindex="-1"></a>nonmem_data_simulate <span class="ot">&lt;-</span> dosing_data <span class="sc">%&gt;%</span> </span>
-<span id="cb972-108"><a href="#cb972-108" aria-hidden="true" tabindex="-1"></a>  <span class="fu">group_by</span>(ID) <span class="sc">%&gt;%</span> </span>
-<span id="cb972-109"><a href="#cb972-109" aria-hidden="true" tabindex="-1"></a>  <span class="fu">slice</span>(<span class="fu">rep</span>(<span class="dv">1</span>, <span class="at">times =</span> <span class="fu">length</span>(times_to_simulate))) <span class="sc">%&gt;%</span> </span>
-<span id="cb972-110"><a href="#cb972-110" aria-hidden="true" tabindex="-1"></a>  <span class="fu">mutate</span>(<span class="at">AMT =</span> <span class="dv">0</span>,</span>
-<span id="cb972-111"><a href="#cb972-111" aria-hidden="true" tabindex="-1"></a>         <span class="at">ADDL =</span> <span class="dv">0</span>,</span>
-<span id="cb972-112"><a href="#cb972-112" aria-hidden="true" tabindex="-1"></a>         <span class="at">II =</span> <span class="dv">0</span>,</span>
-<span id="cb972-113"><a href="#cb972-113" aria-hidden="true" tabindex="-1"></a>         <span class="at">CMT =</span> <span class="dv">2</span>,</span>
-<span id="cb972-114"><a href="#cb972-114" aria-hidden="true" tabindex="-1"></a>         <span class="at">EVID =</span> <span class="dv">0</span>,</span>
-<span id="cb972-115"><a href="#cb972-115" aria-hidden="true" tabindex="-1"></a>         <span class="at">TIME =</span> times_to_simulate) <span class="sc">%&gt;%</span> </span>
-<span id="cb972-116"><a href="#cb972-116" aria-hidden="true" tabindex="-1"></a>  <span class="fu">ungroup</span>() <span class="sc">%&gt;%</span></span>
-<span id="cb972-117"><a href="#cb972-117" aria-hidden="true" tabindex="-1"></a>  <span class="fu">bind_rows</span>(dosing_data) <span class="sc">%&gt;%</span> </span>
-<span id="cb972-118"><a href="#cb972-118" aria-hidden="true" tabindex="-1"></a>  <span class="fu">arrange</span>(ID, TIME, AMT)</span>
-<span id="cb972-119"><a href="#cb972-119" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-120"><a href="#cb972-120" aria-hidden="true" tabindex="-1"></a>n_subjects <span class="ot">&lt;-</span> nonmem_data_simulate <span class="sc">%&gt;%</span>  <span class="co"># number of individuals to simulate</span></span>
-<span id="cb972-121"><a href="#cb972-121" aria-hidden="true" tabindex="-1"></a>  <span class="fu">distinct</span>(ID) <span class="sc">%&gt;%</span> </span>
-<span id="cb972-122"><a href="#cb972-122" aria-hidden="true" tabindex="-1"></a>  <span class="fu">count</span>() <span class="sc">%&gt;%</span> </span>
-<span id="cb972-123"><a href="#cb972-123" aria-hidden="true" tabindex="-1"></a>  <span class="fu">deframe</span>()</span>
-<span id="cb972-124"><a href="#cb972-124" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-125"><a href="#cb972-125" aria-hidden="true" tabindex="-1"></a>n_total <span class="ot">&lt;-</span> <span class="fu">nrow</span>(nonmem_data_simulate) <span class="co"># total number of time points at which to predict</span></span>
-<span id="cb972-126"><a href="#cb972-126" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-127"><a href="#cb972-127" aria-hidden="true" tabindex="-1"></a>subj_start <span class="ot">&lt;-</span> nonmem_data_simulate <span class="sc">%&gt;%</span> </span>
-<span id="cb972-128"><a href="#cb972-128" aria-hidden="true" tabindex="-1"></a>  <span class="fu">mutate</span>(<span class="at">row_num =</span> <span class="dv">1</span><span class="sc">:</span><span class="fu">n</span>()) <span class="sc">%&gt;%</span> </span>
-<span id="cb972-129"><a href="#cb972-129" aria-hidden="true" tabindex="-1"></a>  <span class="fu">group_by</span>(ID) <span class="sc">%&gt;%</span> </span>
-<span id="cb972-130"><a href="#cb972-130" aria-hidden="true" tabindex="-1"></a>  <span class="fu">slice_head</span>(<span class="at">n =</span> <span class="dv">1</span>) <span class="sc">%&gt;%</span></span>
-<span id="cb972-131"><a href="#cb972-131" aria-hidden="true" tabindex="-1"></a>  <span class="fu">ungroup</span>() <span class="sc">%&gt;%</span> </span>
-<span id="cb972-132"><a href="#cb972-132" aria-hidden="true" tabindex="-1"></a>  <span class="fu">select</span>(row_num) <span class="sc">%&gt;%</span> </span>
-<span id="cb972-133"><a href="#cb972-133" aria-hidden="true" tabindex="-1"></a>  <span class="fu">deframe</span>()</span>
-<span id="cb972-134"><a href="#cb972-134" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-135"><a href="#cb972-135" aria-hidden="true" tabindex="-1"></a>subj_end <span class="ot">&lt;-</span> <span class="fu">c</span>(subj_start[<span class="sc">-</span><span class="dv">1</span>] <span class="sc">-</span> <span class="dv">1</span>, n_total) </span>
-<span id="cb972-136"><a href="#cb972-136" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-137"><a href="#cb972-137" aria-hidden="true" tabindex="-1"></a>stan_data <span class="ot">&lt;-</span> <span class="fu">list</span>(<span class="at">n_subjects =</span> n_subjects,</span>
-<span id="cb972-138"><a href="#cb972-138" aria-hidden="true" tabindex="-1"></a>                  <span class="at">n_total =</span> n_total,</span>
-<span id="cb972-139"><a href="#cb972-139" aria-hidden="true" tabindex="-1"></a>                  <span class="at">time =</span> nonmem_data_simulate<span class="sc">$</span>TIME,</span>
-<span id="cb972-140"><a href="#cb972-140" aria-hidden="true" tabindex="-1"></a>                  <span class="at">amt =</span> nonmem_data_simulate<span class="sc">$</span>AMT,</span>
-<span id="cb972-141"><a href="#cb972-141" aria-hidden="true" tabindex="-1"></a>                  <span class="at">cmt =</span> nonmem_data_simulate<span class="sc">$</span>CMT,</span>
-<span id="cb972-142"><a href="#cb972-142" aria-hidden="true" tabindex="-1"></a>                  <span class="at">evid =</span> nonmem_data_simulate<span class="sc">$</span>EVID,</span>
-<span id="cb972-143"><a href="#cb972-143" aria-hidden="true" tabindex="-1"></a>                  <span class="at">rate =</span> nonmem_data_simulate<span class="sc">$</span>RATE,</span>
-<span id="cb972-144"><a href="#cb972-144" aria-hidden="true" tabindex="-1"></a>                  <span class="at">ii =</span> nonmem_data_simulate<span class="sc">$</span>II,</span>
-<span id="cb972-145"><a href="#cb972-145" aria-hidden="true" tabindex="-1"></a>                  <span class="at">addl =</span> nonmem_data_simulate<span class="sc">$</span>ADDL,</span>
-<span id="cb972-146"><a href="#cb972-146" aria-hidden="true" tabindex="-1"></a>                  <span class="at">ss =</span> nonmem_data_simulate<span class="sc">$</span>SS,</span>
-<span id="cb972-147"><a href="#cb972-147" aria-hidden="true" tabindex="-1"></a>                  <span class="at">subj_start =</span> subj_start,</span>
-<span id="cb972-148"><a href="#cb972-148" aria-hidden="true" tabindex="-1"></a>                  <span class="at">subj_end =</span> subj_end,</span>
-<span id="cb972-149"><a href="#cb972-149" aria-hidden="true" tabindex="-1"></a>                  <span class="at">TVCL =</span> TVCL,</span>
-<span id="cb972-150"><a href="#cb972-150" aria-hidden="true" tabindex="-1"></a>                  <span class="at">TVVC =</span> TVVC,</span>
-<span id="cb972-151"><a href="#cb972-151" aria-hidden="true" tabindex="-1"></a>                  <span class="at">TVKA =</span> TVKA,</span>
-<span id="cb972-152"><a href="#cb972-152" aria-hidden="true" tabindex="-1"></a>                  <span class="at">omega_cl =</span> omega_cl,</span>
-<span id="cb972-153"><a href="#cb972-153" aria-hidden="true" tabindex="-1"></a>                  <span class="at">omega_vc =</span> omega_vc,</span>
-<span id="cb972-154"><a href="#cb972-154" aria-hidden="true" tabindex="-1"></a>                  <span class="at">omega_ka =</span> omega_ka,</span>
-<span id="cb972-155"><a href="#cb972-155" aria-hidden="true" tabindex="-1"></a>                  <span class="at">R =</span> R,</span>
-<span id="cb972-156"><a href="#cb972-156" aria-hidden="true" tabindex="-1"></a>                  <span class="at">sigma =</span> sigma,</span>
-<span id="cb972-157"><a href="#cb972-157" aria-hidden="true" tabindex="-1"></a>                  <span class="at">solver =</span> <span class="dv">1</span>) <span class="co"># analytical = 1, mat exp = 2, rk45 = 3</span></span>
-<span id="cb972-158"><a href="#cb972-158" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-159"><a href="#cb972-159" aria-hidden="true" tabindex="-1"></a>model <span class="ot">&lt;-</span> <span class="fu">cmdstan_model</span>(</span>
-<span id="cb972-160"><a href="#cb972-160" aria-hidden="true" tabindex="-1"></a>  here<span class="sc">::</span><span class="fu">here</span>(<span class="st">&quot;M3/depot_1cmt_linear/Stan/Simulate/depot_1cmt_exp.stan&quot;</span>))</span>
-<span id="cb972-161"><a href="#cb972-161" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-162"><a href="#cb972-162" aria-hidden="true" tabindex="-1"></a>model<span class="sc">$</span><span class="fu">print</span>()</span>
-<span id="cb972-163"><a href="#cb972-163" aria-hidden="true" tabindex="-1"></a><span class="in">```</span></span>
-<span id="cb972-164"><a href="#cb972-164" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-165"><a href="#cb972-165" aria-hidden="true" tabindex="-1"></a>:::</span>
-<span id="cb972-166"><a href="#cb972-166" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-169"><a href="#cb972-169" aria-hidden="true" tabindex="-1"></a><span class="in">```{r}</span></span>
-<span id="cb972-170"><a href="#cb972-170" aria-hidden="true" tabindex="-1"></a><span class="co">#| cache: true</span></span>
-<span id="cb972-171"><a href="#cb972-171" aria-hidden="true" tabindex="-1"></a><span class="co">#| output: false</span></span>
-<span id="cb972-172"><a href="#cb972-172" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-173"><a href="#cb972-173" aria-hidden="true" tabindex="-1"></a>simulated_data <span class="ot">&lt;-</span> model<span class="sc">$</span><span class="fu">sample</span>(<span class="at">data =</span> stan_data,</span>
-<span id="cb972-174"><a href="#cb972-174" aria-hidden="true" tabindex="-1"></a>                               <span class="at">fixed_param =</span> <span class="cn">TRUE</span>,</span>
-<span id="cb972-175"><a href="#cb972-175" aria-hidden="true" tabindex="-1"></a>                               <span class="at">seed =</span> <span class="dv">1123</span>,</span>
-<span id="cb972-176"><a href="#cb972-176" aria-hidden="true" tabindex="-1"></a>                               <span class="at">iter_warmup =</span> <span class="dv">0</span>,</span>
-<span id="cb972-177"><a href="#cb972-177" aria-hidden="true" tabindex="-1"></a>                               <span class="at">iter_sampling =</span> <span class="dv">1</span>,</span>
-<span id="cb972-178"><a href="#cb972-178" aria-hidden="true" tabindex="-1"></a>                               <span class="at">chains =</span> <span class="dv">1</span>,</span>
-<span id="cb972-179"><a href="#cb972-179" aria-hidden="true" tabindex="-1"></a>                               <span class="at">parallel_chains =</span> <span class="dv">1</span>)</span>
-<span id="cb972-180"><a href="#cb972-180" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-181"><a href="#cb972-181" aria-hidden="true" tabindex="-1"></a>data_analytical <span class="ot">&lt;-</span> simulated_data<span class="sc">$</span><span class="fu">draws</span>(<span class="fu">c</span>(<span class="st">&quot;dv&quot;</span>, <span class="st">&quot;ipred&quot;</span>)) <span class="sc">%&gt;%</span> </span>
-<span id="cb972-182"><a href="#cb972-182" aria-hidden="true" tabindex="-1"></a>  <span class="fu">spread_draws</span>(dv[i], ipred[i]) <span class="sc">%&gt;%</span> </span>
-<span id="cb972-183"><a href="#cb972-183" aria-hidden="true" tabindex="-1"></a>  <span class="fu">ungroup</span>() <span class="sc">%&gt;%</span> </span>
-<span id="cb972-184"><a href="#cb972-184" aria-hidden="true" tabindex="-1"></a>  <span class="fu">inner_join</span>(nonmem_data_simulate <span class="sc">%&gt;%</span> </span>
-<span id="cb972-185"><a href="#cb972-185" aria-hidden="true" tabindex="-1"></a>               <span class="fu">mutate</span>(<span class="at">i =</span> <span class="dv">1</span><span class="sc">:</span><span class="fu">n</span>()),</span>
-<span id="cb972-186"><a href="#cb972-186" aria-hidden="true" tabindex="-1"></a>             <span class="at">by =</span> <span class="st">&quot;i&quot;</span>) <span class="sc">%&gt;%</span></span>
-<span id="cb972-187"><a href="#cb972-187" aria-hidden="true" tabindex="-1"></a>  <span class="fu">select</span>(ID, AMT, II, ADDL, RATE, CMT, EVID, SS, TIME, </span>
-<span id="cb972-188"><a href="#cb972-188" aria-hidden="true" tabindex="-1"></a>         <span class="at">DV =</span> <span class="st">&quot;dv&quot;</span>, <span class="at">IPRED =</span> <span class="st">&quot;ipred&quot;</span>) <span class="sc">%&gt;%</span> </span>
-<span id="cb972-189"><a href="#cb972-189" aria-hidden="true" tabindex="-1"></a>  <span class="fu">mutate</span>(<span class="at">LLOQ =</span> <span class="fl">1e-6</span>, </span>
-<span id="cb972-190"><a href="#cb972-190" aria-hidden="true" tabindex="-1"></a>         <span class="at">BLOQ =</span> <span class="fu">case_when</span>(EVID <span class="sc">==</span> <span class="dv">1</span> <span class="sc">~</span> <span class="cn">NA_real_</span>,</span>
-<span id="cb972-191"><a href="#cb972-191" aria-hidden="true" tabindex="-1"></a>                          DV <span class="sc">&lt;=</span> LLOQ <span class="sc">~</span> <span class="dv">1</span>,</span>
-<span id="cb972-192"><a href="#cb972-192" aria-hidden="true" tabindex="-1"></a>                          DV <span class="sc">&gt;</span> LLOQ <span class="sc">~</span> <span class="dv">0</span>,</span>
-<span id="cb972-193"><a href="#cb972-193" aria-hidden="true" tabindex="-1"></a>                          <span class="cn">TRUE</span> <span class="sc">~</span> <span class="cn">NA_real_</span>),</span>
-<span id="cb972-194"><a href="#cb972-194" aria-hidden="true" tabindex="-1"></a>         <span class="at">DV =</span> <span class="fu">if_else</span>(EVID <span class="sc">==</span> <span class="dv">1</span> <span class="sc">|</span> BLOQ <span class="sc">==</span> <span class="dv">1</span>, <span class="cn">NA_real_</span>, DV),</span>
-<span id="cb972-195"><a href="#cb972-195" aria-hidden="true" tabindex="-1"></a>         <span class="at">MDV =</span> <span class="fu">if_else</span>(<span class="fu">is.na</span>(DV), <span class="dv">1</span>, <span class="dv">0</span>)) <span class="sc">%&gt;%</span> </span>
-<span id="cb972-196"><a href="#cb972-196" aria-hidden="true" tabindex="-1"></a>  <span class="fu">relocate</span>(DV, <span class="at">.after =</span> <span class="fu">last_col</span>()) <span class="sc">%&gt;%</span> </span>
-<span id="cb972-197"><a href="#cb972-197" aria-hidden="true" tabindex="-1"></a>  <span class="fu">relocate</span>(TIME, <span class="at">.before =</span> DV) <span class="sc">%&gt;%</span> </span>
-<span id="cb972-198"><a href="#cb972-198" aria-hidden="true" tabindex="-1"></a>  <span class="fu">mutate</span>(<span class="at">solver =</span> <span class="st">&quot;analytical&quot;</span>)</span>
-<span id="cb972-199"><a href="#cb972-199" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-200"><a href="#cb972-200" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-201"><a href="#cb972-201" aria-hidden="true" tabindex="-1"></a>stan_data<span class="sc">$</span>solver <span class="ot">&lt;-</span> <span class="dv">2</span></span>
-<span id="cb972-202"><a href="#cb972-202" aria-hidden="true" tabindex="-1"></a>simulated_data <span class="ot">&lt;-</span> model<span class="sc">$</span><span class="fu">sample</span>(<span class="at">data =</span> stan_data,</span>
-<span id="cb972-203"><a href="#cb972-203" aria-hidden="true" tabindex="-1"></a>                               <span class="at">fixed_param =</span> <span class="cn">TRUE</span>,</span>
-<span id="cb972-204"><a href="#cb972-204" aria-hidden="true" tabindex="-1"></a>                               <span class="at">seed =</span> <span class="dv">1123</span>,</span>
-<span id="cb972-205"><a href="#cb972-205" aria-hidden="true" tabindex="-1"></a>                               <span class="at">iter_warmup =</span> <span class="dv">0</span>,</span>
-<span id="cb972-206"><a href="#cb972-206" aria-hidden="true" tabindex="-1"></a>                               <span class="at">iter_sampling =</span> <span class="dv">1</span>,</span>
-<span id="cb972-207"><a href="#cb972-207" aria-hidden="true" tabindex="-1"></a>                               <span class="at">chains =</span> <span class="dv">1</span>,</span>
-<span id="cb972-208"><a href="#cb972-208" aria-hidden="true" tabindex="-1"></a>                               <span class="at">parallel_chains =</span> <span class="dv">1</span>)</span>
-<span id="cb972-209"><a href="#cb972-209" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-210"><a href="#cb972-210" aria-hidden="true" tabindex="-1"></a>data_mat_exp <span class="ot">&lt;-</span> simulated_data<span class="sc">$</span><span class="fu">draws</span>(<span class="fu">c</span>(<span class="st">&quot;dv&quot;</span>, <span class="st">&quot;ipred&quot;</span>)) <span class="sc">%&gt;%</span> </span>
-<span id="cb972-211"><a href="#cb972-211" aria-hidden="true" tabindex="-1"></a>  <span class="fu">spread_draws</span>(dv[i], ipred[i]) <span class="sc">%&gt;%</span> </span>
-<span id="cb972-212"><a href="#cb972-212" aria-hidden="true" tabindex="-1"></a>  <span class="fu">ungroup</span>() <span class="sc">%&gt;%</span> </span>
-<span id="cb972-213"><a href="#cb972-213" aria-hidden="true" tabindex="-1"></a>  <span class="fu">inner_join</span>(nonmem_data_simulate <span class="sc">%&gt;%</span> </span>
-<span id="cb972-214"><a href="#cb972-214" aria-hidden="true" tabindex="-1"></a>               <span class="fu">mutate</span>(<span class="at">i =</span> <span class="dv">1</span><span class="sc">:</span><span class="fu">n</span>()),</span>
-<span id="cb972-215"><a href="#cb972-215" aria-hidden="true" tabindex="-1"></a>             <span class="at">by =</span> <span class="st">&quot;i&quot;</span>) <span class="sc">%&gt;%</span></span>
-<span id="cb972-216"><a href="#cb972-216" aria-hidden="true" tabindex="-1"></a>  <span class="fu">select</span>(ID, AMT, II, ADDL, RATE, CMT, EVID, SS, TIME, </span>
-<span id="cb972-217"><a href="#cb972-217" aria-hidden="true" tabindex="-1"></a>         <span class="at">DV =</span> <span class="st">&quot;dv&quot;</span>, <span class="at">IPRED =</span> <span class="st">&quot;ipred&quot;</span>) <span class="sc">%&gt;%</span> </span>
-<span id="cb972-218"><a href="#cb972-218" aria-hidden="true" tabindex="-1"></a>  <span class="fu">mutate</span>(<span class="at">LLOQ =</span> <span class="fl">1e-6</span>, </span>
-<span id="cb972-219"><a href="#cb972-219" aria-hidden="true" tabindex="-1"></a>         <span class="at">BLOQ =</span> <span class="fu">case_when</span>(EVID <span class="sc">==</span> <span class="dv">1</span> <span class="sc">~</span> <span class="cn">NA_real_</span>,</span>
-<span id="cb972-220"><a href="#cb972-220" aria-hidden="true" tabindex="-1"></a>                          DV <span class="sc">&lt;=</span> LLOQ <span class="sc">~</span> <span class="dv">1</span>,</span>
-<span id="cb972-221"><a href="#cb972-221" aria-hidden="true" tabindex="-1"></a>                          DV <span class="sc">&gt;</span> LLOQ <span class="sc">~</span> <span class="dv">0</span>,</span>
-<span id="cb972-222"><a href="#cb972-222" aria-hidden="true" tabindex="-1"></a>                          <span class="cn">TRUE</span> <span class="sc">~</span> <span class="cn">NA_real_</span>),</span>
-<span id="cb972-223"><a href="#cb972-223" aria-hidden="true" tabindex="-1"></a>         <span class="at">DV =</span> <span class="fu">if_else</span>(EVID <span class="sc">==</span> <span class="dv">1</span> <span class="sc">|</span> BLOQ <span class="sc">==</span> <span class="dv">1</span>, <span class="cn">NA_real_</span>, DV),</span>
-<span id="cb972-224"><a href="#cb972-224" aria-hidden="true" tabindex="-1"></a>         <span class="at">MDV =</span> <span class="fu">if_else</span>(<span class="fu">is.na</span>(DV), <span class="dv">1</span>, <span class="dv">0</span>)) <span class="sc">%&gt;%</span> </span>
-<span id="cb972-225"><a href="#cb972-225" aria-hidden="true" tabindex="-1"></a>  <span class="fu">relocate</span>(DV, <span class="at">.after =</span> <span class="fu">last_col</span>()) <span class="sc">%&gt;%</span> </span>
-<span id="cb972-226"><a href="#cb972-226" aria-hidden="true" tabindex="-1"></a>  <span class="fu">relocate</span>(TIME, <span class="at">.before =</span> DV) <span class="sc">%&gt;%</span> </span>
-<span id="cb972-227"><a href="#cb972-227" aria-hidden="true" tabindex="-1"></a>  <span class="fu">mutate</span>(<span class="at">solver =</span> <span class="st">&quot;mat_exp&quot;</span>)</span>
-<span id="cb972-228"><a href="#cb972-228" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-229"><a href="#cb972-229" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-230"><a href="#cb972-230" aria-hidden="true" tabindex="-1"></a>stan_data<span class="sc">$</span>solver <span class="ot">&lt;-</span> <span class="dv">3</span></span>
-<span id="cb972-231"><a href="#cb972-231" aria-hidden="true" tabindex="-1"></a>simulated_data <span class="ot">&lt;-</span> model<span class="sc">$</span><span class="fu">sample</span>(<span class="at">data =</span> stan_data,</span>
-<span id="cb972-232"><a href="#cb972-232" aria-hidden="true" tabindex="-1"></a>                               <span class="at">fixed_param =</span> <span class="cn">TRUE</span>,</span>
-<span id="cb972-233"><a href="#cb972-233" aria-hidden="true" tabindex="-1"></a>                               <span class="at">seed =</span> <span class="dv">1123</span>,</span>
-<span id="cb972-234"><a href="#cb972-234" aria-hidden="true" tabindex="-1"></a>                               <span class="at">iter_warmup =</span> <span class="dv">0</span>,</span>
-<span id="cb972-235"><a href="#cb972-235" aria-hidden="true" tabindex="-1"></a>                               <span class="at">iter_sampling =</span> <span class="dv">1</span>,</span>
-<span id="cb972-236"><a href="#cb972-236" aria-hidden="true" tabindex="-1"></a>                               <span class="at">chains =</span> <span class="dv">1</span>,</span>
-<span id="cb972-237"><a href="#cb972-237" aria-hidden="true" tabindex="-1"></a>                               <span class="at">parallel_chains =</span> <span class="dv">1</span>)</span>
-<span id="cb972-238"><a href="#cb972-238" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-239"><a href="#cb972-239" aria-hidden="true" tabindex="-1"></a>data_rk45 <span class="ot">&lt;-</span> simulated_data<span class="sc">$</span><span class="fu">draws</span>(<span class="fu">c</span>(<span class="st">&quot;dv&quot;</span>, <span class="st">&quot;ipred&quot;</span>)) <span class="sc">%&gt;%</span> </span>
-<span id="cb972-240"><a href="#cb972-240" aria-hidden="true" tabindex="-1"></a>  <span class="fu">spread_draws</span>(dv[i], ipred[i]) <span class="sc">%&gt;%</span> </span>
-<span id="cb972-241"><a href="#cb972-241" aria-hidden="true" tabindex="-1"></a>  <span class="fu">ungroup</span>() <span class="sc">%&gt;%</span> </span>
-<span id="cb972-242"><a href="#cb972-242" aria-hidden="true" tabindex="-1"></a>  <span class="fu">inner_join</span>(nonmem_data_simulate <span class="sc">%&gt;%</span> </span>
-<span id="cb972-243"><a href="#cb972-243" aria-hidden="true" tabindex="-1"></a>               <span class="fu">mutate</span>(<span class="at">i =</span> <span class="dv">1</span><span class="sc">:</span><span class="fu">n</span>()),</span>
-<span id="cb972-244"><a href="#cb972-244" aria-hidden="true" tabindex="-1"></a>             <span class="at">by =</span> <span class="st">&quot;i&quot;</span>) <span class="sc">%&gt;%</span></span>
-<span id="cb972-245"><a href="#cb972-245" aria-hidden="true" tabindex="-1"></a>  <span class="fu">select</span>(ID, AMT, II, ADDL, RATE, CMT, EVID, SS, TIME, </span>
-<span id="cb972-246"><a href="#cb972-246" aria-hidden="true" tabindex="-1"></a>         <span class="at">DV =</span> <span class="st">&quot;dv&quot;</span>, <span class="at">IPRED =</span> <span class="st">&quot;ipred&quot;</span>) <span class="sc">%&gt;%</span> </span>
-<span id="cb972-247"><a href="#cb972-247" aria-hidden="true" tabindex="-1"></a>  <span class="fu">mutate</span>(<span class="at">LLOQ =</span> <span class="fl">1e-6</span>, </span>
-<span id="cb972-248"><a href="#cb972-248" aria-hidden="true" tabindex="-1"></a>         <span class="at">BLOQ =</span> <span class="fu">case_when</span>(EVID <span class="sc">==</span> <span class="dv">1</span> <span class="sc">~</span> <span class="cn">NA_real_</span>,</span>
-<span id="cb972-249"><a href="#cb972-249" aria-hidden="true" tabindex="-1"></a>                          DV <span class="sc">&lt;=</span> LLOQ <span class="sc">~</span> <span class="dv">1</span>,</span>
-<span id="cb972-250"><a href="#cb972-250" aria-hidden="true" tabindex="-1"></a>                          DV <span class="sc">&gt;</span> LLOQ <span class="sc">~</span> <span class="dv">0</span>,</span>
-<span id="cb972-251"><a href="#cb972-251" aria-hidden="true" tabindex="-1"></a>                          <span class="cn">TRUE</span> <span class="sc">~</span> <span class="cn">NA_real_</span>),</span>
-<span id="cb972-252"><a href="#cb972-252" aria-hidden="true" tabindex="-1"></a>         <span class="at">DV =</span> <span class="fu">if_else</span>(EVID <span class="sc">==</span> <span class="dv">1</span> <span class="sc">|</span> BLOQ <span class="sc">==</span> <span class="dv">1</span>, <span class="cn">NA_real_</span>, DV),</span>
-<span id="cb972-253"><a href="#cb972-253" aria-hidden="true" tabindex="-1"></a>         <span class="at">MDV =</span> <span class="fu">if_else</span>(<span class="fu">is.na</span>(DV), <span class="dv">1</span>, <span class="dv">0</span>)) <span class="sc">%&gt;%</span> </span>
-<span id="cb972-254"><a href="#cb972-254" aria-hidden="true" tabindex="-1"></a>  <span class="fu">relocate</span>(DV, <span class="at">.after =</span> <span class="fu">last_col</span>()) <span class="sc">%&gt;%</span> </span>
-<span id="cb972-255"><a href="#cb972-255" aria-hidden="true" tabindex="-1"></a>  <span class="fu">relocate</span>(TIME, <span class="at">.before =</span> DV) <span class="sc">%&gt;%</span> </span>
-<span id="cb972-256"><a href="#cb972-256" aria-hidden="true" tabindex="-1"></a>  <span class="fu">mutate</span>(<span class="at">solver =</span> <span class="st">&quot;rk45&quot;</span>)</span>
-<span id="cb972-257"><a href="#cb972-257" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-258"><a href="#cb972-258" aria-hidden="true" tabindex="-1"></a><span class="do">## Now do it with mrgsolve to check</span></span>
-<span id="cb972-259"><a href="#cb972-259" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-260"><a href="#cb972-260" aria-hidden="true" tabindex="-1"></a>mod <span class="ot">&lt;-</span> <span class="fu">mread</span>(here<span class="sc">::</span><span class="fu">here</span>(<span class="st">&quot;M3/depot_1cmt_linear/mrgsolve/depot_1cmt_exp.cpp&quot;</span>))</span>
-<span id="cb972-261"><a href="#cb972-261" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-262"><a href="#cb972-262" aria-hidden="true" tabindex="-1"></a>data_mrgsolve <span class="ot">&lt;-</span> mod <span class="sc">%&gt;%</span> </span>
-<span id="cb972-263"><a href="#cb972-263" aria-hidden="true" tabindex="-1"></a>  <span class="fu">param</span>(<span class="fu">tibble</span>(<span class="at">CL =</span> TVCL,</span>
-<span id="cb972-264"><a href="#cb972-264" aria-hidden="true" tabindex="-1"></a>               <span class="at">VC =</span> TVVC,</span>
-<span id="cb972-265"><a href="#cb972-265" aria-hidden="true" tabindex="-1"></a>               <span class="at">KA =</span> TVKA,</span>
-<span id="cb972-266"><a href="#cb972-266" aria-hidden="true" tabindex="-1"></a>               <span class="at">F1 =</span> <span class="dv">1</span>,</span>
-<span id="cb972-267"><a href="#cb972-267" aria-hidden="true" tabindex="-1"></a>               <span class="at">LAGTIME =</span> <span class="dv">0</span>)) <span class="sc">%&gt;%</span> </span>
-<span id="cb972-268"><a href="#cb972-268" aria-hidden="true" tabindex="-1"></a>  <span class="fu">data_set</span>(dosing_data) <span class="sc">%&gt;%</span> </span>
-<span id="cb972-269"><a href="#cb972-269" aria-hidden="true" tabindex="-1"></a>  <span class="fu">mrgsim_df</span>(<span class="at">tgrid =</span> times_to_simulate) <span class="sc">%&gt;%</span> </span>
-<span id="cb972-270"><a href="#cb972-270" aria-hidden="true" tabindex="-1"></a>  <span class="fu">as_tibble</span>() <span class="sc">%&gt;%</span> </span>
-<span id="cb972-271"><a href="#cb972-271" aria-hidden="true" tabindex="-1"></a>  <span class="fu">mutate</span>(<span class="at">solver =</span> <span class="st">&quot;mrgsolve&quot;</span>)</span>
-<span id="cb972-272"><a href="#cb972-272" aria-hidden="true" tabindex="-1"></a><span class="in">```</span></span>
-<span id="cb972-273"><a href="#cb972-273" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-274"><a href="#cb972-274" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-277"><a href="#cb972-277" aria-hidden="true" tabindex="-1"></a><span class="in">```{r}</span></span>
-<span id="cb972-278"><a href="#cb972-278" aria-hidden="true" tabindex="-1"></a><span class="co">#| fig-align: center</span></span>
-<span id="cb972-279"><a href="#cb972-279" aria-hidden="true" tabindex="-1"></a><span class="co">#| </span></span>
-<span id="cb972-280"><a href="#cb972-280" aria-hidden="true" tabindex="-1"></a><span class="fu">mget</span>(<span class="fu">str_subset</span>(<span class="fu">ls</span>(), <span class="st">&quot;^data_&quot;</span>)) <span class="sc">%&gt;%</span></span>
-<span id="cb972-281"><a href="#cb972-281" aria-hidden="true" tabindex="-1"></a>  <span class="fu">bind_rows</span>() <span class="sc">%&gt;%</span> </span>
-<span id="cb972-282"><a href="#cb972-282" aria-hidden="true" tabindex="-1"></a>  <span class="fu">ggplot</span>(<span class="fu">aes</span>(<span class="at">x =</span> TIME, <span class="at">y =</span> IPRED, <span class="at">color =</span> solver)) <span class="sc">+</span></span>
-<span id="cb972-283"><a href="#cb972-283" aria-hidden="true" tabindex="-1"></a>  <span class="fu">geom_line</span>(<span class="fu">aes</span>(<span class="at">linetype =</span> solver)) <span class="sc">+</span></span>
-<span id="cb972-284"><a href="#cb972-284" aria-hidden="true" tabindex="-1"></a>  <span class="fu">theme_bw</span>() <span class="sc">+</span></span>
-<span id="cb972-285"><a href="#cb972-285" aria-hidden="true" tabindex="-1"></a>  <span class="fu">scale_x_continuous</span>(<span class="at">name =</span> <span class="st">&quot;Time (h)&quot;</span>,</span>
-<span id="cb972-286"><a href="#cb972-286" aria-hidden="true" tabindex="-1"></a>                     <span class="at">breaks =</span> <span class="fu">seq</span>(<span class="dv">0</span>, <span class="dv">168</span>, <span class="at">by =</span> <span class="dv">24</span>),</span>
-<span id="cb972-287"><a href="#cb972-287" aria-hidden="true" tabindex="-1"></a>                     <span class="at">labels =</span> <span class="fu">seq</span>(<span class="dv">0</span>, <span class="dv">168</span>, <span class="at">by =</span> <span class="dv">24</span>)) <span class="sc">+</span></span>
-<span id="cb972-288"><a href="#cb972-288" aria-hidden="true" tabindex="-1"></a>  <span class="fu">scale_y_continuous</span>(<span class="at">name =</span> <span class="st">&quot;Drug Conc. (ug/mL)&quot;</span>)</span>
-<span id="cb972-289"><a href="#cb972-289" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-290"><a href="#cb972-290" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-291"><a href="#cb972-291" aria-hidden="true" tabindex="-1"></a><span class="in">```</span></span>
-<span id="cb972-292"><a href="#cb972-292" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-293"><a href="#cb972-293" aria-hidden="true" tabindex="-1"></a>So you can see that the analytical solution spits out a vector of 0s, while the</span>
-<span id="cb972-294"><a href="#cb972-294" aria-hidden="true" tabindex="-1"></a>linear ODE, general ODE, and mrgsolve simulations are all the same.</span>
-<span id="cb972-295"><a href="#cb972-295" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-296"><a href="#cb972-296" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-297"><a href="#cb972-297" aria-hidden="true" tabindex="-1"></a><span class="fu">### Two-Compartment IV with Proportional Error</span></span>
-<span id="cb972-298"><a href="#cb972-298" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-299"><a href="#cb972-299" aria-hidden="true" tabindex="-1"></a>The following code simulates with Stan + Torsten with an analytical solution, </span>
-<span id="cb972-300"><a href="#cb972-300" aria-hidden="true" tabindex="-1"></a>linear ODE solution, and general ODE solution using code I&#39;ve written in the </span>
-<span id="cb972-301"><a href="#cb972-301" aria-hidden="true" tabindex="-1"></a>past, and then also a simulation with mrgsolve as a comparison.</span>
-<span id="cb972-302"><a href="#cb972-302" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-303"><a href="#cb972-303" aria-hidden="true" tabindex="-1"></a>:::{.scrolling_500}</span>
-<span id="cb972-304"><a href="#cb972-304" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-307"><a href="#cb972-307" aria-hidden="true" tabindex="-1"></a><span class="in">```{r}</span></span>
-<span id="cb972-308"><a href="#cb972-308" aria-hidden="true" tabindex="-1"></a><span class="co">#| cache: true</span></span>
-<span id="cb972-309"><a href="#cb972-309" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-310"><a href="#cb972-310" aria-hidden="true" tabindex="-1"></a>TVCL <span class="ot">&lt;-</span> <span class="fl">0.25</span>  <span class="co"># L/d</span></span>
-<span id="cb972-311"><a href="#cb972-311" aria-hidden="true" tabindex="-1"></a>TVVC <span class="ot">&lt;-</span> <span class="dv">3</span>     <span class="co"># L</span></span>
-<span id="cb972-312"><a href="#cb972-312" aria-hidden="true" tabindex="-1"></a>TVQ <span class="ot">&lt;-</span> <span class="dv">1</span>      <span class="co"># L/d</span></span>
-<span id="cb972-313"><a href="#cb972-313" aria-hidden="true" tabindex="-1"></a>TVVP <span class="ot">&lt;-</span> <span class="dv">4</span>     <span class="co"># L</span></span>
-<span id="cb972-314"><a href="#cb972-314" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-315"><a href="#cb972-315" aria-hidden="true" tabindex="-1"></a>omega_cl <span class="ot">&lt;-</span> <span class="dv">0</span></span>
-<span id="cb972-316"><a href="#cb972-316" aria-hidden="true" tabindex="-1"></a>omega_vc <span class="ot">&lt;-</span> <span class="dv">0</span></span>
-<span id="cb972-317"><a href="#cb972-317" aria-hidden="true" tabindex="-1"></a>omega_q <span class="ot">&lt;-</span> <span class="dv">0</span></span>
-<span id="cb972-318"><a href="#cb972-318" aria-hidden="true" tabindex="-1"></a>omega_vp <span class="ot">&lt;-</span> <span class="dv">0</span></span>
-<span id="cb972-319"><a href="#cb972-319" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-320"><a href="#cb972-320" aria-hidden="true" tabindex="-1"></a>R <span class="ot">&lt;-</span> <span class="fu">diag</span>(<span class="fu">rep</span>(<span class="dv">1</span>, <span class="at">times =</span> <span class="dv">4</span>))</span>
-<span id="cb972-321"><a href="#cb972-321" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-322"><a href="#cb972-322" aria-hidden="true" tabindex="-1"></a>sigma_p <span class="ot">&lt;-</span> <span class="fl">0.2</span></span>
-<span id="cb972-323"><a href="#cb972-323" aria-hidden="true" tabindex="-1"></a>sigma_a <span class="ot">&lt;-</span> <span class="fl">0.05</span></span>
-<span id="cb972-324"><a href="#cb972-324" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-325"><a href="#cb972-325" aria-hidden="true" tabindex="-1"></a>cor_p_a <span class="ot">&lt;-</span> <span class="dv">0</span></span>
-<span id="cb972-326"><a href="#cb972-326" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-327"><a href="#cb972-327" aria-hidden="true" tabindex="-1"></a>solver <span class="ot">&lt;-</span> <span class="dv">1</span> <span class="co"># analytical = 1, mat exp = 2, rk45 = 3</span></span>
-<span id="cb972-328"><a href="#cb972-328" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-329"><a href="#cb972-329" aria-hidden="true" tabindex="-1"></a><span class="co"># If using Torsten&#39;s analytical solver, dose into the second compartment </span></span>
-<span id="cb972-330"><a href="#cb972-330" aria-hidden="true" tabindex="-1"></a><span class="co"># (cmt = 2). If using matrix-exponential or ODE, then dose into the first</span></span>
-<span id="cb972-331"><a href="#cb972-331" aria-hidden="true" tabindex="-1"></a><span class="co"># compartment (cmt = 1)</span></span>
-<span id="cb972-332"><a href="#cb972-332" aria-hidden="true" tabindex="-1"></a>dosing_data <span class="ot">&lt;-</span> <span class="fu">expand.ev</span>(<span class="at">ID =</span> <span class="dv">1</span>, <span class="at">addl =</span> <span class="dv">5</span>, <span class="at">ii =</span> <span class="dv">14</span>, </span>
-<span id="cb972-333"><a href="#cb972-333" aria-hidden="true" tabindex="-1"></a>                         <span class="at">cmt =</span> <span class="dv">2</span>, <span class="at">amt =</span> <span class="dv">400</span>, <span class="at">ss =</span> <span class="dv">0</span>, </span>
-<span id="cb972-334"><a href="#cb972-334" aria-hidden="true" tabindex="-1"></a>                         <span class="at">tinf =</span> <span class="dv">1</span><span class="sc">/</span><span class="dv">24</span>, <span class="at">evid =</span> <span class="dv">1</span>) <span class="sc">%&gt;%</span></span>
-<span id="cb972-335"><a href="#cb972-335" aria-hidden="true" tabindex="-1"></a>  <span class="fu">as_tibble</span>() <span class="sc">%&gt;%</span> </span>
-<span id="cb972-336"><a href="#cb972-336" aria-hidden="true" tabindex="-1"></a>  <span class="fu">mutate</span>(<span class="at">cmt =</span> <span class="fu">if_else</span>(solver <span class="sc">==</span> <span class="dv">1</span>, <span class="dv">2</span>, <span class="dv">1</span>)) <span class="sc">%&gt;%</span> </span>
-<span id="cb972-337"><a href="#cb972-337" aria-hidden="true" tabindex="-1"></a>  <span class="fu">rename_all</span>(toupper) <span class="sc">%&gt;%</span></span>
-<span id="cb972-338"><a href="#cb972-338" aria-hidden="true" tabindex="-1"></a>  <span class="fu">select</span>(ID, TIME, <span class="fu">everything</span>()) </span>
-<span id="cb972-339"><a href="#cb972-339" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-340"><a href="#cb972-340" aria-hidden="true" tabindex="-1"></a>times_to_simulate <span class="ot">&lt;-</span> <span class="fu">seq</span>(<span class="dv">0</span>, <span class="dv">84</span><span class="sc">*</span><span class="dv">24</span>, <span class="at">by =</span> <span class="dv">1</span>)<span class="sc">/</span><span class="dv">24</span></span>
-<span id="cb972-341"><a href="#cb972-341" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-342"><a href="#cb972-342" aria-hidden="true" tabindex="-1"></a>nonmem_data_simulate <span class="ot">&lt;-</span> dosing_data <span class="sc">%&gt;%</span> </span>
-<span id="cb972-343"><a href="#cb972-343" aria-hidden="true" tabindex="-1"></a>  <span class="fu">group_by</span>(ID) <span class="sc">%&gt;%</span> </span>
-<span id="cb972-344"><a href="#cb972-344" aria-hidden="true" tabindex="-1"></a>  <span class="fu">slice</span>(<span class="fu">rep</span>(<span class="dv">1</span>, <span class="at">times =</span> <span class="fu">length</span>(times_to_simulate))) <span class="sc">%&gt;%</span> </span>
-<span id="cb972-345"><a href="#cb972-345" aria-hidden="true" tabindex="-1"></a>  <span class="fu">mutate</span>(<span class="at">AMT =</span> <span class="dv">0</span>,</span>
-<span id="cb972-346"><a href="#cb972-346" aria-hidden="true" tabindex="-1"></a>         <span class="at">ADDL =</span> <span class="dv">0</span>,</span>
-<span id="cb972-347"><a href="#cb972-347" aria-hidden="true" tabindex="-1"></a>         <span class="at">II =</span> <span class="dv">0</span>,</span>
-<span id="cb972-348"><a href="#cb972-348" aria-hidden="true" tabindex="-1"></a>         <span class="at">CMT =</span> <span class="fu">if_else</span>(solver <span class="sc">==</span> <span class="dv">1</span>, <span class="dv">2</span>, <span class="dv">1</span>),</span>
-<span id="cb972-349"><a href="#cb972-349" aria-hidden="true" tabindex="-1"></a>         <span class="at">EVID =</span> <span class="dv">0</span>,</span>
-<span id="cb972-350"><a href="#cb972-350" aria-hidden="true" tabindex="-1"></a>         <span class="at">RATE =</span> <span class="dv">0</span>,</span>
-<span id="cb972-351"><a href="#cb972-351" aria-hidden="true" tabindex="-1"></a>         <span class="at">TIME =</span> times_to_simulate) <span class="sc">%&gt;%</span> </span>
-<span id="cb972-352"><a href="#cb972-352" aria-hidden="true" tabindex="-1"></a>  <span class="fu">ungroup</span>() <span class="sc">%&gt;%</span></span>
-<span id="cb972-353"><a href="#cb972-353" aria-hidden="true" tabindex="-1"></a>  <span class="fu">bind_rows</span>(dosing_data) <span class="sc">%&gt;%</span> </span>
-<span id="cb972-354"><a href="#cb972-354" aria-hidden="true" tabindex="-1"></a>  <span class="fu">arrange</span>(ID, TIME, AMT)</span>
-<span id="cb972-355"><a href="#cb972-355" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-356"><a href="#cb972-356" aria-hidden="true" tabindex="-1"></a>n_subjects <span class="ot">&lt;-</span> nonmem_data_simulate <span class="sc">%&gt;%</span>  <span class="co"># number of individuals to simulate</span></span>
-<span id="cb972-357"><a href="#cb972-357" aria-hidden="true" tabindex="-1"></a>  <span class="fu">distinct</span>(ID) <span class="sc">%&gt;%</span> </span>
-<span id="cb972-358"><a href="#cb972-358" aria-hidden="true" tabindex="-1"></a>  <span class="fu">count</span>() <span class="sc">%&gt;%</span> </span>
-<span id="cb972-359"><a href="#cb972-359" aria-hidden="true" tabindex="-1"></a>  <span class="fu">deframe</span>()</span>
-<span id="cb972-360"><a href="#cb972-360" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-361"><a href="#cb972-361" aria-hidden="true" tabindex="-1"></a>n_total <span class="ot">&lt;-</span> <span class="fu">nrow</span>(nonmem_data_simulate) <span class="co"># total number of time points at which to predict</span></span>
-<span id="cb972-362"><a href="#cb972-362" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-363"><a href="#cb972-363" aria-hidden="true" tabindex="-1"></a>subj_start <span class="ot">&lt;-</span> nonmem_data_simulate <span class="sc">%&gt;%</span> </span>
-<span id="cb972-364"><a href="#cb972-364" aria-hidden="true" tabindex="-1"></a>  <span class="fu">mutate</span>(<span class="at">row_num =</span> <span class="dv">1</span><span class="sc">:</span><span class="fu">n</span>()) <span class="sc">%&gt;%</span> </span>
-<span id="cb972-365"><a href="#cb972-365" aria-hidden="true" tabindex="-1"></a>  <span class="fu">group_by</span>(ID) <span class="sc">%&gt;%</span> </span>
-<span id="cb972-366"><a href="#cb972-366" aria-hidden="true" tabindex="-1"></a>  <span class="fu">slice_head</span>(<span class="at">n =</span> <span class="dv">1</span>) <span class="sc">%&gt;%</span></span>
-<span id="cb972-367"><a href="#cb972-367" aria-hidden="true" tabindex="-1"></a>  <span class="fu">ungroup</span>() <span class="sc">%&gt;%</span> </span>
-<span id="cb972-368"><a href="#cb972-368" aria-hidden="true" tabindex="-1"></a>  <span class="fu">select</span>(row_num) <span class="sc">%&gt;%</span> </span>
-<span id="cb972-369"><a href="#cb972-369" aria-hidden="true" tabindex="-1"></a>  <span class="fu">deframe</span>()</span>
-<span id="cb972-370"><a href="#cb972-370" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-371"><a href="#cb972-371" aria-hidden="true" tabindex="-1"></a>subj_end <span class="ot">&lt;-</span> <span class="fu">c</span>(subj_start[<span class="sc">-</span><span class="dv">1</span>] <span class="sc">-</span> <span class="dv">1</span>, n_total) </span>
-<span id="cb972-372"><a href="#cb972-372" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-373"><a href="#cb972-373" aria-hidden="true" tabindex="-1"></a>stan_data <span class="ot">&lt;-</span> <span class="fu">list</span>(<span class="at">n_subjects =</span> n_subjects,</span>
-<span id="cb972-374"><a href="#cb972-374" aria-hidden="true" tabindex="-1"></a>                  <span class="at">n_total =</span> n_total,</span>
-<span id="cb972-375"><a href="#cb972-375" aria-hidden="true" tabindex="-1"></a>                  <span class="at">time =</span> nonmem_data_simulate<span class="sc">$</span>TIME,</span>
-<span id="cb972-376"><a href="#cb972-376" aria-hidden="true" tabindex="-1"></a>                  <span class="at">amt =</span> nonmem_data_simulate<span class="sc">$</span>AMT,</span>
-<span id="cb972-377"><a href="#cb972-377" aria-hidden="true" tabindex="-1"></a>                  <span class="at">cmt =</span> nonmem_data_simulate<span class="sc">$</span>CMT,</span>
-<span id="cb972-378"><a href="#cb972-378" aria-hidden="true" tabindex="-1"></a>                  <span class="at">evid =</span> nonmem_data_simulate<span class="sc">$</span>EVID,</span>
-<span id="cb972-379"><a href="#cb972-379" aria-hidden="true" tabindex="-1"></a>                  <span class="at">rate =</span> nonmem_data_simulate<span class="sc">$</span>RATE,</span>
-<span id="cb972-380"><a href="#cb972-380" aria-hidden="true" tabindex="-1"></a>                  <span class="at">ii =</span> nonmem_data_simulate<span class="sc">$</span>II,</span>
-<span id="cb972-381"><a href="#cb972-381" aria-hidden="true" tabindex="-1"></a>                  <span class="at">addl =</span> nonmem_data_simulate<span class="sc">$</span>ADDL,</span>
-<span id="cb972-382"><a href="#cb972-382" aria-hidden="true" tabindex="-1"></a>                  <span class="at">ss =</span> nonmem_data_simulate<span class="sc">$</span>SS,</span>
-<span id="cb972-383"><a href="#cb972-383" aria-hidden="true" tabindex="-1"></a>                  <span class="at">subj_start =</span> subj_start,</span>
-<span id="cb972-384"><a href="#cb972-384" aria-hidden="true" tabindex="-1"></a>                  <span class="at">subj_end =</span> subj_end,</span>
-<span id="cb972-385"><a href="#cb972-385" aria-hidden="true" tabindex="-1"></a>                  <span class="at">TVCL =</span> TVCL,</span>
-<span id="cb972-386"><a href="#cb972-386" aria-hidden="true" tabindex="-1"></a>                  <span class="at">TVVC =</span> TVVC,</span>
-<span id="cb972-387"><a href="#cb972-387" aria-hidden="true" tabindex="-1"></a>                  <span class="at">TVQ =</span> TVQ,</span>
-<span id="cb972-388"><a href="#cb972-388" aria-hidden="true" tabindex="-1"></a>                  <span class="at">TVVP =</span> TVVP,</span>
-<span id="cb972-389"><a href="#cb972-389" aria-hidden="true" tabindex="-1"></a>                  <span class="at">omega_cl =</span> omega_cl,</span>
-<span id="cb972-390"><a href="#cb972-390" aria-hidden="true" tabindex="-1"></a>                  <span class="at">omega_vc =</span> omega_vc,</span>
-<span id="cb972-391"><a href="#cb972-391" aria-hidden="true" tabindex="-1"></a>                  <span class="at">omega_q =</span> omega_q,</span>
-<span id="cb972-392"><a href="#cb972-392" aria-hidden="true" tabindex="-1"></a>                  <span class="at">omega_vp =</span> omega_vp,</span>
-<span id="cb972-393"><a href="#cb972-393" aria-hidden="true" tabindex="-1"></a>                  <span class="at">R =</span> R,</span>
-<span id="cb972-394"><a href="#cb972-394" aria-hidden="true" tabindex="-1"></a>                  <span class="at">sigma_p =</span> sigma_p,</span>
-<span id="cb972-395"><a href="#cb972-395" aria-hidden="true" tabindex="-1"></a>                  <span class="at">sigma_a =</span> sigma_a,</span>
-<span id="cb972-396"><a href="#cb972-396" aria-hidden="true" tabindex="-1"></a>                  <span class="at">cor_p_a =</span> cor_p_a,</span>
-<span id="cb972-397"><a href="#cb972-397" aria-hidden="true" tabindex="-1"></a>                  <span class="at">solver =</span> solver) <span class="co"># analytical = 1, mat exp = 2, rk45 = 3</span></span>
-<span id="cb972-398"><a href="#cb972-398" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-399"><a href="#cb972-399" aria-hidden="true" tabindex="-1"></a>model <span class="ot">&lt;-</span> <span class="fu">cmdstan_model</span>(</span>
-<span id="cb972-400"><a href="#cb972-400" aria-hidden="true" tabindex="-1"></a>  here<span class="sc">::</span><span class="fu">here</span>(<span class="st">&quot;M3/iv_2cmt_linear/Stan/Simulate/iv_2cmt_ppa.stan&quot;</span>))</span>
-<span id="cb972-401"><a href="#cb972-401" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-402"><a href="#cb972-402" aria-hidden="true" tabindex="-1"></a>model<span class="sc">$</span><span class="fu">print</span>()</span>
-<span id="cb972-403"><a href="#cb972-403" aria-hidden="true" tabindex="-1"></a><span class="in">```</span></span>
-<span id="cb972-404"><a href="#cb972-404" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-405"><a href="#cb972-405" aria-hidden="true" tabindex="-1"></a>:::</span>
-<span id="cb972-406"><a href="#cb972-406" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-409"><a href="#cb972-409" aria-hidden="true" tabindex="-1"></a><span class="in">```{r}</span></span>
-<span id="cb972-410"><a href="#cb972-410" aria-hidden="true" tabindex="-1"></a><span class="co">#| cache: true</span></span>
-<span id="cb972-411"><a href="#cb972-411" aria-hidden="true" tabindex="-1"></a><span class="co">#| output: false</span></span>
-<span id="cb972-412"><a href="#cb972-412" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-413"><a href="#cb972-413" aria-hidden="true" tabindex="-1"></a>simulated_data <span class="ot">&lt;-</span> model<span class="sc">$</span><span class="fu">sample</span>(<span class="at">data =</span> stan_data,</span>
-<span id="cb972-414"><a href="#cb972-414" aria-hidden="true" tabindex="-1"></a>                               <span class="at">fixed_param =</span> <span class="cn">TRUE</span>,</span>
-<span id="cb972-415"><a href="#cb972-415" aria-hidden="true" tabindex="-1"></a>                               <span class="at">seed =</span> <span class="dv">112358</span>,</span>
-<span id="cb972-416"><a href="#cb972-416" aria-hidden="true" tabindex="-1"></a>                               <span class="at">iter_warmup =</span> <span class="dv">0</span>,</span>
-<span id="cb972-417"><a href="#cb972-417" aria-hidden="true" tabindex="-1"></a>                               <span class="at">iter_sampling =</span> <span class="dv">1</span>,</span>
-<span id="cb972-418"><a href="#cb972-418" aria-hidden="true" tabindex="-1"></a>                               <span class="at">chains =</span> <span class="dv">1</span>,</span>
-<span id="cb972-419"><a href="#cb972-419" aria-hidden="true" tabindex="-1"></a>                               <span class="at">parallel_chains =</span> <span class="dv">1</span>)</span>
-<span id="cb972-420"><a href="#cb972-420" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-421"><a href="#cb972-421" aria-hidden="true" tabindex="-1"></a>data_analytical <span class="ot">&lt;-</span> simulated_data<span class="sc">$</span><span class="fu">draws</span>(<span class="fu">c</span>(<span class="st">&quot;dv&quot;</span>, <span class="st">&quot;ipred&quot;</span>)) <span class="sc">%&gt;%</span> </span>
-<span id="cb972-422"><a href="#cb972-422" aria-hidden="true" tabindex="-1"></a>  <span class="fu">spread_draws</span>(dv[i], ipred[i]) <span class="sc">%&gt;%</span> </span>
-<span id="cb972-423"><a href="#cb972-423" aria-hidden="true" tabindex="-1"></a>  <span class="fu">ungroup</span>() <span class="sc">%&gt;%</span> </span>
-<span id="cb972-424"><a href="#cb972-424" aria-hidden="true" tabindex="-1"></a>  <span class="fu">inner_join</span>(nonmem_data_simulate <span class="sc">%&gt;%</span> </span>
-<span id="cb972-425"><a href="#cb972-425" aria-hidden="true" tabindex="-1"></a>               <span class="fu">mutate</span>(<span class="at">i =</span> <span class="dv">1</span><span class="sc">:</span><span class="fu">n</span>()),</span>
-<span id="cb972-426"><a href="#cb972-426" aria-hidden="true" tabindex="-1"></a>             <span class="at">by =</span> <span class="st">&quot;i&quot;</span>) <span class="sc">%&gt;%</span></span>
-<span id="cb972-427"><a href="#cb972-427" aria-hidden="true" tabindex="-1"></a>  <span class="fu">select</span>(ID, AMT, II, ADDL, RATE, CMT, EVID, SS, TIME, </span>
-<span id="cb972-428"><a href="#cb972-428" aria-hidden="true" tabindex="-1"></a>         <span class="at">DV =</span> <span class="st">&quot;dv&quot;</span>, <span class="at">IPRED =</span> <span class="st">&quot;ipred&quot;</span>) <span class="sc">%&gt;%</span> </span>
-<span id="cb972-429"><a href="#cb972-429" aria-hidden="true" tabindex="-1"></a>  <span class="fu">mutate</span>(<span class="at">LLOQ =</span> <span class="fl">1e-6</span>, </span>
-<span id="cb972-430"><a href="#cb972-430" aria-hidden="true" tabindex="-1"></a>         <span class="at">BLOQ =</span> <span class="fu">case_when</span>(EVID <span class="sc">==</span> <span class="dv">1</span> <span class="sc">~</span> <span class="cn">NA_real_</span>,</span>
-<span id="cb972-431"><a href="#cb972-431" aria-hidden="true" tabindex="-1"></a>                          DV <span class="sc">&lt;=</span> LLOQ <span class="sc">~</span> <span class="dv">1</span>,</span>
-<span id="cb972-432"><a href="#cb972-432" aria-hidden="true" tabindex="-1"></a>                          DV <span class="sc">&gt;</span> LLOQ <span class="sc">~</span> <span class="dv">0</span>,</span>
-<span id="cb972-433"><a href="#cb972-433" aria-hidden="true" tabindex="-1"></a>                          <span class="cn">TRUE</span> <span class="sc">~</span> <span class="cn">NA_real_</span>),</span>
-<span id="cb972-434"><a href="#cb972-434" aria-hidden="true" tabindex="-1"></a>         <span class="at">DV =</span> <span class="fu">if_else</span>(EVID <span class="sc">==</span> <span class="dv">1</span> <span class="sc">|</span> BLOQ <span class="sc">==</span> <span class="dv">1</span>, <span class="cn">NA_real_</span>, DV),</span>
-<span id="cb972-435"><a href="#cb972-435" aria-hidden="true" tabindex="-1"></a>         <span class="at">MDV =</span> <span class="fu">if_else</span>(<span class="fu">is.na</span>(DV), <span class="dv">1</span>, <span class="dv">0</span>)) <span class="sc">%&gt;%</span> </span>
-<span id="cb972-436"><a href="#cb972-436" aria-hidden="true" tabindex="-1"></a>  <span class="fu">relocate</span>(DV, <span class="at">.after =</span> <span class="fu">last_col</span>()) <span class="sc">%&gt;%</span> </span>
-<span id="cb972-437"><a href="#cb972-437" aria-hidden="true" tabindex="-1"></a>  <span class="fu">relocate</span>(TIME, <span class="at">.before =</span> DV) <span class="sc">%&gt;%</span> </span>
-<span id="cb972-438"><a href="#cb972-438" aria-hidden="true" tabindex="-1"></a>  <span class="fu">mutate</span>(<span class="at">solver =</span> <span class="st">&quot;analytical&quot;</span>)</span>
-<span id="cb972-439"><a href="#cb972-439" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-440"><a href="#cb972-440" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-441"><a href="#cb972-441" aria-hidden="true" tabindex="-1"></a>solver <span class="ot">&lt;-</span> <span class="dv">2</span></span>
-<span id="cb972-442"><a href="#cb972-442" aria-hidden="true" tabindex="-1"></a>dosing_data <span class="ot">&lt;-</span> dosing_data <span class="sc">%&gt;%</span> </span>
-<span id="cb972-443"><a href="#cb972-443" aria-hidden="true" tabindex="-1"></a>  <span class="fu">mutate</span>(<span class="at">CMT =</span> <span class="fu">if_else</span>(solver <span class="sc">==</span> <span class="dv">1</span>, <span class="dv">2</span>, <span class="dv">1</span>)) </span>
-<span id="cb972-444"><a href="#cb972-444" aria-hidden="true" tabindex="-1"></a>  </span>
-<span id="cb972-445"><a href="#cb972-445" aria-hidden="true" tabindex="-1"></a>nonmem_data_simulate <span class="ot">&lt;-</span> dosing_data <span class="sc">%&gt;%</span> </span>
-<span id="cb972-446"><a href="#cb972-446" aria-hidden="true" tabindex="-1"></a>  <span class="fu">group_by</span>(ID) <span class="sc">%&gt;%</span> </span>
-<span id="cb972-447"><a href="#cb972-447" aria-hidden="true" tabindex="-1"></a>  <span class="fu">slice</span>(<span class="fu">rep</span>(<span class="dv">1</span>, <span class="at">times =</span> <span class="fu">length</span>(times_to_simulate))) <span class="sc">%&gt;%</span> </span>
-<span id="cb972-448"><a href="#cb972-448" aria-hidden="true" tabindex="-1"></a>  <span class="fu">mutate</span>(<span class="at">AMT =</span> <span class="dv">0</span>,</span>
-<span id="cb972-449"><a href="#cb972-449" aria-hidden="true" tabindex="-1"></a>         <span class="at">ADDL =</span> <span class="dv">0</span>,</span>
-<span id="cb972-450"><a href="#cb972-450" aria-hidden="true" tabindex="-1"></a>         <span class="at">II =</span> <span class="dv">0</span>,</span>
-<span id="cb972-451"><a href="#cb972-451" aria-hidden="true" tabindex="-1"></a>         <span class="at">CMT =</span> <span class="fu">if_else</span>(solver <span class="sc">==</span> <span class="dv">1</span>, <span class="dv">2</span>, <span class="dv">1</span>),</span>
-<span id="cb972-452"><a href="#cb972-452" aria-hidden="true" tabindex="-1"></a>         <span class="at">EVID =</span> <span class="dv">0</span>,</span>
-<span id="cb972-453"><a href="#cb972-453" aria-hidden="true" tabindex="-1"></a>         <span class="at">RATE =</span> <span class="dv">0</span>,</span>
-<span id="cb972-454"><a href="#cb972-454" aria-hidden="true" tabindex="-1"></a>         <span class="at">TIME =</span> times_to_simulate) <span class="sc">%&gt;%</span> </span>
-<span id="cb972-455"><a href="#cb972-455" aria-hidden="true" tabindex="-1"></a>  <span class="fu">ungroup</span>() <span class="sc">%&gt;%</span></span>
-<span id="cb972-456"><a href="#cb972-456" aria-hidden="true" tabindex="-1"></a>  <span class="fu">bind_rows</span>(dosing_data) <span class="sc">%&gt;%</span> </span>
-<span id="cb972-457"><a href="#cb972-457" aria-hidden="true" tabindex="-1"></a>  <span class="fu">arrange</span>(ID, TIME, AMT) </span>
-<span id="cb972-458"><a href="#cb972-458" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-459"><a href="#cb972-459" aria-hidden="true" tabindex="-1"></a>stan_data <span class="ot">&lt;-</span> <span class="fu">list</span>(<span class="at">n_subjects =</span> n_subjects,</span>
-<span id="cb972-460"><a href="#cb972-460" aria-hidden="true" tabindex="-1"></a>                  <span class="at">n_total =</span> n_total,</span>
-<span id="cb972-461"><a href="#cb972-461" aria-hidden="true" tabindex="-1"></a>                  <span class="at">time =</span> nonmem_data_simulate<span class="sc">$</span>TIME,</span>
-<span id="cb972-462"><a href="#cb972-462" aria-hidden="true" tabindex="-1"></a>                  <span class="at">amt =</span> nonmem_data_simulate<span class="sc">$</span>AMT,</span>
-<span id="cb972-463"><a href="#cb972-463" aria-hidden="true" tabindex="-1"></a>                  <span class="at">cmt =</span> nonmem_data_simulate<span class="sc">$</span>CMT,</span>
-<span id="cb972-464"><a href="#cb972-464" aria-hidden="true" tabindex="-1"></a>                  <span class="at">evid =</span> nonmem_data_simulate<span class="sc">$</span>EVID,</span>
-<span id="cb972-465"><a href="#cb972-465" aria-hidden="true" tabindex="-1"></a>                  <span class="at">rate =</span> nonmem_data_simulate<span class="sc">$</span>RATE,</span>
-<span id="cb972-466"><a href="#cb972-466" aria-hidden="true" tabindex="-1"></a>                  <span class="at">ii =</span> nonmem_data_simulate<span class="sc">$</span>II,</span>
-<span id="cb972-467"><a href="#cb972-467" aria-hidden="true" tabindex="-1"></a>                  <span class="at">addl =</span> nonmem_data_simulate<span class="sc">$</span>ADDL,</span>
-<span id="cb972-468"><a href="#cb972-468" aria-hidden="true" tabindex="-1"></a>                  <span class="at">ss =</span> nonmem_data_simulate<span class="sc">$</span>SS,</span>
-<span id="cb972-469"><a href="#cb972-469" aria-hidden="true" tabindex="-1"></a>                  <span class="at">subj_start =</span> subj_start,</span>
-<span id="cb972-470"><a href="#cb972-470" aria-hidden="true" tabindex="-1"></a>                  <span class="at">subj_end =</span> subj_end,</span>
-<span id="cb972-471"><a href="#cb972-471" aria-hidden="true" tabindex="-1"></a>                  <span class="at">TVCL =</span> TVCL,</span>
-<span id="cb972-472"><a href="#cb972-472" aria-hidden="true" tabindex="-1"></a>                  <span class="at">TVVC =</span> TVVC,</span>
-<span id="cb972-473"><a href="#cb972-473" aria-hidden="true" tabindex="-1"></a>                  <span class="at">TVQ =</span> TVQ,</span>
-<span id="cb972-474"><a href="#cb972-474" aria-hidden="true" tabindex="-1"></a>                  <span class="at">TVVP =</span> TVVP,</span>
-<span id="cb972-475"><a href="#cb972-475" aria-hidden="true" tabindex="-1"></a>                  <span class="at">omega_cl =</span> omega_cl,</span>
-<span id="cb972-476"><a href="#cb972-476" aria-hidden="true" tabindex="-1"></a>                  <span class="at">omega_vc =</span> omega_vc,</span>
-<span id="cb972-477"><a href="#cb972-477" aria-hidden="true" tabindex="-1"></a>                  <span class="at">omega_q =</span> omega_q,</span>
-<span id="cb972-478"><a href="#cb972-478" aria-hidden="true" tabindex="-1"></a>                  <span class="at">omega_vp =</span> omega_vp,</span>
-<span id="cb972-479"><a href="#cb972-479" aria-hidden="true" tabindex="-1"></a>                  <span class="at">R =</span> R,</span>
-<span id="cb972-480"><a href="#cb972-480" aria-hidden="true" tabindex="-1"></a>                  <span class="at">sigma_p =</span> sigma_p,</span>
-<span id="cb972-481"><a href="#cb972-481" aria-hidden="true" tabindex="-1"></a>                  <span class="at">sigma_a =</span> sigma_a,</span>
-<span id="cb972-482"><a href="#cb972-482" aria-hidden="true" tabindex="-1"></a>                  <span class="at">cor_p_a =</span> cor_p_a,</span>
-<span id="cb972-483"><a href="#cb972-483" aria-hidden="true" tabindex="-1"></a>                  <span class="at">solver =</span> solver) </span>
-<span id="cb972-484"><a href="#cb972-484" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-485"><a href="#cb972-485" aria-hidden="true" tabindex="-1"></a>simulated_data <span class="ot">&lt;-</span> model<span class="sc">$</span><span class="fu">sample</span>(<span class="at">data =</span> stan_data,</span>
-<span id="cb972-486"><a href="#cb972-486" aria-hidden="true" tabindex="-1"></a>                               <span class="at">fixed_param =</span> <span class="cn">TRUE</span>,</span>
-<span id="cb972-487"><a href="#cb972-487" aria-hidden="true" tabindex="-1"></a>                               <span class="at">seed =</span> <span class="dv">112358</span>,</span>
-<span id="cb972-488"><a href="#cb972-488" aria-hidden="true" tabindex="-1"></a>                               <span class="at">iter_warmup =</span> <span class="dv">0</span>,</span>
-<span id="cb972-489"><a href="#cb972-489" aria-hidden="true" tabindex="-1"></a>                               <span class="at">iter_sampling =</span> <span class="dv">1</span>,</span>
-<span id="cb972-490"><a href="#cb972-490" aria-hidden="true" tabindex="-1"></a>                               <span class="at">chains =</span> <span class="dv">1</span>,</span>
-<span id="cb972-491"><a href="#cb972-491" aria-hidden="true" tabindex="-1"></a>                               <span class="at">parallel_chains =</span> <span class="dv">1</span>)</span>
-<span id="cb972-492"><a href="#cb972-492" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-493"><a href="#cb972-493" aria-hidden="true" tabindex="-1"></a>data_mat_exp <span class="ot">&lt;-</span> simulated_data<span class="sc">$</span><span class="fu">draws</span>(<span class="fu">c</span>(<span class="st">&quot;dv&quot;</span>, <span class="st">&quot;ipred&quot;</span>)) <span class="sc">%&gt;%</span> </span>
-<span id="cb972-494"><a href="#cb972-494" aria-hidden="true" tabindex="-1"></a>  <span class="fu">spread_draws</span>(dv[i], ipred[i]) <span class="sc">%&gt;%</span> </span>
-<span id="cb972-495"><a href="#cb972-495" aria-hidden="true" tabindex="-1"></a>  <span class="fu">ungroup</span>() <span class="sc">%&gt;%</span> </span>
-<span id="cb972-496"><a href="#cb972-496" aria-hidden="true" tabindex="-1"></a>  <span class="fu">inner_join</span>(nonmem_data_simulate <span class="sc">%&gt;%</span> </span>
-<span id="cb972-497"><a href="#cb972-497" aria-hidden="true" tabindex="-1"></a>               <span class="fu">mutate</span>(<span class="at">i =</span> <span class="dv">1</span><span class="sc">:</span><span class="fu">n</span>()),</span>
-<span id="cb972-498"><a href="#cb972-498" aria-hidden="true" tabindex="-1"></a>             <span class="at">by =</span> <span class="st">&quot;i&quot;</span>) <span class="sc">%&gt;%</span></span>
-<span id="cb972-499"><a href="#cb972-499" aria-hidden="true" tabindex="-1"></a>  <span class="fu">select</span>(ID, AMT, II, ADDL, RATE, CMT, EVID, SS, TIME, </span>
-<span id="cb972-500"><a href="#cb972-500" aria-hidden="true" tabindex="-1"></a>         <span class="at">DV =</span> <span class="st">&quot;dv&quot;</span>, <span class="at">IPRED =</span> <span class="st">&quot;ipred&quot;</span>) <span class="sc">%&gt;%</span> </span>
-<span id="cb972-501"><a href="#cb972-501" aria-hidden="true" tabindex="-1"></a>  <span class="fu">mutate</span>(<span class="at">LLOQ =</span> <span class="fl">1e-6</span>, </span>
-<span id="cb972-502"><a href="#cb972-502" aria-hidden="true" tabindex="-1"></a>         <span class="at">BLOQ =</span> <span class="fu">case_when</span>(EVID <span class="sc">==</span> <span class="dv">1</span> <span class="sc">~</span> <span class="cn">NA_real_</span>,</span>
-<span id="cb972-503"><a href="#cb972-503" aria-hidden="true" tabindex="-1"></a>                          DV <span class="sc">&lt;=</span> LLOQ <span class="sc">~</span> <span class="dv">1</span>,</span>
-<span id="cb972-504"><a href="#cb972-504" aria-hidden="true" tabindex="-1"></a>                          DV <span class="sc">&gt;</span> LLOQ <span class="sc">~</span> <span class="dv">0</span>,</span>
-<span id="cb972-505"><a href="#cb972-505" aria-hidden="true" tabindex="-1"></a>                          <span class="cn">TRUE</span> <span class="sc">~</span> <span class="cn">NA_real_</span>),</span>
-<span id="cb972-506"><a href="#cb972-506" aria-hidden="true" tabindex="-1"></a>         <span class="at">DV =</span> <span class="fu">if_else</span>(EVID <span class="sc">==</span> <span class="dv">1</span> <span class="sc">|</span> BLOQ <span class="sc">==</span> <span class="dv">1</span>, <span class="cn">NA_real_</span>, DV),</span>
-<span id="cb972-507"><a href="#cb972-507" aria-hidden="true" tabindex="-1"></a>         <span class="at">MDV =</span> <span class="fu">if_else</span>(<span class="fu">is.na</span>(DV), <span class="dv">1</span>, <span class="dv">0</span>)) <span class="sc">%&gt;%</span> </span>
-<span id="cb972-508"><a href="#cb972-508" aria-hidden="true" tabindex="-1"></a>  <span class="fu">relocate</span>(DV, <span class="at">.after =</span> <span class="fu">last_col</span>()) <span class="sc">%&gt;%</span> </span>
-<span id="cb972-509"><a href="#cb972-509" aria-hidden="true" tabindex="-1"></a>  <span class="fu">relocate</span>(TIME, <span class="at">.before =</span> DV) <span class="sc">%&gt;%</span> </span>
-<span id="cb972-510"><a href="#cb972-510" aria-hidden="true" tabindex="-1"></a>  <span class="fu">mutate</span>(<span class="at">solver =</span> <span class="st">&quot;mat_exp&quot;</span>)</span>
-<span id="cb972-511"><a href="#cb972-511" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-512"><a href="#cb972-512" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-513"><a href="#cb972-513" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-514"><a href="#cb972-514" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-515"><a href="#cb972-515" aria-hidden="true" tabindex="-1"></a>solver <span class="ot">&lt;-</span> <span class="dv">3</span></span>
-<span id="cb972-516"><a href="#cb972-516" aria-hidden="true" tabindex="-1"></a>stan_data<span class="sc">$</span>solver <span class="ot">&lt;-</span> solver</span>
-<span id="cb972-517"><a href="#cb972-517" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-518"><a href="#cb972-518" aria-hidden="true" tabindex="-1"></a>simulated_data <span class="ot">&lt;-</span> model<span class="sc">$</span><span class="fu">sample</span>(<span class="at">data =</span> stan_data,</span>
-<span id="cb972-519"><a href="#cb972-519" aria-hidden="true" tabindex="-1"></a>                               <span class="at">fixed_param =</span> <span class="cn">TRUE</span>,</span>
-<span id="cb972-520"><a href="#cb972-520" aria-hidden="true" tabindex="-1"></a>                               <span class="at">seed =</span> <span class="dv">112358</span>,</span>
-<span id="cb972-521"><a href="#cb972-521" aria-hidden="true" tabindex="-1"></a>                               <span class="at">iter_warmup =</span> <span class="dv">0</span>,</span>
-<span id="cb972-522"><a href="#cb972-522" aria-hidden="true" tabindex="-1"></a>                               <span class="at">iter_sampling =</span> <span class="dv">1</span>,</span>
-<span id="cb972-523"><a href="#cb972-523" aria-hidden="true" tabindex="-1"></a>                               <span class="at">chains =</span> <span class="dv">1</span>,</span>
-<span id="cb972-524"><a href="#cb972-524" aria-hidden="true" tabindex="-1"></a>                               <span class="at">parallel_chains =</span> <span class="dv">1</span>)</span>
-<span id="cb972-525"><a href="#cb972-525" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-526"><a href="#cb972-526" aria-hidden="true" tabindex="-1"></a>data_rk45 <span class="ot">&lt;-</span> simulated_data<span class="sc">$</span><span class="fu">draws</span>(<span class="fu">c</span>(<span class="st">&quot;dv&quot;</span>, <span class="st">&quot;ipred&quot;</span>)) <span class="sc">%&gt;%</span> </span>
-<span id="cb972-527"><a href="#cb972-527" aria-hidden="true" tabindex="-1"></a>  <span class="fu">spread_draws</span>(dv[i], ipred[i]) <span class="sc">%&gt;%</span> </span>
-<span id="cb972-528"><a href="#cb972-528" aria-hidden="true" tabindex="-1"></a>  <span class="fu">ungroup</span>() <span class="sc">%&gt;%</span> </span>
-<span id="cb972-529"><a href="#cb972-529" aria-hidden="true" tabindex="-1"></a>  <span class="fu">inner_join</span>(nonmem_data_simulate <span class="sc">%&gt;%</span> </span>
-<span id="cb972-530"><a href="#cb972-530" aria-hidden="true" tabindex="-1"></a>               <span class="fu">mutate</span>(<span class="at">i =</span> <span class="dv">1</span><span class="sc">:</span><span class="fu">n</span>()),</span>
-<span id="cb972-531"><a href="#cb972-531" aria-hidden="true" tabindex="-1"></a>             <span class="at">by =</span> <span class="st">&quot;i&quot;</span>) <span class="sc">%&gt;%</span></span>
-<span id="cb972-532"><a href="#cb972-532" aria-hidden="true" tabindex="-1"></a>  <span class="fu">select</span>(ID, AMT, II, ADDL, RATE, CMT, EVID, SS, TIME, </span>
-<span id="cb972-533"><a href="#cb972-533" aria-hidden="true" tabindex="-1"></a>         <span class="at">DV =</span> <span class="st">&quot;dv&quot;</span>, <span class="at">IPRED =</span> <span class="st">&quot;ipred&quot;</span>) <span class="sc">%&gt;%</span> </span>
-<span id="cb972-534"><a href="#cb972-534" aria-hidden="true" tabindex="-1"></a>  <span class="fu">mutate</span>(<span class="at">LLOQ =</span> <span class="fl">1e-6</span>, </span>
-<span id="cb972-535"><a href="#cb972-535" aria-hidden="true" tabindex="-1"></a>         <span class="at">BLOQ =</span> <span class="fu">case_when</span>(EVID <span class="sc">==</span> <span class="dv">1</span> <span class="sc">~</span> <span class="cn">NA_real_</span>,</span>
-<span id="cb972-536"><a href="#cb972-536" aria-hidden="true" tabindex="-1"></a>                          DV <span class="sc">&lt;=</span> LLOQ <span class="sc">~</span> <span class="dv">1</span>,</span>
-<span id="cb972-537"><a href="#cb972-537" aria-hidden="true" tabindex="-1"></a>                          DV <span class="sc">&gt;</span> LLOQ <span class="sc">~</span> <span class="dv">0</span>,</span>
-<span id="cb972-538"><a href="#cb972-538" aria-hidden="true" tabindex="-1"></a>                          <span class="cn">TRUE</span> <span class="sc">~</span> <span class="cn">NA_real_</span>),</span>
-<span id="cb972-539"><a href="#cb972-539" aria-hidden="true" tabindex="-1"></a>         <span class="at">DV =</span> <span class="fu">if_else</span>(EVID <span class="sc">==</span> <span class="dv">1</span> <span class="sc">|</span> BLOQ <span class="sc">==</span> <span class="dv">1</span>, <span class="cn">NA_real_</span>, DV),</span>
-<span id="cb972-540"><a href="#cb972-540" aria-hidden="true" tabindex="-1"></a>         <span class="at">MDV =</span> <span class="fu">if_else</span>(<span class="fu">is.na</span>(DV), <span class="dv">1</span>, <span class="dv">0</span>)) <span class="sc">%&gt;%</span> </span>
-<span id="cb972-541"><a href="#cb972-541" aria-hidden="true" tabindex="-1"></a>  <span class="fu">relocate</span>(DV, <span class="at">.after =</span> <span class="fu">last_col</span>()) <span class="sc">%&gt;%</span> </span>
-<span id="cb972-542"><a href="#cb972-542" aria-hidden="true" tabindex="-1"></a>  <span class="fu">relocate</span>(TIME, <span class="at">.before =</span> DV) <span class="sc">%&gt;%</span> </span>
-<span id="cb972-543"><a href="#cb972-543" aria-hidden="true" tabindex="-1"></a>  <span class="fu">mutate</span>(<span class="at">solver =</span> <span class="st">&quot;rk45&quot;</span>)</span>
-<span id="cb972-544"><a href="#cb972-544" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-545"><a href="#cb972-545" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-546"><a href="#cb972-546" aria-hidden="true" tabindex="-1"></a><span class="do">## Now do it with mrgsolve to check</span></span>
-<span id="cb972-547"><a href="#cb972-547" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-548"><a href="#cb972-548" aria-hidden="true" tabindex="-1"></a>mod <span class="ot">&lt;-</span> <span class="fu">mread</span>(here<span class="sc">::</span><span class="fu">here</span>(<span class="st">&quot;M3/iv_2cmt_linear/mrgsolve/iv_2cmt_ppa.cpp&quot;</span>))</span>
-<span id="cb972-549"><a href="#cb972-549" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-550"><a href="#cb972-550" aria-hidden="true" tabindex="-1"></a>data_mrgsolve <span class="ot">&lt;-</span> mod <span class="sc">%&gt;%</span> </span>
-<span id="cb972-551"><a href="#cb972-551" aria-hidden="true" tabindex="-1"></a>  <span class="fu">param</span>(<span class="fu">tibble</span>(<span class="at">TVCL =</span> TVCL,</span>
-<span id="cb972-552"><a href="#cb972-552" aria-hidden="true" tabindex="-1"></a>               <span class="at">TVVC =</span> TVVC,</span>
-<span id="cb972-553"><a href="#cb972-553" aria-hidden="true" tabindex="-1"></a>               <span class="at">TVQ =</span> TVQ,</span>
-<span id="cb972-554"><a href="#cb972-554" aria-hidden="true" tabindex="-1"></a>               <span class="at">TVVP =</span> TVVP)) <span class="sc">%&gt;%</span> </span>
-<span id="cb972-555"><a href="#cb972-555" aria-hidden="true" tabindex="-1"></a>  <span class="fu">data_set</span>(dosing_data) <span class="sc">%&gt;%</span> </span>
-<span id="cb972-556"><a href="#cb972-556" aria-hidden="true" tabindex="-1"></a>  <span class="fu">mrgsim_df</span>(<span class="at">tgrid =</span> times_to_simulate) <span class="sc">%&gt;%</span> </span>
-<span id="cb972-557"><a href="#cb972-557" aria-hidden="true" tabindex="-1"></a>  <span class="fu">as_tibble</span>() <span class="sc">%&gt;%</span> </span>
-<span id="cb972-558"><a href="#cb972-558" aria-hidden="true" tabindex="-1"></a>  <span class="fu">mutate</span>(<span class="at">solver =</span> <span class="st">&quot;mrgsolve&quot;</span>)</span>
-<span id="cb972-559"><a href="#cb972-559" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-560"><a href="#cb972-560" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-561"><a href="#cb972-561" aria-hidden="true" tabindex="-1"></a><span class="in">```</span></span>
-<span id="cb972-562"><a href="#cb972-562" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-563"><a href="#cb972-563" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-566"><a href="#cb972-566" aria-hidden="true" tabindex="-1"></a><span class="in">```{r}</span></span>
-<span id="cb972-567"><a href="#cb972-567" aria-hidden="true" tabindex="-1"></a><span class="co">#| fig-align: center</span></span>
-<span id="cb972-568"><a href="#cb972-568" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-569"><a href="#cb972-569" aria-hidden="true" tabindex="-1"></a><span class="fu">mget</span>(<span class="fu">str_subset</span>(<span class="fu">ls</span>(), <span class="st">&quot;^data_&quot;</span>)) <span class="sc">%&gt;%</span></span>
-<span id="cb972-570"><a href="#cb972-570" aria-hidden="true" tabindex="-1"></a>  <span class="fu">bind_rows</span>() <span class="sc">%&gt;%</span> </span>
-<span id="cb972-571"><a href="#cb972-571" aria-hidden="true" tabindex="-1"></a>  <span class="fu">ggplot</span>(<span class="fu">aes</span>(<span class="at">x =</span> TIME, <span class="at">y =</span> IPRED, <span class="at">color =</span> solver)) <span class="sc">+</span></span>
-<span id="cb972-572"><a href="#cb972-572" aria-hidden="true" tabindex="-1"></a>  <span class="fu">geom_line</span>(<span class="fu">aes</span>(<span class="at">linetype =</span> solver)) <span class="sc">+</span></span>
-<span id="cb972-573"><a href="#cb972-573" aria-hidden="true" tabindex="-1"></a>  <span class="fu">theme_bw</span>() <span class="sc">+</span></span>
-<span id="cb972-574"><a href="#cb972-574" aria-hidden="true" tabindex="-1"></a>  <span class="fu">scale_x_continuous</span>(<span class="at">name =</span> <span class="st">&quot;Time (h)&quot;</span>,</span>
-<span id="cb972-575"><a href="#cb972-575" aria-hidden="true" tabindex="-1"></a>                     <span class="at">breaks =</span> <span class="fu">seq</span>(<span class="dv">0</span>, <span class="dv">168</span>, <span class="at">by =</span> <span class="dv">24</span>),</span>
-<span id="cb972-576"><a href="#cb972-576" aria-hidden="true" tabindex="-1"></a>                     <span class="at">labels =</span> <span class="fu">seq</span>(<span class="dv">0</span>, <span class="dv">168</span>, <span class="at">by =</span> <span class="dv">24</span>)) <span class="sc">+</span></span>
-<span id="cb972-577"><a href="#cb972-577" aria-hidden="true" tabindex="-1"></a>  <span class="fu">scale_y_continuous</span>(<span class="at">name =</span> <span class="st">&quot;Drug Conc. (ug/mL)&quot;</span>)</span>
-<span id="cb972-578"><a href="#cb972-578" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-579"><a href="#cb972-579" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-580"><a href="#cb972-580" aria-hidden="true" tabindex="-1"></a><span class="in">```</span></span>
-<span id="cb972-581"><a href="#cb972-581" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-582"><a href="#cb972-582" aria-hidden="true" tabindex="-1"></a>So you can see that the analytical solution spits out a vector of 0s, while the</span>
-<span id="cb972-583"><a href="#cb972-583" aria-hidden="true" tabindex="-1"></a>linear ODE, general ODE, and mrgsolve simulations are all the same.</span>
-<span id="cb972-584"><a href="#cb972-584" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-585"><a href="#cb972-585" aria-hidden="true" tabindex="-1"></a><span class="fu">## Fitting ```pk2cpt```, ```pk2cpt_linode```, ```pk2cpt_ode``` from ```example-models/```</span></span>
-<span id="cb972-586"><a href="#cb972-586" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-587"><a href="#cb972-587" aria-hidden="true" tabindex="-1"></a>I made a few modifications in the R script to fit the project and a couple </span>
-<span id="cb972-588"><a href="#cb972-588" aria-hidden="true" tabindex="-1"></a>small changes in the general ODE model while trying to debug it, but no changes </span>
-<span id="cb972-589"><a href="#cb972-589" aria-hidden="true" tabindex="-1"></a>of any major substance.</span>
-<span id="cb972-590"><a href="#cb972-590" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-591"><a href="#cb972-591" aria-hidden="true" tabindex="-1"></a><span class="fu">### ```pk2cpt```</span></span>
-<span id="cb972-592"><a href="#cb972-592" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-593"><a href="#cb972-593" aria-hidden="true" tabindex="-1"></a>:::{.scrolling_500}</span>
-<span id="cb972-594"><a href="#cb972-594" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-597"><a href="#cb972-597" aria-hidden="true" tabindex="-1"></a><span class="in">```{r}</span></span>
-<span id="cb972-598"><a href="#cb972-598" aria-hidden="true" tabindex="-1"></a>model_analytical <span class="ot">&lt;-</span> <span class="fu">cmdstan_model</span>(</span>
-<span id="cb972-599"><a href="#cb972-599" aria-hidden="true" tabindex="-1"></a>  here<span class="sc">::</span><span class="fu">here</span>(<span class="st">&quot;M3/example_models_metrum/pk2cpt/pk2cpt.stan&quot;</span>))</span>
-<span id="cb972-600"><a href="#cb972-600" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-601"><a href="#cb972-601" aria-hidden="true" tabindex="-1"></a>fit_analytical <span class="ot">&lt;-</span> model_analytical<span class="sc">$</span><span class="fu">sample</span>(</span>
-<span id="cb972-602"><a href="#cb972-602" aria-hidden="true" tabindex="-1"></a>  <span class="at">data =</span> here<span class="sc">::</span><span class="fu">here</span>(<span class="st">&quot;M3/example_models_metrum/pk2cpt/pk2cpt.data.R&quot;</span>), </span>
-<span id="cb972-603"><a href="#cb972-603" aria-hidden="true" tabindex="-1"></a>  <span class="at">init =</span> here<span class="sc">::</span><span class="fu">here</span>(<span class="st">&quot;M3/example_models_metrum/pk2cpt/pk2cpt.init.R&quot;</span>), </span>
-<span id="cb972-604"><a href="#cb972-604" aria-hidden="true" tabindex="-1"></a>  <span class="at">seed =</span> <span class="dv">3191951</span>,</span>
-<span id="cb972-605"><a href="#cb972-605" aria-hidden="true" tabindex="-1"></a>  <span class="at">chains =</span> <span class="dv">1</span>,</span>
-<span id="cb972-606"><a href="#cb972-606" aria-hidden="true" tabindex="-1"></a>  <span class="at">parallel_chains =</span> <span class="dv">1</span>,</span>
-<span id="cb972-607"><a href="#cb972-607" aria-hidden="true" tabindex="-1"></a>  <span class="at">iter_warmup =</span> <span class="dv">500</span>,</span>
-<span id="cb972-608"><a href="#cb972-608" aria-hidden="true" tabindex="-1"></a>  <span class="at">iter_sampling =</span> <span class="dv">1000</span>,</span>
-<span id="cb972-609"><a href="#cb972-609" aria-hidden="true" tabindex="-1"></a>  <span class="at">adapt_delta =</span> <span class="fl">0.80</span>)</span>
-<span id="cb972-610"><a href="#cb972-610" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-611"><a href="#cb972-611" aria-hidden="true" tabindex="-1"></a><span class="in">```</span></span>
-<span id="cb972-612"><a href="#cb972-612" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-613"><a href="#cb972-613" aria-hidden="true" tabindex="-1"></a>:::</span>
-<span id="cb972-614"><a href="#cb972-614" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-615"><a href="#cb972-615" aria-hidden="true" tabindex="-1"></a>In particular, </span>
-<span id="cb972-616"><a href="#cb972-616" aria-hidden="true" tabindex="-1"></a>```Chain 1 Exception: normal_lpdf: Location parameter<span class="co">[</span><span class="ot">1</span><span class="co">]</span> is -inf, but must be finite!```</span>
-<span id="cb972-617"><a href="#cb972-617" aria-hidden="true" tabindex="-1"></a>implies that the prediction is 0.</span>
-<span id="cb972-618"><a href="#cb972-618" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-619"><a href="#cb972-619" aria-hidden="true" tabindex="-1"></a><span class="fu">### ```pk2cpt_linode```</span></span>
-<span id="cb972-620"><a href="#cb972-620" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-621"><a href="#cb972-621" aria-hidden="true" tabindex="-1"></a>:::{.scrolling_500}</span>
-<span id="cb972-622"><a href="#cb972-622" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-625"><a href="#cb972-625" aria-hidden="true" tabindex="-1"></a><span class="in">```{r}</span></span>
-<span id="cb972-626"><a href="#cb972-626" aria-hidden="true" tabindex="-1"></a><span class="co">#| cache: true</span></span>
-<span id="cb972-627"><a href="#cb972-627" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-628"><a href="#cb972-628" aria-hidden="true" tabindex="-1"></a>model_mat_exp <span class="ot">&lt;-</span> <span class="fu">cmdstan_model</span>(</span>
-<span id="cb972-629"><a href="#cb972-629" aria-hidden="true" tabindex="-1"></a>  here<span class="sc">::</span><span class="fu">here</span>(<span class="st">&quot;M3/example_models_metrum/pk2cpt_linode/pk2cpt_linode.stan&quot;</span>))</span>
-<span id="cb972-630"><a href="#cb972-630" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-631"><a href="#cb972-631" aria-hidden="true" tabindex="-1"></a>fit_mat_exp <span class="ot">&lt;-</span> model_mat_exp<span class="sc">$</span><span class="fu">sample</span>(</span>
-<span id="cb972-632"><a href="#cb972-632" aria-hidden="true" tabindex="-1"></a>  <span class="at">data =</span> here<span class="sc">::</span><span class="fu">here</span>(<span class="st">&quot;M3/example_models_metrum/pk2cpt_linode/pk2cpt_linode.data.R&quot;</span>), </span>
-<span id="cb972-633"><a href="#cb972-633" aria-hidden="true" tabindex="-1"></a>  <span class="at">init =</span> here<span class="sc">::</span><span class="fu">here</span>(<span class="st">&quot;M3/example_models_metrum/pk2cpt_linode/pk2cpt_linode.init.R&quot;</span>), </span>
-<span id="cb972-634"><a href="#cb972-634" aria-hidden="true" tabindex="-1"></a>  <span class="at">seed =</span> <span class="dv">3191951</span>,</span>
-<span id="cb972-635"><a href="#cb972-635" aria-hidden="true" tabindex="-1"></a>  <span class="at">chains =</span> <span class="dv">4</span>,</span>
-<span id="cb972-636"><a href="#cb972-636" aria-hidden="true" tabindex="-1"></a>  <span class="at">parallel_chains =</span> <span class="dv">4</span>,</span>
-<span id="cb972-637"><a href="#cb972-637" aria-hidden="true" tabindex="-1"></a>  <span class="at">iter_warmup =</span> <span class="dv">500</span>,</span>
-<span id="cb972-638"><a href="#cb972-638" aria-hidden="true" tabindex="-1"></a>  <span class="at">iter_sampling =</span> <span class="dv">1000</span>,</span>
-<span id="cb972-639"><a href="#cb972-639" aria-hidden="true" tabindex="-1"></a>  <span class="at">refresh =</span> <span class="dv">0</span>,</span>
-<span id="cb972-640"><a href="#cb972-640" aria-hidden="true" tabindex="-1"></a>  <span class="at">adapt_delta =</span> <span class="fl">0.80</span>)</span>
-<span id="cb972-641"><a href="#cb972-641" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-642"><a href="#cb972-642" aria-hidden="true" tabindex="-1"></a><span class="in">```</span></span>
-<span id="cb972-643"><a href="#cb972-643" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-644"><a href="#cb972-644" aria-hidden="true" tabindex="-1"></a>:::</span>
-<span id="cb972-645"><a href="#cb972-645" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-646"><a href="#cb972-646" aria-hidden="true" tabindex="-1"></a>Works fine. I also fit the ```pk2cpt``` and ```pk2cpt_ode``` data with this </span>
-<span id="cb972-647"><a href="#cb972-647" aria-hidden="true" tabindex="-1"></a>model with no issues.</span>
-<span id="cb972-648"><a href="#cb972-648" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-649"><a href="#cb972-649" aria-hidden="true" tabindex="-1"></a><span class="fu">### ```pk2cpt_ode```</span></span>
-<span id="cb972-650"><a href="#cb972-650" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-651"><a href="#cb972-651" aria-hidden="true" tabindex="-1"></a>:::{.scrolling_500}</span>
-<span id="cb972-652"><a href="#cb972-652" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-655"><a href="#cb972-655" aria-hidden="true" tabindex="-1"></a><span class="in">```{r}</span></span>
-<span id="cb972-656"><a href="#cb972-656" aria-hidden="true" tabindex="-1"></a><span class="co">#| cache: true</span></span>
-<span id="cb972-657"><a href="#cb972-657" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-658"><a href="#cb972-658" aria-hidden="true" tabindex="-1"></a>model_rk45 <span class="ot">&lt;-</span> <span class="fu">cmdstan_model</span>(</span>
-<span id="cb972-659"><a href="#cb972-659" aria-hidden="true" tabindex="-1"></a>  here<span class="sc">::</span><span class="fu">here</span>(<span class="st">&quot;M3/example_models_metrum/pk2cpt_ode/pk2cpt_ode.stan&quot;</span>))</span>
-<span id="cb972-660"><a href="#cb972-660" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-661"><a href="#cb972-661" aria-hidden="true" tabindex="-1"></a>stan_data_rk45 <span class="ot">&lt;-</span> rstan<span class="sc">::</span><span class="fu">read_rdump</span>(</span>
-<span id="cb972-662"><a href="#cb972-662" aria-hidden="true" tabindex="-1"></a>  here<span class="sc">::</span><span class="fu">here</span>(<span class="st">&quot;M3/example_models_metrum/pk2cpt_ode/pk2cpt_ode.data.R&quot;</span>))</span>
-<span id="cb972-663"><a href="#cb972-663" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-664"><a href="#cb972-664" aria-hidden="true" tabindex="-1"></a>stan_data_rk45<span class="sc">$</span>prior_only <span class="ot">&lt;-</span> <span class="dv">1</span></span>
-<span id="cb972-665"><a href="#cb972-665" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-666"><a href="#cb972-666" aria-hidden="true" tabindex="-1"></a>fit_rk45 <span class="ot">&lt;-</span> model_rk45<span class="sc">$</span><span class="fu">sample</span>(</span>
-<span id="cb972-667"><a href="#cb972-667" aria-hidden="true" tabindex="-1"></a>  <span class="at">data =</span> stan_data_rk45, </span>
-<span id="cb972-668"><a href="#cb972-668" aria-hidden="true" tabindex="-1"></a>  <span class="at">init =</span> here<span class="sc">::</span><span class="fu">here</span>(<span class="st">&quot;M3/example_models_metrum/pk2cpt_ode/pk2cpt_ode.init.R&quot;</span>), </span>
-<span id="cb972-669"><a href="#cb972-669" aria-hidden="true" tabindex="-1"></a>  <span class="at">seed =</span> <span class="dv">3191951</span>,</span>
-<span id="cb972-670"><a href="#cb972-670" aria-hidden="true" tabindex="-1"></a>  <span class="at">chains =</span> <span class="dv">1</span>,</span>
-<span id="cb972-671"><a href="#cb972-671" aria-hidden="true" tabindex="-1"></a>  <span class="at">parallel_chains =</span> <span class="dv">1</span>,</span>
-<span id="cb972-672"><a href="#cb972-672" aria-hidden="true" tabindex="-1"></a>  <span class="at">iter_warmup =</span> <span class="dv">1</span>,</span>
-<span id="cb972-673"><a href="#cb972-673" aria-hidden="true" tabindex="-1"></a>  <span class="at">iter_sampling =</span> <span class="dv">1</span>,</span>
-<span id="cb972-674"><a href="#cb972-674" aria-hidden="true" tabindex="-1"></a>  <span class="at">adapt_delta =</span> <span class="fl">0.80</span>)</span>
-<span id="cb972-675"><a href="#cb972-675" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-676"><a href="#cb972-676" aria-hidden="true" tabindex="-1"></a><span class="in">```</span></span>
-<span id="cb972-677"><a href="#cb972-677" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-678"><a href="#cb972-678" aria-hidden="true" tabindex="-1"></a>:::</span>
-<span id="cb972-679"><a href="#cb972-679" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-680"><a href="#cb972-680" aria-hidden="true" tabindex="-1"></a>As you can see, it&#39;s returning a vector of 0s as the solution.</span>
-<span id="cb972-681"><a href="#cb972-681" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-682"><a href="#cb972-682" aria-hidden="true" tabindex="-1"></a><span class="fu">## Fitting ```poppk2cpt``` from ```example-models/```</span></span>
-<span id="cb972-683"><a href="#cb972-683" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-684"><a href="#cb972-684" aria-hidden="true" tabindex="-1"></a>I made a couple adjustments in ```poppk2cpt.stan``` so that it can be fit with</span>
-<span id="cb972-685"><a href="#cb972-685" aria-hidden="true" tabindex="-1"></a>an analytical solver, the linear ODE, or the general ODE.</span>
-<span id="cb972-686"><a href="#cb972-686" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-687"><a href="#cb972-687" aria-hidden="true" tabindex="-1"></a><span class="fu">### Analytical Solution</span></span>
-<span id="cb972-688"><a href="#cb972-688" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-689"><a href="#cb972-689" aria-hidden="true" tabindex="-1"></a>:::{.scrolling_500}</span>
-<span id="cb972-690"><a href="#cb972-690" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-693"><a href="#cb972-693" aria-hidden="true" tabindex="-1"></a><span class="in">```{r}</span></span>
-<span id="cb972-694"><a href="#cb972-694" aria-hidden="true" tabindex="-1"></a><span class="co">#| cache: true</span></span>
-<span id="cb972-695"><a href="#cb972-695" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-696"><a href="#cb972-696" aria-hidden="true" tabindex="-1"></a>model <span class="ot">&lt;-</span> <span class="fu">cmdstan_model</span>(</span>
-<span id="cb972-697"><a href="#cb972-697" aria-hidden="true" tabindex="-1"></a>  here<span class="sc">::</span><span class="fu">here</span>(<span class="st">&quot;M3/example_models_metrum/poppk2cpt/poppk2cpt.stan&quot;</span>))</span>
-<span id="cb972-698"><a href="#cb972-698" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-699"><a href="#cb972-699" aria-hidden="true" tabindex="-1"></a>stan_data <span class="ot">&lt;-</span> rstan<span class="sc">::</span><span class="fu">read_rdump</span>(</span>
-<span id="cb972-700"><a href="#cb972-700" aria-hidden="true" tabindex="-1"></a>  here<span class="sc">::</span><span class="fu">here</span>(<span class="st">&quot;M3/example_models_metrum/poppk2cpt/poppk2cpt.data.R&quot;</span>))</span>
-<span id="cb972-701"><a href="#cb972-701" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-702"><a href="#cb972-702" aria-hidden="true" tabindex="-1"></a>stan_data<span class="sc">$</span>solver <span class="ot">&lt;-</span> <span class="dv">1</span></span>
-<span id="cb972-703"><a href="#cb972-703" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-704"><a href="#cb972-704" aria-hidden="true" tabindex="-1"></a>fit_analytical <span class="ot">&lt;-</span> model<span class="sc">$</span><span class="fu">sample</span>(</span>
-<span id="cb972-705"><a href="#cb972-705" aria-hidden="true" tabindex="-1"></a>  <span class="at">data =</span> stan_data, </span>
-<span id="cb972-706"><a href="#cb972-706" aria-hidden="true" tabindex="-1"></a>  <span class="at">init =</span> here<span class="sc">::</span><span class="fu">here</span>(<span class="st">&quot;M3/example_models_metrum/poppk2cpt/poppk2cpt.init.R&quot;</span>), </span>
-<span id="cb972-707"><a href="#cb972-707" aria-hidden="true" tabindex="-1"></a>  <span class="at">seed =</span> <span class="dv">3191951</span>,</span>
-<span id="cb972-708"><a href="#cb972-708" aria-hidden="true" tabindex="-1"></a>  <span class="at">chains =</span> <span class="dv">4</span>,</span>
-<span id="cb972-709"><a href="#cb972-709" aria-hidden="true" tabindex="-1"></a>  <span class="at">parallel_chains =</span> <span class="dv">4</span>,</span>
-<span id="cb972-710"><a href="#cb972-710" aria-hidden="true" tabindex="-1"></a>  <span class="at">iter_warmup =</span> <span class="dv">500</span>,</span>
-<span id="cb972-711"><a href="#cb972-711" aria-hidden="true" tabindex="-1"></a>  <span class="at">iter_sampling =</span> <span class="dv">500</span>,</span>
-<span id="cb972-712"><a href="#cb972-712" aria-hidden="true" tabindex="-1"></a>  <span class="at">adapt_delta =</span> <span class="fl">0.80</span>)</span>
-<span id="cb972-713"><a href="#cb972-713" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-714"><a href="#cb972-714" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-715"><a href="#cb972-715" aria-hidden="true" tabindex="-1"></a><span class="in">```</span></span>
-<span id="cb972-716"><a href="#cb972-716" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-717"><a href="#cb972-717" aria-hidden="true" tabindex="-1"></a>:::</span>
-<span id="cb972-718"><a href="#cb972-718" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-719"><a href="#cb972-719" aria-hidden="true" tabindex="-1"></a>This one fits fine.</span>
-<span id="cb972-720"><a href="#cb972-720" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-721"><a href="#cb972-721" aria-hidden="true" tabindex="-1"></a><span class="fu">### Linear ODE Solution</span></span>
-<span id="cb972-722"><a href="#cb972-722" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-723"><a href="#cb972-723" aria-hidden="true" tabindex="-1"></a>:::{.scrolling_500}</span>
-<span id="cb972-724"><a href="#cb972-724" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-727"><a href="#cb972-727" aria-hidden="true" tabindex="-1"></a><span class="in">```{r}</span></span>
-<span id="cb972-728"><a href="#cb972-728" aria-hidden="true" tabindex="-1"></a><span class="co">#| cache: true</span></span>
-<span id="cb972-729"><a href="#cb972-729" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-730"><a href="#cb972-730" aria-hidden="true" tabindex="-1"></a>stan_data<span class="sc">$</span>solver <span class="ot">&lt;-</span> <span class="dv">2</span></span>
-<span id="cb972-731"><a href="#cb972-731" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-732"><a href="#cb972-732" aria-hidden="true" tabindex="-1"></a>fit_mat_exp <span class="ot">&lt;-</span> model<span class="sc">$</span><span class="fu">sample</span>(</span>
-<span id="cb972-733"><a href="#cb972-733" aria-hidden="true" tabindex="-1"></a>  <span class="at">data =</span> stan_data, </span>
-<span id="cb972-734"><a href="#cb972-734" aria-hidden="true" tabindex="-1"></a>  <span class="at">init =</span> here<span class="sc">::</span><span class="fu">here</span>(<span class="st">&quot;M3/example_models_metrum/poppk2cpt/poppk2cpt.init.R&quot;</span>), </span>
-<span id="cb972-735"><a href="#cb972-735" aria-hidden="true" tabindex="-1"></a>  <span class="at">seed =</span> <span class="dv">3191951</span>,</span>
-<span id="cb972-736"><a href="#cb972-736" aria-hidden="true" tabindex="-1"></a>  <span class="at">chains =</span> <span class="dv">4</span>,</span>
-<span id="cb972-737"><a href="#cb972-737" aria-hidden="true" tabindex="-1"></a>  <span class="at">parallel_chains =</span> <span class="dv">4</span>,</span>
-<span id="cb972-738"><a href="#cb972-738" aria-hidden="true" tabindex="-1"></a>  <span class="at">iter_warmup =</span> <span class="dv">1</span>,</span>
-<span id="cb972-739"><a href="#cb972-739" aria-hidden="true" tabindex="-1"></a>  <span class="at">iter_sampling =</span> <span class="dv">1</span>,</span>
-<span id="cb972-740"><a href="#cb972-740" aria-hidden="true" tabindex="-1"></a>  <span class="at">adapt_delta =</span> <span class="fl">0.80</span>)</span>
-<span id="cb972-741"><a href="#cb972-741" aria-hidden="true" tabindex="-1"></a><span class="in">```</span></span>
-<span id="cb972-742"><a href="#cb972-742" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-743"><a href="#cb972-743" aria-hidden="true" tabindex="-1"></a>:::</span>
-<span id="cb972-744"><a href="#cb972-744" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-745"><a href="#cb972-745" aria-hidden="true" tabindex="-1"></a>This one doesn&#39;t work.</span>
-<span id="cb972-746"><a href="#cb972-746" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-747"><a href="#cb972-747" aria-hidden="true" tabindex="-1"></a><span class="fu">### General ODE Solution</span></span>
-<span id="cb972-748"><a href="#cb972-748" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-749"><a href="#cb972-749" aria-hidden="true" tabindex="-1"></a>:::{.scrolling_500}</span>
-<span id="cb972-750"><a href="#cb972-750" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-753"><a href="#cb972-753" aria-hidden="true" tabindex="-1"></a><span class="in">```{r}</span></span>
-<span id="cb972-754"><a href="#cb972-754" aria-hidden="true" tabindex="-1"></a><span class="co">#| cache: true</span></span>
-<span id="cb972-755"><a href="#cb972-755" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-756"><a href="#cb972-756" aria-hidden="true" tabindex="-1"></a>stan_data<span class="sc">$</span>solver <span class="ot">&lt;-</span> <span class="dv">3</span></span>
-<span id="cb972-757"><a href="#cb972-757" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-758"><a href="#cb972-758" aria-hidden="true" tabindex="-1"></a>fit_rk45 <span class="ot">&lt;-</span> model<span class="sc">$</span><span class="fu">sample</span>(</span>
-<span id="cb972-759"><a href="#cb972-759" aria-hidden="true" tabindex="-1"></a>  <span class="at">data =</span> stan_data, </span>
-<span id="cb972-760"><a href="#cb972-760" aria-hidden="true" tabindex="-1"></a>  <span class="at">init =</span> here<span class="sc">::</span><span class="fu">here</span>(<span class="st">&quot;M3/example_models_metrum/poppk2cpt/poppk2cpt.init.R&quot;</span>), </span>
-<span id="cb972-761"><a href="#cb972-761" aria-hidden="true" tabindex="-1"></a>  <span class="at">seed =</span> <span class="dv">3191951</span>,</span>
-<span id="cb972-762"><a href="#cb972-762" aria-hidden="true" tabindex="-1"></a>  <span class="at">chains =</span> <span class="dv">4</span>,</span>
-<span id="cb972-763"><a href="#cb972-763" aria-hidden="true" tabindex="-1"></a>  <span class="at">parallel_chains =</span> <span class="dv">4</span>,</span>
-<span id="cb972-764"><a href="#cb972-764" aria-hidden="true" tabindex="-1"></a>  <span class="at">iter_warmup =</span> <span class="dv">300</span>,</span>
-<span id="cb972-765"><a href="#cb972-765" aria-hidden="true" tabindex="-1"></a>  <span class="at">iter_sampling =</span> <span class="dv">100</span>,</span>
-<span id="cb972-766"><a href="#cb972-766" aria-hidden="true" tabindex="-1"></a>  <span class="at">adapt_delta =</span> <span class="fl">0.80</span>)</span>
-<span id="cb972-767"><a href="#cb972-767" aria-hidden="true" tabindex="-1"></a><span class="in">```</span></span>
-<span id="cb972-768"><a href="#cb972-768" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-769"><a href="#cb972-769" aria-hidden="true" tabindex="-1"></a>:::</span>
-<span id="cb972-770"><a href="#cb972-770" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-771"><a href="#cb972-771" aria-hidden="true" tabindex="-1"></a>This one works.</span>
-<span id="cb972-772"><a href="#cb972-772" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-773"><a href="#cb972-773" aria-hidden="true" tabindex="-1"></a><span class="fu">## Fitting ```poppk2cpt``` from ```example-models/``` With My Own Models</span></span>
-<span id="cb972-774"><a href="#cb972-774" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-775"><a href="#cb972-775" aria-hidden="true" tabindex="-1"></a>I&#39;ve previously written this model to fit with the analytical, linear ODE, and</span>
-<span id="cb972-776"><a href="#cb972-776" aria-hidden="true" tabindex="-1"></a>general ODE solutions with proportional error, so I&#39;m just going to use that, </span>
-<span id="cb972-777"><a href="#cb972-777" aria-hidden="true" tabindex="-1"></a>but it shouldn&#39;t make a difference.</span>
-<span id="cb972-778"><a href="#cb972-778" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-779"><a href="#cb972-779" aria-hidden="true" tabindex="-1"></a><span class="fu">### Data Wrangling</span></span>
-<span id="cb972-780"><a href="#cb972-780" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-781"><a href="#cb972-781" aria-hidden="true" tabindex="-1"></a>My models should work from a NONMEM dataset in .csv format, so I&#39;ll wrangle the</span>
-<span id="cb972-782"><a href="#cb972-782" aria-hidden="true" tabindex="-1"></a>data into something like that first.</span>
-<span id="cb972-783"><a href="#cb972-783" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-786"><a href="#cb972-786" aria-hidden="true" tabindex="-1"></a><span class="in">```{r}</span></span>
-<span id="cb972-787"><a href="#cb972-787" aria-hidden="true" tabindex="-1"></a>dv <span class="ot">&lt;-</span> <span class="fu">rep</span>(<span class="cn">NA</span>, stan_data<span class="sc">$</span>nt)</span>
-<span id="cb972-788"><a href="#cb972-788" aria-hidden="true" tabindex="-1"></a>dv[stan_data<span class="sc">$</span>iObs] <span class="ot">&lt;-</span> stan_data<span class="sc">$</span>cObs</span>
-<span id="cb972-789"><a href="#cb972-789" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-790"><a href="#cb972-790" aria-hidden="true" tabindex="-1"></a>nonmem_data <span class="ot">&lt;-</span> <span class="fu">with</span>(stan_data, </span>
-<span id="cb972-791"><a href="#cb972-791" aria-hidden="true" tabindex="-1"></a>                    <span class="fu">tibble</span>(<span class="at">ID =</span> <span class="fu">rep</span>(<span class="dv">1</span><span class="sc">:</span>stan_data<span class="sc">$</span>nSubj, <span class="at">each =</span> <span class="dv">54</span>),</span>
-<span id="cb972-792"><a href="#cb972-792" aria-hidden="true" tabindex="-1"></a>                           <span class="at">amt =</span> amt, </span>
-<span id="cb972-793"><a href="#cb972-793" aria-hidden="true" tabindex="-1"></a>                           <span class="at">ii =</span> ii,</span>
-<span id="cb972-794"><a href="#cb972-794" aria-hidden="true" tabindex="-1"></a>                           <span class="at">addl =</span> addl,</span>
-<span id="cb972-795"><a href="#cb972-795" aria-hidden="true" tabindex="-1"></a>                           <span class="at">rate =</span> rate,</span>
-<span id="cb972-796"><a href="#cb972-796" aria-hidden="true" tabindex="-1"></a>                           <span class="at">cmt =</span> cmt,</span>
-<span id="cb972-797"><a href="#cb972-797" aria-hidden="true" tabindex="-1"></a>                           <span class="at">evid =</span> evid, </span>
-<span id="cb972-798"><a href="#cb972-798" aria-hidden="true" tabindex="-1"></a>                           <span class="at">ss =</span> ss,</span>
-<span id="cb972-799"><a href="#cb972-799" aria-hidden="true" tabindex="-1"></a>                           <span class="at">lloq =</span> <span class="dv">0</span>,</span>
-<span id="cb972-800"><a href="#cb972-800" aria-hidden="true" tabindex="-1"></a>                           <span class="at">bloq =</span> <span class="dv">0</span>,</span>
-<span id="cb972-801"><a href="#cb972-801" aria-hidden="true" tabindex="-1"></a>                           <span class="at">time =</span> time,</span>
-<span id="cb972-802"><a href="#cb972-802" aria-hidden="true" tabindex="-1"></a>                           <span class="at">DV =</span> dv)) <span class="sc">%&gt;%</span> </span>
-<span id="cb972-803"><a href="#cb972-803" aria-hidden="true" tabindex="-1"></a>  <span class="fu">mutate</span>(<span class="at">DV =</span> <span class="fu">if_else</span>(<span class="fu">is.na</span>(DV), <span class="dv">5555555</span>, DV),    <span class="co"># This value can be anything except NA. It&#39;ll be indexed away </span></span>
-<span id="cb972-804"><a href="#cb972-804" aria-hidden="true" tabindex="-1"></a>         <span class="at">bloq =</span> <span class="fu">if_else</span>(<span class="fu">is.na</span>(bloq), <span class="sc">-</span><span class="dv">999</span>, bloq)) <span class="co"># This value can be anything except NA. It&#39;ll be indexed away </span></span>
-<span id="cb972-805"><a href="#cb972-805" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-806"><a href="#cb972-806" aria-hidden="true" tabindex="-1"></a>n_subjects <span class="ot">&lt;-</span> nonmem_data <span class="sc">%&gt;%</span>  <span class="co"># number of individuals</span></span>
-<span id="cb972-807"><a href="#cb972-807" aria-hidden="true" tabindex="-1"></a>  <span class="fu">distinct</span>(ID) <span class="sc">%&gt;%</span></span>
-<span id="cb972-808"><a href="#cb972-808" aria-hidden="true" tabindex="-1"></a>  <span class="fu">count</span>() <span class="sc">%&gt;%</span></span>
-<span id="cb972-809"><a href="#cb972-809" aria-hidden="true" tabindex="-1"></a>  <span class="fu">deframe</span>()</span>
-<span id="cb972-810"><a href="#cb972-810" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-811"><a href="#cb972-811" aria-hidden="true" tabindex="-1"></a>n_total <span class="ot">&lt;-</span> <span class="fu">nrow</span>(nonmem_data)   <span class="co"># total number of records</span></span>
-<span id="cb972-812"><a href="#cb972-812" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-813"><a href="#cb972-813" aria-hidden="true" tabindex="-1"></a>i_obs <span class="ot">&lt;-</span> nonmem_data <span class="sc">%&gt;%</span></span>
-<span id="cb972-814"><a href="#cb972-814" aria-hidden="true" tabindex="-1"></a>  <span class="fu">mutate</span>(<span class="at">row_num =</span> <span class="dv">1</span><span class="sc">:</span><span class="fu">n</span>()) <span class="sc">%&gt;%</span></span>
-<span id="cb972-815"><a href="#cb972-815" aria-hidden="true" tabindex="-1"></a>  <span class="fu">filter</span>(evid <span class="sc">==</span> <span class="dv">0</span>) <span class="sc">%&gt;%</span></span>
-<span id="cb972-816"><a href="#cb972-816" aria-hidden="true" tabindex="-1"></a>  <span class="fu">select</span>(row_num) <span class="sc">%&gt;%</span></span>
-<span id="cb972-817"><a href="#cb972-817" aria-hidden="true" tabindex="-1"></a>  <span class="fu">deframe</span>()</span>
-<span id="cb972-818"><a href="#cb972-818" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-819"><a href="#cb972-819" aria-hidden="true" tabindex="-1"></a>n_obs <span class="ot">&lt;-</span> <span class="fu">length</span>(i_obs)</span>
-<span id="cb972-820"><a href="#cb972-820" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-821"><a href="#cb972-821" aria-hidden="true" tabindex="-1"></a>subj_start <span class="ot">&lt;-</span> nonmem_data <span class="sc">%&gt;%</span></span>
-<span id="cb972-822"><a href="#cb972-822" aria-hidden="true" tabindex="-1"></a>  <span class="fu">mutate</span>(<span class="at">row_num =</span> <span class="dv">1</span><span class="sc">:</span><span class="fu">n</span>()) <span class="sc">%&gt;%</span></span>
-<span id="cb972-823"><a href="#cb972-823" aria-hidden="true" tabindex="-1"></a>  <span class="fu">group_by</span>(ID) <span class="sc">%&gt;%</span></span>
-<span id="cb972-824"><a href="#cb972-824" aria-hidden="true" tabindex="-1"></a>  <span class="fu">slice_head</span>(<span class="at">n =</span> <span class="dv">1</span>) <span class="sc">%&gt;%</span></span>
-<span id="cb972-825"><a href="#cb972-825" aria-hidden="true" tabindex="-1"></a>  <span class="fu">ungroup</span>() <span class="sc">%&gt;%</span></span>
-<span id="cb972-826"><a href="#cb972-826" aria-hidden="true" tabindex="-1"></a>  <span class="fu">select</span>(row_num) <span class="sc">%&gt;%</span></span>
-<span id="cb972-827"><a href="#cb972-827" aria-hidden="true" tabindex="-1"></a>  <span class="fu">deframe</span>()</span>
-<span id="cb972-828"><a href="#cb972-828" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-829"><a href="#cb972-829" aria-hidden="true" tabindex="-1"></a>subj_end <span class="ot">&lt;-</span> <span class="fu">c</span>(subj_start[<span class="sc">-</span><span class="dv">1</span>] <span class="sc">-</span> <span class="dv">1</span>, n_total)</span>
-<span id="cb972-830"><a href="#cb972-830" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-831"><a href="#cb972-831" aria-hidden="true" tabindex="-1"></a>stan_data <span class="ot">&lt;-</span> <span class="fu">list</span>(<span class="at">n_subjects =</span> n_subjects,</span>
-<span id="cb972-832"><a href="#cb972-832" aria-hidden="true" tabindex="-1"></a>                  <span class="at">n_total =</span> n_total,</span>
-<span id="cb972-833"><a href="#cb972-833" aria-hidden="true" tabindex="-1"></a>                  <span class="at">n_obs =</span> n_obs,</span>
-<span id="cb972-834"><a href="#cb972-834" aria-hidden="true" tabindex="-1"></a>                  <span class="at">i_obs =</span> i_obs,</span>
-<span id="cb972-835"><a href="#cb972-835" aria-hidden="true" tabindex="-1"></a>                  <span class="at">ID =</span> nonmem_data<span class="sc">$</span>ID,</span>
-<span id="cb972-836"><a href="#cb972-836" aria-hidden="true" tabindex="-1"></a>                  <span class="at">amt =</span> nonmem_data<span class="sc">$</span>amt,</span>
-<span id="cb972-837"><a href="#cb972-837" aria-hidden="true" tabindex="-1"></a>                  <span class="at">cmt =</span> nonmem_data<span class="sc">$</span>cmt,</span>
-<span id="cb972-838"><a href="#cb972-838" aria-hidden="true" tabindex="-1"></a>                  <span class="at">evid =</span> nonmem_data<span class="sc">$</span>evid,</span>
-<span id="cb972-839"><a href="#cb972-839" aria-hidden="true" tabindex="-1"></a>                  <span class="at">rate =</span> nonmem_data<span class="sc">$</span>rate,</span>
-<span id="cb972-840"><a href="#cb972-840" aria-hidden="true" tabindex="-1"></a>                  <span class="at">ii =</span> nonmem_data<span class="sc">$</span>ii,</span>
-<span id="cb972-841"><a href="#cb972-841" aria-hidden="true" tabindex="-1"></a>                  <span class="at">addl =</span> nonmem_data<span class="sc">$</span>addl,</span>
-<span id="cb972-842"><a href="#cb972-842" aria-hidden="true" tabindex="-1"></a>                  <span class="at">ss =</span> nonmem_data<span class="sc">$</span>ss,</span>
-<span id="cb972-843"><a href="#cb972-843" aria-hidden="true" tabindex="-1"></a>                  <span class="at">time =</span> nonmem_data<span class="sc">$</span>time,</span>
-<span id="cb972-844"><a href="#cb972-844" aria-hidden="true" tabindex="-1"></a>                  <span class="at">dv =</span> nonmem_data<span class="sc">$</span>DV,</span>
-<span id="cb972-845"><a href="#cb972-845" aria-hidden="true" tabindex="-1"></a>                  <span class="at">subj_start =</span> subj_start,</span>
-<span id="cb972-846"><a href="#cb972-846" aria-hidden="true" tabindex="-1"></a>                  <span class="at">subj_end =</span> subj_end,</span>
-<span id="cb972-847"><a href="#cb972-847" aria-hidden="true" tabindex="-1"></a>                  <span class="at">lloq =</span> nonmem_data<span class="sc">$</span>lloq,</span>
-<span id="cb972-848"><a href="#cb972-848" aria-hidden="true" tabindex="-1"></a>                  <span class="at">bloq =</span> nonmem_data<span class="sc">$</span>bloq,</span>
-<span id="cb972-849"><a href="#cb972-849" aria-hidden="true" tabindex="-1"></a>                  <span class="at">location_tvcl =</span> <span class="fl">0.75</span>,</span>
-<span id="cb972-850"><a href="#cb972-850" aria-hidden="true" tabindex="-1"></a>                  <span class="at">location_tvvc =</span> <span class="dv">18</span>,</span>
-<span id="cb972-851"><a href="#cb972-851" aria-hidden="true" tabindex="-1"></a>                  <span class="at">location_tvq =</span> <span class="dv">3</span>,</span>
-<span id="cb972-852"><a href="#cb972-852" aria-hidden="true" tabindex="-1"></a>                  <span class="at">location_tvvp =</span> <span class="dv">35</span>,</span>
-<span id="cb972-853"><a href="#cb972-853" aria-hidden="true" tabindex="-1"></a>                  <span class="at">location_tvka =</span> <span class="fl">0.8</span>,</span>
-<span id="cb972-854"><a href="#cb972-854" aria-hidden="true" tabindex="-1"></a>                  <span class="at">scale_tvcl =</span> <span class="dv">1</span>,</span>
-<span id="cb972-855"><a href="#cb972-855" aria-hidden="true" tabindex="-1"></a>                  <span class="at">scale_tvvc =</span> <span class="dv">1</span>,</span>
-<span id="cb972-856"><a href="#cb972-856" aria-hidden="true" tabindex="-1"></a>                  <span class="at">scale_tvq =</span> <span class="dv">1</span>,</span>
-<span id="cb972-857"><a href="#cb972-857" aria-hidden="true" tabindex="-1"></a>                  <span class="at">scale_tvvp =</span> <span class="dv">1</span>,</span>
-<span id="cb972-858"><a href="#cb972-858" aria-hidden="true" tabindex="-1"></a>                  <span class="at">scale_tvka =</span> <span class="dv">1</span>,</span>
-<span id="cb972-859"><a href="#cb972-859" aria-hidden="true" tabindex="-1"></a>                  <span class="at">scale_omega_cl =</span> <span class="fl">0.4</span>,</span>
-<span id="cb972-860"><a href="#cb972-860" aria-hidden="true" tabindex="-1"></a>                  <span class="at">scale_omega_vc =</span> <span class="fl">0.4</span>,</span>
-<span id="cb972-861"><a href="#cb972-861" aria-hidden="true" tabindex="-1"></a>                  <span class="at">scale_omega_q =</span> <span class="fl">0.4</span>,</span>
-<span id="cb972-862"><a href="#cb972-862" aria-hidden="true" tabindex="-1"></a>                  <span class="at">scale_omega_vp =</span> <span class="fl">0.4</span>,</span>
-<span id="cb972-863"><a href="#cb972-863" aria-hidden="true" tabindex="-1"></a>                  <span class="at">scale_omega_ka =</span> <span class="fl">0.4</span>,</span>
-<span id="cb972-864"><a href="#cb972-864" aria-hidden="true" tabindex="-1"></a>                  <span class="at">lkj_df_omega =</span> <span class="dv">2</span>,</span>
-<span id="cb972-865"><a href="#cb972-865" aria-hidden="true" tabindex="-1"></a>                  <span class="at">scale_sigma_p =</span> <span class="fl">0.5</span>,</span>
-<span id="cb972-866"><a href="#cb972-866" aria-hidden="true" tabindex="-1"></a>                  <span class="at">prior_only =</span> <span class="dv">0</span>)</span>
-<span id="cb972-867"><a href="#cb972-867" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-868"><a href="#cb972-868" aria-hidden="true" tabindex="-1"></a>model <span class="ot">&lt;-</span> <span class="fu">cmdstan_model</span>(</span>
-<span id="cb972-869"><a href="#cb972-869" aria-hidden="true" tabindex="-1"></a>  here<span class="sc">::</span><span class="fu">here</span>(<span class="st">&quot;M3/depot_2cmt_linear/Stan/Fit/depot_2cmt_prop_all_solvers.stan&quot;</span>),</span>
-<span id="cb972-870"><a href="#cb972-870" aria-hidden="true" tabindex="-1"></a>  <span class="at">cpp_options =</span> <span class="fu">list</span>(<span class="at">stan_threads =</span> <span class="cn">TRUE</span>))</span>
-<span id="cb972-871"><a href="#cb972-871" aria-hidden="true" tabindex="-1"></a><span class="in">```</span></span>
-<span id="cb972-872"><a href="#cb972-872" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-873"><a href="#cb972-873" aria-hidden="true" tabindex="-1"></a><span class="fu">### Analytical Solution</span></span>
-<span id="cb972-874"><a href="#cb972-874" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-875"><a href="#cb972-875" aria-hidden="true" tabindex="-1"></a>:::{.scrolling_500}</span>
-<span id="cb972-876"><a href="#cb972-876" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-879"><a href="#cb972-879" aria-hidden="true" tabindex="-1"></a><span class="in">```{r}</span></span>
-<span id="cb972-880"><a href="#cb972-880" aria-hidden="true" tabindex="-1"></a><span class="co">#| cache: true</span></span>
-<span id="cb972-881"><a href="#cb972-881" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-882"><a href="#cb972-882" aria-hidden="true" tabindex="-1"></a>stan_data<span class="sc">$</span>solver <span class="ot">&lt;-</span> <span class="dv">1</span></span>
-<span id="cb972-883"><a href="#cb972-883" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-884"><a href="#cb972-884" aria-hidden="true" tabindex="-1"></a>fit <span class="ot">&lt;-</span> model<span class="sc">$</span><span class="fu">sample</span>(<span class="at">data =</span> stan_data,</span>
-<span id="cb972-885"><a href="#cb972-885" aria-hidden="true" tabindex="-1"></a>                    <span class="at">seed =</span> <span class="dv">11235</span>,</span>
-<span id="cb972-886"><a href="#cb972-886" aria-hidden="true" tabindex="-1"></a>                    <span class="at">chains =</span> <span class="dv">4</span>,</span>
-<span id="cb972-887"><a href="#cb972-887" aria-hidden="true" tabindex="-1"></a>                    <span class="at">parallel_chains =</span> <span class="dv">4</span>,</span>
-<span id="cb972-888"><a href="#cb972-888" aria-hidden="true" tabindex="-1"></a>                    <span class="at">threads_per_chain =</span> parallel<span class="sc">::</span><span class="fu">detectCores</span>()<span class="sc">/</span><span class="dv">4</span>,</span>
-<span id="cb972-889"><a href="#cb972-889" aria-hidden="true" tabindex="-1"></a>                    <span class="at">iter_warmup =</span> <span class="dv">500</span>,</span>
-<span id="cb972-890"><a href="#cb972-890" aria-hidden="true" tabindex="-1"></a>                    <span class="at">iter_sampling =</span> <span class="dv">1000</span>,</span>
-<span id="cb972-891"><a href="#cb972-891" aria-hidden="true" tabindex="-1"></a>                    <span class="at">adapt_delta =</span> <span class="fl">0.8</span>,</span>
-<span id="cb972-892"><a href="#cb972-892" aria-hidden="true" tabindex="-1"></a>                    <span class="at">refresh =</span> <span class="dv">500</span>,</span>
-<span id="cb972-893"><a href="#cb972-893" aria-hidden="true" tabindex="-1"></a>                    <span class="at">max_treedepth =</span> <span class="dv">10</span>,</span>
-<span id="cb972-894"><a href="#cb972-894" aria-hidden="true" tabindex="-1"></a>                    <span class="at">init =</span> <span class="cf">function</span>() <span class="fu">list</span>(<span class="at">TVCL =</span> <span class="fu">rlnorm</span>(<span class="dv">1</span>, <span class="fu">log</span>(<span class="dv">5</span>), <span class="fl">0.1</span>),</span>
-<span id="cb972-895"><a href="#cb972-895" aria-hidden="true" tabindex="-1"></a>                                           <span class="at">TVVC =</span> <span class="fu">rlnorm</span>(<span class="dv">1</span>, <span class="fu">log</span>(<span class="dv">20</span>), <span class="fl">0.1</span>),</span>
-<span id="cb972-896"><a href="#cb972-896" aria-hidden="true" tabindex="-1"></a>                                           <span class="at">TVQ =</span> <span class="fu">rlnorm</span>(<span class="dv">1</span>, <span class="fu">log</span>(<span class="dv">7</span>), <span class="fl">0.1</span>),</span>
-<span id="cb972-897"><a href="#cb972-897" aria-hidden="true" tabindex="-1"></a>                                           <span class="at">TVVP =</span> <span class="fu">rlnorm</span>(<span class="dv">1</span>, <span class="fu">log</span>(<span class="dv">70</span>), <span class="fl">0.1</span>),</span>
-<span id="cb972-898"><a href="#cb972-898" aria-hidden="true" tabindex="-1"></a>                                           <span class="at">TVKA =</span> <span class="fu">rlnorm</span>(<span class="dv">1</span>, <span class="fu">log</span>(<span class="fl">1.2</span>), <span class="fl">0.1</span>),</span>
-<span id="cb972-899"><a href="#cb972-899" aria-hidden="true" tabindex="-1"></a>                                           <span class="at">omega =</span> <span class="fu">rlnorm</span>(<span class="dv">5</span>, <span class="fu">log</span>(<span class="fl">0.1</span>), <span class="fl">0.1</span>),</span>
-<span id="cb972-900"><a href="#cb972-900" aria-hidden="true" tabindex="-1"></a>                                           <span class="at">sigma_p =</span> <span class="fu">rlnorm</span>(<span class="dv">1</span>, <span class="fu">log</span>(<span class="fl">0.1</span>), <span class="fl">0.1</span>)))</span>
-<span id="cb972-901"><a href="#cb972-901" aria-hidden="true" tabindex="-1"></a><span class="in">```</span></span>
-<span id="cb972-902"><a href="#cb972-902" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-903"><a href="#cb972-903" aria-hidden="true" tabindex="-1"></a>:::</span>
-<span id="cb972-904"><a href="#cb972-904" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-905"><a href="#cb972-905" aria-hidden="true" tabindex="-1"></a>Doesn&#39;t work.</span>
-<span id="cb972-906"><a href="#cb972-906" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-907"><a href="#cb972-907" aria-hidden="true" tabindex="-1"></a><span class="fu">### Linear ODE</span></span>
-<span id="cb972-908"><a href="#cb972-908" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-909"><a href="#cb972-909" aria-hidden="true" tabindex="-1"></a>:::{.scrolling_500}</span>
-<span id="cb972-910"><a href="#cb972-910" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-913"><a href="#cb972-913" aria-hidden="true" tabindex="-1"></a><span class="in">```{r}</span></span>
-<span id="cb972-914"><a href="#cb972-914" aria-hidden="true" tabindex="-1"></a><span class="co">#| cache: true</span></span>
-<span id="cb972-915"><a href="#cb972-915" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-916"><a href="#cb972-916" aria-hidden="true" tabindex="-1"></a>stan_data<span class="sc">$</span>solver <span class="ot">&lt;-</span> <span class="dv">2</span></span>
-<span id="cb972-917"><a href="#cb972-917" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-918"><a href="#cb972-918" aria-hidden="true" tabindex="-1"></a>fit_mat_exp_cd <span class="ot">&lt;-</span> model<span class="sc">$</span><span class="fu">sample</span>(</span>
-<span id="cb972-919"><a href="#cb972-919" aria-hidden="true" tabindex="-1"></a>  <span class="at">data =</span> stan_data,</span>
-<span id="cb972-920"><a href="#cb972-920" aria-hidden="true" tabindex="-1"></a>  <span class="at">seed =</span> <span class="dv">11235</span>,</span>
-<span id="cb972-921"><a href="#cb972-921" aria-hidden="true" tabindex="-1"></a>  <span class="at">chains =</span> <span class="dv">4</span>,</span>
-<span id="cb972-922"><a href="#cb972-922" aria-hidden="true" tabindex="-1"></a>  <span class="at">parallel_chains =</span> <span class="dv">4</span>,</span>
-<span id="cb972-923"><a href="#cb972-923" aria-hidden="true" tabindex="-1"></a>  <span class="at">threads_per_chain =</span> parallel<span class="sc">::</span><span class="fu">detectCores</span>()<span class="sc">/</span><span class="dv">4</span>,</span>
-<span id="cb972-924"><a href="#cb972-924" aria-hidden="true" tabindex="-1"></a>  <span class="at">iter_warmup =</span> <span class="dv">500</span>,</span>
-<span id="cb972-925"><a href="#cb972-925" aria-hidden="true" tabindex="-1"></a>  <span class="at">iter_sampling =</span> <span class="dv">1000</span>,</span>
-<span id="cb972-926"><a href="#cb972-926" aria-hidden="true" tabindex="-1"></a>  <span class="at">adapt_delta =</span> <span class="fl">0.8</span>,</span>
-<span id="cb972-927"><a href="#cb972-927" aria-hidden="true" tabindex="-1"></a>  <span class="at">refresh =</span> <span class="dv">500</span>,</span>
-<span id="cb972-928"><a href="#cb972-928" aria-hidden="true" tabindex="-1"></a>  <span class="at">max_treedepth =</span> <span class="dv">10</span>,</span>
-<span id="cb972-929"><a href="#cb972-929" aria-hidden="true" tabindex="-1"></a>  <span class="at">init =</span> <span class="cf">function</span>() <span class="fu">list</span>(<span class="at">TVCL =</span> <span class="fu">rlnorm</span>(<span class="dv">1</span>, <span class="fu">log</span>(<span class="dv">5</span>), <span class="fl">0.1</span>),</span>
-<span id="cb972-930"><a href="#cb972-930" aria-hidden="true" tabindex="-1"></a>                         <span class="at">TVVC =</span> <span class="fu">rlnorm</span>(<span class="dv">1</span>, <span class="fu">log</span>(<span class="dv">20</span>), <span class="fl">0.1</span>),</span>
-<span id="cb972-931"><a href="#cb972-931" aria-hidden="true" tabindex="-1"></a>                         <span class="at">TVQ =</span> <span class="fu">rlnorm</span>(<span class="dv">1</span>, <span class="fu">log</span>(<span class="dv">7</span>), <span class="fl">0.1</span>),</span>
-<span id="cb972-932"><a href="#cb972-932" aria-hidden="true" tabindex="-1"></a>                         <span class="at">TVVP =</span> <span class="fu">rlnorm</span>(<span class="dv">1</span>, <span class="fu">log</span>(<span class="dv">70</span>), <span class="fl">0.1</span>),</span>
-<span id="cb972-933"><a href="#cb972-933" aria-hidden="true" tabindex="-1"></a>                         <span class="at">TVKA =</span> <span class="fu">rlnorm</span>(<span class="dv">1</span>, <span class="fu">log</span>(<span class="fl">1.2</span>), <span class="fl">0.1</span>),</span>
-<span id="cb972-934"><a href="#cb972-934" aria-hidden="true" tabindex="-1"></a>                         <span class="at">omega =</span> <span class="fu">rlnorm</span>(<span class="dv">5</span>, <span class="fu">log</span>(<span class="fl">0.1</span>), <span class="fl">0.1</span>),</span>
-<span id="cb972-935"><a href="#cb972-935" aria-hidden="true" tabindex="-1"></a>                         <span class="at">sigma_p =</span> <span class="fu">rlnorm</span>(<span class="dv">1</span>, <span class="fu">log</span>(<span class="fl">0.1</span>), <span class="fl">0.1</span>)))</span>
-<span id="cb972-936"><a href="#cb972-936" aria-hidden="true" tabindex="-1"></a><span class="in">```</span></span>
-<span id="cb972-937"><a href="#cb972-937" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-938"><a href="#cb972-938" aria-hidden="true" tabindex="-1"></a>:::</span>
-<span id="cb972-939"><a href="#cb972-939" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-940"><a href="#cb972-940" aria-hidden="true" tabindex="-1"></a>This one works fine.</span>
-<span id="cb972-941"><a href="#cb972-941" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-942"><a href="#cb972-942" aria-hidden="true" tabindex="-1"></a><span class="fu">### General ODE</span></span>
-<span id="cb972-943"><a href="#cb972-943" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-944"><a href="#cb972-944" aria-hidden="true" tabindex="-1"></a>:::{.scrolling_500}</span>
-<span id="cb972-945"><a href="#cb972-945" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-948"><a href="#cb972-948" aria-hidden="true" tabindex="-1"></a><span class="in">```{r}</span></span>
-<span id="cb972-949"><a href="#cb972-949" aria-hidden="true" tabindex="-1"></a><span class="co">#| cache: true</span></span>
-<span id="cb972-950"><a href="#cb972-950" aria-hidden="true" tabindex="-1"></a> </span>
-<span id="cb972-951"><a href="#cb972-951" aria-hidden="true" tabindex="-1"></a>stan_data<span class="sc">$</span>solver <span class="ot">&lt;-</span> <span class="dv">3</span></span>
-<span id="cb972-952"><a href="#cb972-952" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-953"><a href="#cb972-953" aria-hidden="true" tabindex="-1"></a>fit_rk45_cd <span class="ot">&lt;-</span> model<span class="sc">$</span><span class="fu">sample</span>(</span>
-<span id="cb972-954"><a href="#cb972-954" aria-hidden="true" tabindex="-1"></a>  <span class="at">data =</span> stan_data,</span>
-<span id="cb972-955"><a href="#cb972-955" aria-hidden="true" tabindex="-1"></a>  <span class="at">seed =</span> <span class="dv">11235</span>,</span>
-<span id="cb972-956"><a href="#cb972-956" aria-hidden="true" tabindex="-1"></a>  <span class="at">chains =</span> <span class="dv">4</span>,</span>
-<span id="cb972-957"><a href="#cb972-957" aria-hidden="true" tabindex="-1"></a>  <span class="at">parallel_chains =</span> <span class="dv">4</span>,</span>
-<span id="cb972-958"><a href="#cb972-958" aria-hidden="true" tabindex="-1"></a>  <span class="at">threads_per_chain =</span> parallel<span class="sc">::</span><span class="fu">detectCores</span>()<span class="sc">/</span><span class="dv">4</span>,</span>
-<span id="cb972-959"><a href="#cb972-959" aria-hidden="true" tabindex="-1"></a>  <span class="at">iter_warmup =</span> <span class="dv">300</span>,</span>
-<span id="cb972-960"><a href="#cb972-960" aria-hidden="true" tabindex="-1"></a>  <span class="at">iter_sampling =</span> <span class="dv">100</span>,</span>
-<span id="cb972-961"><a href="#cb972-961" aria-hidden="true" tabindex="-1"></a>  <span class="at">adapt_delta =</span> <span class="fl">0.8</span>,</span>
-<span id="cb972-962"><a href="#cb972-962" aria-hidden="true" tabindex="-1"></a>  <span class="at">refresh =</span> <span class="dv">0</span>,</span>
-<span id="cb972-963"><a href="#cb972-963" aria-hidden="true" tabindex="-1"></a>  <span class="at">max_treedepth =</span> <span class="dv">10</span>,</span>
-<span id="cb972-964"><a href="#cb972-964" aria-hidden="true" tabindex="-1"></a>  <span class="at">init =</span> <span class="cf">function</span>() <span class="fu">list</span>(<span class="at">TVCL =</span> <span class="fu">rlnorm</span>(<span class="dv">1</span>, <span class="fu">log</span>(<span class="dv">5</span>), <span class="fl">0.1</span>),</span>
-<span id="cb972-965"><a href="#cb972-965" aria-hidden="true" tabindex="-1"></a>                         <span class="at">TVVC =</span> <span class="fu">rlnorm</span>(<span class="dv">1</span>, <span class="fu">log</span>(<span class="dv">20</span>), <span class="fl">0.1</span>),</span>
-<span id="cb972-966"><a href="#cb972-966" aria-hidden="true" tabindex="-1"></a>                         <span class="at">TVQ =</span> <span class="fu">rlnorm</span>(<span class="dv">1</span>, <span class="fu">log</span>(<span class="dv">7</span>), <span class="fl">0.1</span>),</span>
-<span id="cb972-967"><a href="#cb972-967" aria-hidden="true" tabindex="-1"></a>                         <span class="at">TVVP =</span> <span class="fu">rlnorm</span>(<span class="dv">1</span>, <span class="fu">log</span>(<span class="dv">70</span>), <span class="fl">0.1</span>),</span>
-<span id="cb972-968"><a href="#cb972-968" aria-hidden="true" tabindex="-1"></a>                         <span class="at">TVKA =</span> <span class="fu">rlnorm</span>(<span class="dv">1</span>, <span class="fu">log</span>(<span class="fl">1.2</span>), <span class="fl">0.1</span>),</span>
-<span id="cb972-969"><a href="#cb972-969" aria-hidden="true" tabindex="-1"></a>                         <span class="at">omega =</span> <span class="fu">rlnorm</span>(<span class="dv">5</span>, <span class="fu">log</span>(<span class="fl">0.1</span>), <span class="fl">0.1</span>),</span>
-<span id="cb972-970"><a href="#cb972-970" aria-hidden="true" tabindex="-1"></a>                         <span class="at">sigma_p =</span> <span class="fu">rlnorm</span>(<span class="dv">1</span>, <span class="fu">log</span>(<span class="fl">0.1</span>), <span class="fl">0.1</span>)))</span>
-<span id="cb972-971"><a href="#cb972-971" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-972"><a href="#cb972-972" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-973"><a href="#cb972-973" aria-hidden="true" tabindex="-1"></a><span class="in">```</span></span>
-<span id="cb972-974"><a href="#cb972-974" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-975"><a href="#cb972-975" aria-hidden="true" tabindex="-1"></a>:::</span>
-<span id="cb972-976"><a href="#cb972-976" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-977"><a href="#cb972-977" aria-hidden="true" tabindex="-1"></a>This one works fine.</span>
-<span id="cb972-978"><a href="#cb972-978" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-979"><a href="#cb972-979" aria-hidden="true" tabindex="-1"></a><span class="fu"># Summary</span></span>
-<span id="cb972-980"><a href="#cb972-980" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-981"><a href="#cb972-981" aria-hidden="true" tabindex="-1"></a>Basically, I haven&#39;t figured out if there&#39;s any rhyme or reason to when the </span>
-<span id="cb972-982"><a href="#cb972-982" aria-hidden="true" tabindex="-1"></a>analytical, linear ODE, or general ODE solution works or not. </span>
-<span id="cb972-983"><a href="#cb972-983" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-984"><a href="#cb972-984" aria-hidden="true" tabindex="-1"></a><span class="fu"># Session Info</span></span>
-<span id="cb972-985"><a href="#cb972-985" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-988"><a href="#cb972-988" aria-hidden="true" tabindex="-1"></a><span class="in">```{r}</span></span>
-<span id="cb972-989"><a href="#cb972-989" aria-hidden="true" tabindex="-1"></a><span class="fu">sessionInfo</span>()</span>
-<span id="cb972-990"><a href="#cb972-990" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb972-991"><a href="#cb972-991" aria-hidden="true" tabindex="-1"></a><span class="in">```</span></span>
+<div class="sourceCode" id="cb2945" data-shortcodes="false"><pre class="sourceCode markdown code-with-copy"><code class="sourceCode markdown"><span id="cb2945-1"><a href="#cb2945-1" aria-hidden="true" tabindex="-1"></a><span class="co">---</span></span>
+<span id="cb2945-2"><a href="#cb2945-2" aria-hidden="true" tabindex="-1"></a><span class="an">title:</span><span class="co"> &quot;Torsten Testing on an M2&quot;</span></span>
+<span id="cb2945-3"><a href="#cb2945-3" aria-hidden="true" tabindex="-1"></a><span class="an">author:</span><span class="co"> &quot;Casey Davis&quot;</span></span>
+<span id="cb2945-4"><a href="#cb2945-4" aria-hidden="true" tabindex="-1"></a><span class="an">date:</span><span class="co"> &quot;`r format(Sys.time(), &#39;%B %d, %Y&#39;)`&quot;</span></span>
+<span id="cb2945-5"><a href="#cb2945-5" aria-hidden="true" tabindex="-1"></a><span class="an">format:</span></span>
+<span id="cb2945-6"><a href="#cb2945-6" aria-hidden="true" tabindex="-1"></a><span class="co">  html:</span></span>
+<span id="cb2945-7"><a href="#cb2945-7" aria-hidden="true" tabindex="-1"></a><span class="co">    code-fold: true  </span></span>
+<span id="cb2945-8"><a href="#cb2945-8" aria-hidden="true" tabindex="-1"></a><span class="co">    code-summary: &quot;Code&quot;</span></span>
+<span id="cb2945-9"><a href="#cb2945-9" aria-hidden="true" tabindex="-1"></a><span class="co">    code-tools: true</span></span>
+<span id="cb2945-10"><a href="#cb2945-10" aria-hidden="true" tabindex="-1"></a><span class="co">    number-sections: true</span></span>
+<span id="cb2945-11"><a href="#cb2945-11" aria-hidden="true" tabindex="-1"></a><span class="co">    toc: true</span></span>
+<span id="cb2945-12"><a href="#cb2945-12" aria-hidden="true" tabindex="-1"></a><span class="co">    toc-depth: 5</span></span>
+<span id="cb2945-13"><a href="#cb2945-13" aria-hidden="true" tabindex="-1"></a><span class="co">    embed-resources: true  </span></span>
+<span id="cb2945-14"><a href="#cb2945-14" aria-hidden="true" tabindex="-1"></a><span class="an">editor_options:</span><span class="co"> </span></span>
+<span id="cb2945-15"><a href="#cb2945-15" aria-hidden="true" tabindex="-1"></a><span class="co">  chunk_output_type: console</span></span>
+<span id="cb2945-16"><a href="#cb2945-16" aria-hidden="true" tabindex="-1"></a><span class="co">---</span></span>
+<span id="cb2945-17"><a href="#cb2945-17" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-18"><a href="#cb2945-18" aria-hidden="true" tabindex="-1"></a><span class="in">```{css, echo = FALSE}</span></span>
+<span id="cb2945-19"><a href="#cb2945-19" aria-hidden="true" tabindex="-1"></a><span class="op">.</span><span class="fu">scrolling_500</span> <span class="op">{</span></span>
+<span id="cb2945-20"><a href="#cb2945-20" aria-hidden="true" tabindex="-1"></a>  max<span class="op">-</span>height<span class="op">:</span> 500px<span class="op">;</span></span>
+<span id="cb2945-21"><a href="#cb2945-21" aria-hidden="true" tabindex="-1"></a>  overflow<span class="op">-</span>y<span class="op">:</span> auto<span class="op">;</span></span>
+<span id="cb2945-22"><a href="#cb2945-22" aria-hidden="true" tabindex="-1"></a><span class="op">}</span></span>
+<span id="cb2945-23"><a href="#cb2945-23" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-24"><a href="#cb2945-24" aria-hidden="true" tabindex="-1"></a><span class="op">.</span><span class="fu">scrolling_700</span> <span class="op">{</span></span>
+<span id="cb2945-25"><a href="#cb2945-25" aria-hidden="true" tabindex="-1"></a>  max<span class="op">-</span>height<span class="op">:</span> 700px<span class="op">;</span></span>
+<span id="cb2945-26"><a href="#cb2945-26" aria-hidden="true" tabindex="-1"></a>  overflow<span class="op">-</span>y<span class="op">:</span> auto<span class="op">;</span></span>
+<span id="cb2945-27"><a href="#cb2945-27" aria-hidden="true" tabindex="-1"></a><span class="op">}</span></span>
+<span id="cb2945-28"><a href="#cb2945-28" aria-hidden="true" tabindex="-1"></a><span class="in">```</span></span>
+<span id="cb2945-29"><a href="#cb2945-29" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-32"><a href="#cb2945-32" aria-hidden="true" tabindex="-1"></a><span class="in">```{r}</span></span>
+<span id="cb2945-33"><a href="#cb2945-33" aria-hidden="true" tabindex="-1"></a><span class="co">#| label: package-load</span></span>
+<span id="cb2945-34"><a href="#cb2945-34" aria-hidden="true" tabindex="-1"></a><span class="co">#| include: true</span></span>
+<span id="cb2945-35"><a href="#cb2945-35" aria-hidden="true" tabindex="-1"></a><span class="co">#| message: false</span></span>
+<span id="cb2945-36"><a href="#cb2945-36" aria-hidden="true" tabindex="-1"></a><span class="co">#| warning: false</span></span>
+<span id="cb2945-37"><a href="#cb2945-37" aria-hidden="true" tabindex="-1"></a><span class="co">#| echo: false</span></span>
+<span id="cb2945-38"><a href="#cb2945-38" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-39"><a href="#cb2945-39" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(mrgsolve)</span>
+<span id="cb2945-40"><a href="#cb2945-40" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(tidybayes)</span>
+<span id="cb2945-41"><a href="#cb2945-41" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(posterior)</span>
+<span id="cb2945-42"><a href="#cb2945-42" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(cmdstanr)</span>
+<span id="cb2945-43"><a href="#cb2945-43" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(tidyverse)</span>
+<span id="cb2945-44"><a href="#cb2945-44" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-45"><a href="#cb2945-45" aria-hidden="true" tabindex="-1"></a><span class="fu">set_cmdstan_path</span>(here<span class="sc">::</span><span class="fu">here</span>(<span class="st">&quot;~/Torsten/cmdstan&quot;</span>))</span>
+<span id="cb2945-46"><a href="#cb2945-46" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-47"><a href="#cb2945-47" aria-hidden="true" tabindex="-1"></a><span class="in">```</span></span>
+<span id="cb2945-48"><a href="#cb2945-48" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-49"><a href="#cb2945-49" aria-hidden="true" tabindex="-1"></a><span class="fu"># Introduction</span></span>
+<span id="cb2945-50"><a href="#cb2945-50" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-51"><a href="#cb2945-51" aria-hidden="true" tabindex="-1"></a>I&#39;ve been doing some testing with the new Torsten release (v0.91.0) on an M3 </span>
+<span id="cb2945-52"><a href="#cb2945-52" aria-hidden="true" tabindex="-1"></a>Macbook Pro. I brought up an issue with M3 compatibility</span>
+<span id="cb2945-53"><a href="#cb2945-53" aria-hidden="true" tabindex="-1"></a><span class="co">[</span><span class="ot">here</span><span class="co">](https://discourse.mc-stan.org/t/problem-installing-torsten-0-90/27585/12)</span>.</span>
+<span id="cb2945-54"><a href="#cb2945-54" aria-hidden="true" tabindex="-1"></a>Thank you for fixing that issue. Now I&#39;m doing some more testing, and I&#39;m </span>
+<span id="cb2945-55"><a href="#cb2945-55" aria-hidden="true" tabindex="-1"></a>finding some issues with the Torsten solvers.</span>
+<span id="cb2945-56"><a href="#cb2945-56" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-57"><a href="#cb2945-57" aria-hidden="true" tabindex="-1"></a><span class="co">&lt;!-- I&#39;ve mostly done testing on my own models, but I&#39;ve also worked on the  --&gt;</span></span>
+<span id="cb2945-58"><a href="#cb2945-58" aria-hidden="true" tabindex="-1"></a><span class="co">&lt;!-- ```pk2cpt```, ```pk2cpt_linode```, ```pk2cpt_ode```, and ```poppk2cpt``` models, --&gt;</span></span>
+<span id="cb2945-59"><a href="#cb2945-59" aria-hidden="true" tabindex="-1"></a><span class="co">&lt;!-- For the single subject models, the analytical solution didn&#39;t work, the linear  --&gt;</span></span>
+<span id="cb2945-60"><a href="#cb2945-60" aria-hidden="true" tabindex="-1"></a><span class="co">&lt;!-- ODE solution worked, and the ODE solution didn&#39;t work (although I&#39;m not exactly  --&gt;</span></span>
+<span id="cb2945-61"><a href="#cb2945-61" aria-hidden="true" tabindex="-1"></a><span class="co">&lt;!-- sure why the ODE solution didn&#39;t work. Still needs worked on, I guess.) For the  --&gt;</span></span>
+<span id="cb2945-62"><a href="#cb2945-62" aria-hidden="true" tabindex="-1"></a><span class="co">&lt;!-- population model, the analytical solution and the ODE solution worked with the --&gt;</span></span>
+<span id="cb2945-63"><a href="#cb2945-63" aria-hidden="true" tabindex="-1"></a><span class="co">&lt;!-- model that you&#39;ve written, but the linear ODE soolution didn&#39;t work. So I then --&gt;</span></span>
+<span id="cb2945-64"><a href="#cb2945-64" aria-hidden="true" tabindex="-1"></a><span class="co">&lt;!-- used the data in ```poppk2cpt``` and fit it with a model I&#39;ve written, and the --&gt;</span></span>
+<span id="cb2945-65"><a href="#cb2945-65" aria-hidden="true" tabindex="-1"></a><span class="co">&lt;!-- linear ODE and general ODE solutions worked, but the analytical solution didn&#39;t. --&gt;</span></span>
+<span id="cb2945-66"><a href="#cb2945-66" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-67"><a href="#cb2945-67" aria-hidden="true" tabindex="-1"></a><span class="fu"># Some Examples</span></span>
+<span id="cb2945-68"><a href="#cb2945-68" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-69"><a href="#cb2945-69" aria-hidden="true" tabindex="-1"></a><span class="fu">## Simulate from My Models</span></span>
+<span id="cb2945-70"><a href="#cb2945-70" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-71"><a href="#cb2945-71" aria-hidden="true" tabindex="-1"></a>I&#39;m starting out with simulations, mainly because it&#39;s simpler and faster.</span>
+<span id="cb2945-72"><a href="#cb2945-72" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-73"><a href="#cb2945-73" aria-hidden="true" tabindex="-1"></a><span class="fu">### One-Compartment Oral with Lognormal Error</span></span>
+<span id="cb2945-74"><a href="#cb2945-74" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-75"><a href="#cb2945-75" aria-hidden="true" tabindex="-1"></a>The following code simulates with Stan + Torsten with an analytical solution, </span>
+<span id="cb2945-76"><a href="#cb2945-76" aria-hidden="true" tabindex="-1"></a>linear ODE solution, and general ODE solution using code I&#39;ve written in the </span>
+<span id="cb2945-77"><a href="#cb2945-77" aria-hidden="true" tabindex="-1"></a>past, and then also a simulation with mrgsolve as a comparison.</span>
+<span id="cb2945-78"><a href="#cb2945-78" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-79"><a href="#cb2945-79" aria-hidden="true" tabindex="-1"></a>:::{.scrolling_500}</span>
+<span id="cb2945-80"><a href="#cb2945-80" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-83"><a href="#cb2945-83" aria-hidden="true" tabindex="-1"></a><span class="in">```{r}</span></span>
+<span id="cb2945-84"><a href="#cb2945-84" aria-hidden="true" tabindex="-1"></a><span class="co">#| cache: true</span></span>
+<span id="cb2945-85"><a href="#cb2945-85" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-86"><a href="#cb2945-86" aria-hidden="true" tabindex="-1"></a>TVCL <span class="ot">&lt;-</span> <span class="fl">0.5</span></span>
+<span id="cb2945-87"><a href="#cb2945-87" aria-hidden="true" tabindex="-1"></a>TVVC <span class="ot">&lt;-</span> <span class="dv">12</span></span>
+<span id="cb2945-88"><a href="#cb2945-88" aria-hidden="true" tabindex="-1"></a>TVKA <span class="ot">&lt;-</span> <span class="dv">1</span></span>
+<span id="cb2945-89"><a href="#cb2945-89" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-90"><a href="#cb2945-90" aria-hidden="true" tabindex="-1"></a>omega_cl <span class="ot">&lt;-</span> <span class="dv">0</span></span>
+<span id="cb2945-91"><a href="#cb2945-91" aria-hidden="true" tabindex="-1"></a>omega_vc <span class="ot">&lt;-</span> <span class="dv">0</span></span>
+<span id="cb2945-92"><a href="#cb2945-92" aria-hidden="true" tabindex="-1"></a>omega_ka <span class="ot">&lt;-</span> <span class="dv">0</span></span>
+<span id="cb2945-93"><a href="#cb2945-93" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-94"><a href="#cb2945-94" aria-hidden="true" tabindex="-1"></a>R <span class="ot">&lt;-</span> <span class="fu">diag</span>(<span class="fu">rep</span>(<span class="dv">1</span>, <span class="at">times =</span> <span class="dv">3</span>))</span>
+<span id="cb2945-95"><a href="#cb2945-95" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-96"><a href="#cb2945-96" aria-hidden="true" tabindex="-1"></a>sigma <span class="ot">&lt;-</span> <span class="fl">0.2</span></span>
+<span id="cb2945-97"><a href="#cb2945-97" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-98"><a href="#cb2945-98" aria-hidden="true" tabindex="-1"></a>dosing_data <span class="ot">&lt;-</span> <span class="fu">expand.ev</span>(<span class="at">ID =</span> <span class="dv">1</span>, <span class="at">addl =</span> <span class="dv">6</span>, <span class="at">ii =</span> <span class="dv">24</span>, </span>
+<span id="cb2945-99"><a href="#cb2945-99" aria-hidden="true" tabindex="-1"></a>                         <span class="at">cmt =</span> <span class="dv">1</span>, <span class="at">amt =</span> <span class="dv">200</span>, <span class="at">ss =</span> <span class="dv">0</span>, <span class="at">tinf =</span> <span class="dv">0</span>, </span>
+<span id="cb2945-100"><a href="#cb2945-100" aria-hidden="true" tabindex="-1"></a>                         <span class="at">evid =</span> <span class="dv">1</span>) <span class="sc">%&gt;%</span></span>
+<span id="cb2945-101"><a href="#cb2945-101" aria-hidden="true" tabindex="-1"></a>  <span class="fu">as_tibble</span>() <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-102"><a href="#cb2945-102" aria-hidden="true" tabindex="-1"></a>  <span class="fu">rename_all</span>(toupper) <span class="sc">%&gt;%</span></span>
+<span id="cb2945-103"><a href="#cb2945-103" aria-hidden="true" tabindex="-1"></a>  <span class="fu">select</span>(ID, TIME, <span class="fu">everything</span>()) </span>
+<span id="cb2945-104"><a href="#cb2945-104" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-105"><a href="#cb2945-105" aria-hidden="true" tabindex="-1"></a>times_to_simulate <span class="ot">&lt;-</span> <span class="fu">c</span>(<span class="fl">0.25</span>, <span class="fu">seq</span>(<span class="fl">0.5</span>, <span class="dv">24</span><span class="sc">*</span><span class="dv">7</span>, <span class="at">by =</span> <span class="fl">0.5</span>))</span>
+<span id="cb2945-106"><a href="#cb2945-106" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-107"><a href="#cb2945-107" aria-hidden="true" tabindex="-1"></a>nonmem_data_simulate <span class="ot">&lt;-</span> dosing_data <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-108"><a href="#cb2945-108" aria-hidden="true" tabindex="-1"></a>  <span class="fu">group_by</span>(ID) <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-109"><a href="#cb2945-109" aria-hidden="true" tabindex="-1"></a>  <span class="fu">slice</span>(<span class="fu">rep</span>(<span class="dv">1</span>, <span class="at">times =</span> <span class="fu">length</span>(times_to_simulate))) <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-110"><a href="#cb2945-110" aria-hidden="true" tabindex="-1"></a>  <span class="fu">mutate</span>(<span class="at">AMT =</span> <span class="dv">0</span>,</span>
+<span id="cb2945-111"><a href="#cb2945-111" aria-hidden="true" tabindex="-1"></a>         <span class="at">ADDL =</span> <span class="dv">0</span>,</span>
+<span id="cb2945-112"><a href="#cb2945-112" aria-hidden="true" tabindex="-1"></a>         <span class="at">II =</span> <span class="dv">0</span>,</span>
+<span id="cb2945-113"><a href="#cb2945-113" aria-hidden="true" tabindex="-1"></a>         <span class="at">CMT =</span> <span class="dv">2</span>,</span>
+<span id="cb2945-114"><a href="#cb2945-114" aria-hidden="true" tabindex="-1"></a>         <span class="at">EVID =</span> <span class="dv">0</span>,</span>
+<span id="cb2945-115"><a href="#cb2945-115" aria-hidden="true" tabindex="-1"></a>         <span class="at">TIME =</span> times_to_simulate) <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-116"><a href="#cb2945-116" aria-hidden="true" tabindex="-1"></a>  <span class="fu">ungroup</span>() <span class="sc">%&gt;%</span></span>
+<span id="cb2945-117"><a href="#cb2945-117" aria-hidden="true" tabindex="-1"></a>  <span class="fu">bind_rows</span>(dosing_data) <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-118"><a href="#cb2945-118" aria-hidden="true" tabindex="-1"></a>  <span class="fu">arrange</span>(ID, TIME, AMT)</span>
+<span id="cb2945-119"><a href="#cb2945-119" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-120"><a href="#cb2945-120" aria-hidden="true" tabindex="-1"></a>n_subjects <span class="ot">&lt;-</span> nonmem_data_simulate <span class="sc">%&gt;%</span>  <span class="co"># number of individuals to simulate</span></span>
+<span id="cb2945-121"><a href="#cb2945-121" aria-hidden="true" tabindex="-1"></a>  <span class="fu">distinct</span>(ID) <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-122"><a href="#cb2945-122" aria-hidden="true" tabindex="-1"></a>  <span class="fu">count</span>() <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-123"><a href="#cb2945-123" aria-hidden="true" tabindex="-1"></a>  <span class="fu">deframe</span>()</span>
+<span id="cb2945-124"><a href="#cb2945-124" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-125"><a href="#cb2945-125" aria-hidden="true" tabindex="-1"></a>n_total <span class="ot">&lt;-</span> <span class="fu">nrow</span>(nonmem_data_simulate) <span class="co"># total number of time points at which to predict</span></span>
+<span id="cb2945-126"><a href="#cb2945-126" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-127"><a href="#cb2945-127" aria-hidden="true" tabindex="-1"></a>subj_start <span class="ot">&lt;-</span> nonmem_data_simulate <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-128"><a href="#cb2945-128" aria-hidden="true" tabindex="-1"></a>  <span class="fu">mutate</span>(<span class="at">row_num =</span> <span class="dv">1</span><span class="sc">:</span><span class="fu">n</span>()) <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-129"><a href="#cb2945-129" aria-hidden="true" tabindex="-1"></a>  <span class="fu">group_by</span>(ID) <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-130"><a href="#cb2945-130" aria-hidden="true" tabindex="-1"></a>  <span class="fu">slice_head</span>(<span class="at">n =</span> <span class="dv">1</span>) <span class="sc">%&gt;%</span></span>
+<span id="cb2945-131"><a href="#cb2945-131" aria-hidden="true" tabindex="-1"></a>  <span class="fu">ungroup</span>() <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-132"><a href="#cb2945-132" aria-hidden="true" tabindex="-1"></a>  <span class="fu">select</span>(row_num) <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-133"><a href="#cb2945-133" aria-hidden="true" tabindex="-1"></a>  <span class="fu">deframe</span>()</span>
+<span id="cb2945-134"><a href="#cb2945-134" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-135"><a href="#cb2945-135" aria-hidden="true" tabindex="-1"></a>subj_end <span class="ot">&lt;-</span> <span class="fu">c</span>(subj_start[<span class="sc">-</span><span class="dv">1</span>] <span class="sc">-</span> <span class="dv">1</span>, n_total) </span>
+<span id="cb2945-136"><a href="#cb2945-136" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-137"><a href="#cb2945-137" aria-hidden="true" tabindex="-1"></a>stan_data <span class="ot">&lt;-</span> <span class="fu">list</span>(<span class="at">n_subjects =</span> n_subjects,</span>
+<span id="cb2945-138"><a href="#cb2945-138" aria-hidden="true" tabindex="-1"></a>                  <span class="at">n_total =</span> n_total,</span>
+<span id="cb2945-139"><a href="#cb2945-139" aria-hidden="true" tabindex="-1"></a>                  <span class="at">time =</span> nonmem_data_simulate<span class="sc">$</span>TIME,</span>
+<span id="cb2945-140"><a href="#cb2945-140" aria-hidden="true" tabindex="-1"></a>                  <span class="at">amt =</span> nonmem_data_simulate<span class="sc">$</span>AMT,</span>
+<span id="cb2945-141"><a href="#cb2945-141" aria-hidden="true" tabindex="-1"></a>                  <span class="at">cmt =</span> nonmem_data_simulate<span class="sc">$</span>CMT,</span>
+<span id="cb2945-142"><a href="#cb2945-142" aria-hidden="true" tabindex="-1"></a>                  <span class="at">evid =</span> nonmem_data_simulate<span class="sc">$</span>EVID,</span>
+<span id="cb2945-143"><a href="#cb2945-143" aria-hidden="true" tabindex="-1"></a>                  <span class="at">rate =</span> nonmem_data_simulate<span class="sc">$</span>RATE,</span>
+<span id="cb2945-144"><a href="#cb2945-144" aria-hidden="true" tabindex="-1"></a>                  <span class="at">ii =</span> nonmem_data_simulate<span class="sc">$</span>II,</span>
+<span id="cb2945-145"><a href="#cb2945-145" aria-hidden="true" tabindex="-1"></a>                  <span class="at">addl =</span> nonmem_data_simulate<span class="sc">$</span>ADDL,</span>
+<span id="cb2945-146"><a href="#cb2945-146" aria-hidden="true" tabindex="-1"></a>                  <span class="at">ss =</span> nonmem_data_simulate<span class="sc">$</span>SS,</span>
+<span id="cb2945-147"><a href="#cb2945-147" aria-hidden="true" tabindex="-1"></a>                  <span class="at">subj_start =</span> subj_start,</span>
+<span id="cb2945-148"><a href="#cb2945-148" aria-hidden="true" tabindex="-1"></a>                  <span class="at">subj_end =</span> subj_end,</span>
+<span id="cb2945-149"><a href="#cb2945-149" aria-hidden="true" tabindex="-1"></a>                  <span class="at">TVCL =</span> TVCL,</span>
+<span id="cb2945-150"><a href="#cb2945-150" aria-hidden="true" tabindex="-1"></a>                  <span class="at">TVVC =</span> TVVC,</span>
+<span id="cb2945-151"><a href="#cb2945-151" aria-hidden="true" tabindex="-1"></a>                  <span class="at">TVKA =</span> TVKA,</span>
+<span id="cb2945-152"><a href="#cb2945-152" aria-hidden="true" tabindex="-1"></a>                  <span class="at">omega_cl =</span> omega_cl,</span>
+<span id="cb2945-153"><a href="#cb2945-153" aria-hidden="true" tabindex="-1"></a>                  <span class="at">omega_vc =</span> omega_vc,</span>
+<span id="cb2945-154"><a href="#cb2945-154" aria-hidden="true" tabindex="-1"></a>                  <span class="at">omega_ka =</span> omega_ka,</span>
+<span id="cb2945-155"><a href="#cb2945-155" aria-hidden="true" tabindex="-1"></a>                  <span class="at">R =</span> R,</span>
+<span id="cb2945-156"><a href="#cb2945-156" aria-hidden="true" tabindex="-1"></a>                  <span class="at">sigma =</span> sigma,</span>
+<span id="cb2945-157"><a href="#cb2945-157" aria-hidden="true" tabindex="-1"></a>                  <span class="at">solver =</span> <span class="dv">1</span>) <span class="co"># analytical = 1, mat exp = 2, rk45 = 3</span></span>
+<span id="cb2945-158"><a href="#cb2945-158" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-159"><a href="#cb2945-159" aria-hidden="true" tabindex="-1"></a>model <span class="ot">&lt;-</span> <span class="fu">cmdstan_model</span>(</span>
+<span id="cb2945-160"><a href="#cb2945-160" aria-hidden="true" tabindex="-1"></a>  here<span class="sc">::</span><span class="fu">here</span>(<span class="st">&quot;M3/depot_1cmt_linear/Stan/Simulate/depot_1cmt_exp.stan&quot;</span>))</span>
+<span id="cb2945-161"><a href="#cb2945-161" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-162"><a href="#cb2945-162" aria-hidden="true" tabindex="-1"></a>model<span class="sc">$</span><span class="fu">print</span>()</span>
+<span id="cb2945-163"><a href="#cb2945-163" aria-hidden="true" tabindex="-1"></a><span class="in">```</span></span>
+<span id="cb2945-164"><a href="#cb2945-164" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-165"><a href="#cb2945-165" aria-hidden="true" tabindex="-1"></a>:::</span>
+<span id="cb2945-166"><a href="#cb2945-166" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-169"><a href="#cb2945-169" aria-hidden="true" tabindex="-1"></a><span class="in">```{r}</span></span>
+<span id="cb2945-170"><a href="#cb2945-170" aria-hidden="true" tabindex="-1"></a><span class="co">#| cache: true</span></span>
+<span id="cb2945-171"><a href="#cb2945-171" aria-hidden="true" tabindex="-1"></a><span class="co">#| output: false</span></span>
+<span id="cb2945-172"><a href="#cb2945-172" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-173"><a href="#cb2945-173" aria-hidden="true" tabindex="-1"></a>simulated_data <span class="ot">&lt;-</span> model<span class="sc">$</span><span class="fu">sample</span>(<span class="at">data =</span> stan_data,</span>
+<span id="cb2945-174"><a href="#cb2945-174" aria-hidden="true" tabindex="-1"></a>                               <span class="at">fixed_param =</span> <span class="cn">TRUE</span>,</span>
+<span id="cb2945-175"><a href="#cb2945-175" aria-hidden="true" tabindex="-1"></a>                               <span class="at">seed =</span> <span class="dv">1123</span>,</span>
+<span id="cb2945-176"><a href="#cb2945-176" aria-hidden="true" tabindex="-1"></a>                               <span class="at">iter_warmup =</span> <span class="dv">0</span>,</span>
+<span id="cb2945-177"><a href="#cb2945-177" aria-hidden="true" tabindex="-1"></a>                               <span class="at">iter_sampling =</span> <span class="dv">1</span>,</span>
+<span id="cb2945-178"><a href="#cb2945-178" aria-hidden="true" tabindex="-1"></a>                               <span class="at">chains =</span> <span class="dv">1</span>,</span>
+<span id="cb2945-179"><a href="#cb2945-179" aria-hidden="true" tabindex="-1"></a>                               <span class="at">parallel_chains =</span> <span class="dv">1</span>)</span>
+<span id="cb2945-180"><a href="#cb2945-180" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-181"><a href="#cb2945-181" aria-hidden="true" tabindex="-1"></a>data_analytical <span class="ot">&lt;-</span> simulated_data<span class="sc">$</span><span class="fu">draws</span>(<span class="fu">c</span>(<span class="st">&quot;dv&quot;</span>, <span class="st">&quot;ipred&quot;</span>)) <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-182"><a href="#cb2945-182" aria-hidden="true" tabindex="-1"></a>  <span class="fu">spread_draws</span>(dv[i], ipred[i]) <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-183"><a href="#cb2945-183" aria-hidden="true" tabindex="-1"></a>  <span class="fu">ungroup</span>() <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-184"><a href="#cb2945-184" aria-hidden="true" tabindex="-1"></a>  <span class="fu">inner_join</span>(nonmem_data_simulate <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-185"><a href="#cb2945-185" aria-hidden="true" tabindex="-1"></a>               <span class="fu">mutate</span>(<span class="at">i =</span> <span class="dv">1</span><span class="sc">:</span><span class="fu">n</span>()),</span>
+<span id="cb2945-186"><a href="#cb2945-186" aria-hidden="true" tabindex="-1"></a>             <span class="at">by =</span> <span class="st">&quot;i&quot;</span>) <span class="sc">%&gt;%</span></span>
+<span id="cb2945-187"><a href="#cb2945-187" aria-hidden="true" tabindex="-1"></a>  <span class="fu">select</span>(ID, AMT, II, ADDL, RATE, CMT, EVID, SS, TIME, </span>
+<span id="cb2945-188"><a href="#cb2945-188" aria-hidden="true" tabindex="-1"></a>         <span class="at">DV =</span> <span class="st">&quot;dv&quot;</span>, <span class="at">IPRED =</span> <span class="st">&quot;ipred&quot;</span>) <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-189"><a href="#cb2945-189" aria-hidden="true" tabindex="-1"></a>  <span class="fu">mutate</span>(<span class="at">LLOQ =</span> <span class="fl">1e-6</span>, </span>
+<span id="cb2945-190"><a href="#cb2945-190" aria-hidden="true" tabindex="-1"></a>         <span class="at">BLOQ =</span> <span class="fu">case_when</span>(EVID <span class="sc">==</span> <span class="dv">1</span> <span class="sc">~</span> <span class="cn">NA_real_</span>,</span>
+<span id="cb2945-191"><a href="#cb2945-191" aria-hidden="true" tabindex="-1"></a>                          DV <span class="sc">&lt;=</span> LLOQ <span class="sc">~</span> <span class="dv">1</span>,</span>
+<span id="cb2945-192"><a href="#cb2945-192" aria-hidden="true" tabindex="-1"></a>                          DV <span class="sc">&gt;</span> LLOQ <span class="sc">~</span> <span class="dv">0</span>,</span>
+<span id="cb2945-193"><a href="#cb2945-193" aria-hidden="true" tabindex="-1"></a>                          <span class="cn">TRUE</span> <span class="sc">~</span> <span class="cn">NA_real_</span>),</span>
+<span id="cb2945-194"><a href="#cb2945-194" aria-hidden="true" tabindex="-1"></a>         <span class="at">DV =</span> <span class="fu">if_else</span>(EVID <span class="sc">==</span> <span class="dv">1</span> <span class="sc">|</span> BLOQ <span class="sc">==</span> <span class="dv">1</span>, <span class="cn">NA_real_</span>, DV),</span>
+<span id="cb2945-195"><a href="#cb2945-195" aria-hidden="true" tabindex="-1"></a>         <span class="at">MDV =</span> <span class="fu">if_else</span>(<span class="fu">is.na</span>(DV), <span class="dv">1</span>, <span class="dv">0</span>)) <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-196"><a href="#cb2945-196" aria-hidden="true" tabindex="-1"></a>  <span class="fu">relocate</span>(DV, <span class="at">.after =</span> <span class="fu">last_col</span>()) <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-197"><a href="#cb2945-197" aria-hidden="true" tabindex="-1"></a>  <span class="fu">relocate</span>(TIME, <span class="at">.before =</span> DV) <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-198"><a href="#cb2945-198" aria-hidden="true" tabindex="-1"></a>  <span class="fu">mutate</span>(<span class="at">solver =</span> <span class="st">&quot;analytical&quot;</span>)</span>
+<span id="cb2945-199"><a href="#cb2945-199" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-200"><a href="#cb2945-200" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-201"><a href="#cb2945-201" aria-hidden="true" tabindex="-1"></a>stan_data<span class="sc">$</span>solver <span class="ot">&lt;-</span> <span class="dv">2</span></span>
+<span id="cb2945-202"><a href="#cb2945-202" aria-hidden="true" tabindex="-1"></a>simulated_data <span class="ot">&lt;-</span> model<span class="sc">$</span><span class="fu">sample</span>(<span class="at">data =</span> stan_data,</span>
+<span id="cb2945-203"><a href="#cb2945-203" aria-hidden="true" tabindex="-1"></a>                               <span class="at">fixed_param =</span> <span class="cn">TRUE</span>,</span>
+<span id="cb2945-204"><a href="#cb2945-204" aria-hidden="true" tabindex="-1"></a>                               <span class="at">seed =</span> <span class="dv">1123</span>,</span>
+<span id="cb2945-205"><a href="#cb2945-205" aria-hidden="true" tabindex="-1"></a>                               <span class="at">iter_warmup =</span> <span class="dv">0</span>,</span>
+<span id="cb2945-206"><a href="#cb2945-206" aria-hidden="true" tabindex="-1"></a>                               <span class="at">iter_sampling =</span> <span class="dv">1</span>,</span>
+<span id="cb2945-207"><a href="#cb2945-207" aria-hidden="true" tabindex="-1"></a>                               <span class="at">chains =</span> <span class="dv">1</span>,</span>
+<span id="cb2945-208"><a href="#cb2945-208" aria-hidden="true" tabindex="-1"></a>                               <span class="at">parallel_chains =</span> <span class="dv">1</span>)</span>
+<span id="cb2945-209"><a href="#cb2945-209" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-210"><a href="#cb2945-210" aria-hidden="true" tabindex="-1"></a>data_mat_exp <span class="ot">&lt;-</span> simulated_data<span class="sc">$</span><span class="fu">draws</span>(<span class="fu">c</span>(<span class="st">&quot;dv&quot;</span>, <span class="st">&quot;ipred&quot;</span>)) <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-211"><a href="#cb2945-211" aria-hidden="true" tabindex="-1"></a>  <span class="fu">spread_draws</span>(dv[i], ipred[i]) <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-212"><a href="#cb2945-212" aria-hidden="true" tabindex="-1"></a>  <span class="fu">ungroup</span>() <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-213"><a href="#cb2945-213" aria-hidden="true" tabindex="-1"></a>  <span class="fu">inner_join</span>(nonmem_data_simulate <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-214"><a href="#cb2945-214" aria-hidden="true" tabindex="-1"></a>               <span class="fu">mutate</span>(<span class="at">i =</span> <span class="dv">1</span><span class="sc">:</span><span class="fu">n</span>()),</span>
+<span id="cb2945-215"><a href="#cb2945-215" aria-hidden="true" tabindex="-1"></a>             <span class="at">by =</span> <span class="st">&quot;i&quot;</span>) <span class="sc">%&gt;%</span></span>
+<span id="cb2945-216"><a href="#cb2945-216" aria-hidden="true" tabindex="-1"></a>  <span class="fu">select</span>(ID, AMT, II, ADDL, RATE, CMT, EVID, SS, TIME, </span>
+<span id="cb2945-217"><a href="#cb2945-217" aria-hidden="true" tabindex="-1"></a>         <span class="at">DV =</span> <span class="st">&quot;dv&quot;</span>, <span class="at">IPRED =</span> <span class="st">&quot;ipred&quot;</span>) <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-218"><a href="#cb2945-218" aria-hidden="true" tabindex="-1"></a>  <span class="fu">mutate</span>(<span class="at">LLOQ =</span> <span class="fl">1e-6</span>, </span>
+<span id="cb2945-219"><a href="#cb2945-219" aria-hidden="true" tabindex="-1"></a>         <span class="at">BLOQ =</span> <span class="fu">case_when</span>(EVID <span class="sc">==</span> <span class="dv">1</span> <span class="sc">~</span> <span class="cn">NA_real_</span>,</span>
+<span id="cb2945-220"><a href="#cb2945-220" aria-hidden="true" tabindex="-1"></a>                          DV <span class="sc">&lt;=</span> LLOQ <span class="sc">~</span> <span class="dv">1</span>,</span>
+<span id="cb2945-221"><a href="#cb2945-221" aria-hidden="true" tabindex="-1"></a>                          DV <span class="sc">&gt;</span> LLOQ <span class="sc">~</span> <span class="dv">0</span>,</span>
+<span id="cb2945-222"><a href="#cb2945-222" aria-hidden="true" tabindex="-1"></a>                          <span class="cn">TRUE</span> <span class="sc">~</span> <span class="cn">NA_real_</span>),</span>
+<span id="cb2945-223"><a href="#cb2945-223" aria-hidden="true" tabindex="-1"></a>         <span class="at">DV =</span> <span class="fu">if_else</span>(EVID <span class="sc">==</span> <span class="dv">1</span> <span class="sc">|</span> BLOQ <span class="sc">==</span> <span class="dv">1</span>, <span class="cn">NA_real_</span>, DV),</span>
+<span id="cb2945-224"><a href="#cb2945-224" aria-hidden="true" tabindex="-1"></a>         <span class="at">MDV =</span> <span class="fu">if_else</span>(<span class="fu">is.na</span>(DV), <span class="dv">1</span>, <span class="dv">0</span>)) <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-225"><a href="#cb2945-225" aria-hidden="true" tabindex="-1"></a>  <span class="fu">relocate</span>(DV, <span class="at">.after =</span> <span class="fu">last_col</span>()) <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-226"><a href="#cb2945-226" aria-hidden="true" tabindex="-1"></a>  <span class="fu">relocate</span>(TIME, <span class="at">.before =</span> DV) <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-227"><a href="#cb2945-227" aria-hidden="true" tabindex="-1"></a>  <span class="fu">mutate</span>(<span class="at">solver =</span> <span class="st">&quot;mat_exp&quot;</span>)</span>
+<span id="cb2945-228"><a href="#cb2945-228" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-229"><a href="#cb2945-229" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-230"><a href="#cb2945-230" aria-hidden="true" tabindex="-1"></a>stan_data<span class="sc">$</span>solver <span class="ot">&lt;-</span> <span class="dv">3</span></span>
+<span id="cb2945-231"><a href="#cb2945-231" aria-hidden="true" tabindex="-1"></a>simulated_data <span class="ot">&lt;-</span> model<span class="sc">$</span><span class="fu">sample</span>(<span class="at">data =</span> stan_data,</span>
+<span id="cb2945-232"><a href="#cb2945-232" aria-hidden="true" tabindex="-1"></a>                               <span class="at">fixed_param =</span> <span class="cn">TRUE</span>,</span>
+<span id="cb2945-233"><a href="#cb2945-233" aria-hidden="true" tabindex="-1"></a>                               <span class="at">seed =</span> <span class="dv">1123</span>,</span>
+<span id="cb2945-234"><a href="#cb2945-234" aria-hidden="true" tabindex="-1"></a>                               <span class="at">iter_warmup =</span> <span class="dv">0</span>,</span>
+<span id="cb2945-235"><a href="#cb2945-235" aria-hidden="true" tabindex="-1"></a>                               <span class="at">iter_sampling =</span> <span class="dv">1</span>,</span>
+<span id="cb2945-236"><a href="#cb2945-236" aria-hidden="true" tabindex="-1"></a>                               <span class="at">chains =</span> <span class="dv">1</span>,</span>
+<span id="cb2945-237"><a href="#cb2945-237" aria-hidden="true" tabindex="-1"></a>                               <span class="at">parallel_chains =</span> <span class="dv">1</span>)</span>
+<span id="cb2945-238"><a href="#cb2945-238" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-239"><a href="#cb2945-239" aria-hidden="true" tabindex="-1"></a>data_rk45 <span class="ot">&lt;-</span> simulated_data<span class="sc">$</span><span class="fu">draws</span>(<span class="fu">c</span>(<span class="st">&quot;dv&quot;</span>, <span class="st">&quot;ipred&quot;</span>)) <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-240"><a href="#cb2945-240" aria-hidden="true" tabindex="-1"></a>  <span class="fu">spread_draws</span>(dv[i], ipred[i]) <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-241"><a href="#cb2945-241" aria-hidden="true" tabindex="-1"></a>  <span class="fu">ungroup</span>() <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-242"><a href="#cb2945-242" aria-hidden="true" tabindex="-1"></a>  <span class="fu">inner_join</span>(nonmem_data_simulate <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-243"><a href="#cb2945-243" aria-hidden="true" tabindex="-1"></a>               <span class="fu">mutate</span>(<span class="at">i =</span> <span class="dv">1</span><span class="sc">:</span><span class="fu">n</span>()),</span>
+<span id="cb2945-244"><a href="#cb2945-244" aria-hidden="true" tabindex="-1"></a>             <span class="at">by =</span> <span class="st">&quot;i&quot;</span>) <span class="sc">%&gt;%</span></span>
+<span id="cb2945-245"><a href="#cb2945-245" aria-hidden="true" tabindex="-1"></a>  <span class="fu">select</span>(ID, AMT, II, ADDL, RATE, CMT, EVID, SS, TIME, </span>
+<span id="cb2945-246"><a href="#cb2945-246" aria-hidden="true" tabindex="-1"></a>         <span class="at">DV =</span> <span class="st">&quot;dv&quot;</span>, <span class="at">IPRED =</span> <span class="st">&quot;ipred&quot;</span>) <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-247"><a href="#cb2945-247" aria-hidden="true" tabindex="-1"></a>  <span class="fu">mutate</span>(<span class="at">LLOQ =</span> <span class="fl">1e-6</span>, </span>
+<span id="cb2945-248"><a href="#cb2945-248" aria-hidden="true" tabindex="-1"></a>         <span class="at">BLOQ =</span> <span class="fu">case_when</span>(EVID <span class="sc">==</span> <span class="dv">1</span> <span class="sc">~</span> <span class="cn">NA_real_</span>,</span>
+<span id="cb2945-249"><a href="#cb2945-249" aria-hidden="true" tabindex="-1"></a>                          DV <span class="sc">&lt;=</span> LLOQ <span class="sc">~</span> <span class="dv">1</span>,</span>
+<span id="cb2945-250"><a href="#cb2945-250" aria-hidden="true" tabindex="-1"></a>                          DV <span class="sc">&gt;</span> LLOQ <span class="sc">~</span> <span class="dv">0</span>,</span>
+<span id="cb2945-251"><a href="#cb2945-251" aria-hidden="true" tabindex="-1"></a>                          <span class="cn">TRUE</span> <span class="sc">~</span> <span class="cn">NA_real_</span>),</span>
+<span id="cb2945-252"><a href="#cb2945-252" aria-hidden="true" tabindex="-1"></a>         <span class="at">DV =</span> <span class="fu">if_else</span>(EVID <span class="sc">==</span> <span class="dv">1</span> <span class="sc">|</span> BLOQ <span class="sc">==</span> <span class="dv">1</span>, <span class="cn">NA_real_</span>, DV),</span>
+<span id="cb2945-253"><a href="#cb2945-253" aria-hidden="true" tabindex="-1"></a>         <span class="at">MDV =</span> <span class="fu">if_else</span>(<span class="fu">is.na</span>(DV), <span class="dv">1</span>, <span class="dv">0</span>)) <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-254"><a href="#cb2945-254" aria-hidden="true" tabindex="-1"></a>  <span class="fu">relocate</span>(DV, <span class="at">.after =</span> <span class="fu">last_col</span>()) <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-255"><a href="#cb2945-255" aria-hidden="true" tabindex="-1"></a>  <span class="fu">relocate</span>(TIME, <span class="at">.before =</span> DV) <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-256"><a href="#cb2945-256" aria-hidden="true" tabindex="-1"></a>  <span class="fu">mutate</span>(<span class="at">solver =</span> <span class="st">&quot;rk45&quot;</span>)</span>
+<span id="cb2945-257"><a href="#cb2945-257" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-258"><a href="#cb2945-258" aria-hidden="true" tabindex="-1"></a><span class="do">## Now do it with mrgsolve to check</span></span>
+<span id="cb2945-259"><a href="#cb2945-259" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-260"><a href="#cb2945-260" aria-hidden="true" tabindex="-1"></a>mod <span class="ot">&lt;-</span> <span class="fu">mread</span>(here<span class="sc">::</span><span class="fu">here</span>(<span class="st">&quot;M3/depot_1cmt_linear/mrgsolve/depot_1cmt_exp.cpp&quot;</span>))</span>
+<span id="cb2945-261"><a href="#cb2945-261" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-262"><a href="#cb2945-262" aria-hidden="true" tabindex="-1"></a>data_mrgsolve <span class="ot">&lt;-</span> mod <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-263"><a href="#cb2945-263" aria-hidden="true" tabindex="-1"></a>  <span class="fu">param</span>(<span class="fu">tibble</span>(<span class="at">CL =</span> TVCL,</span>
+<span id="cb2945-264"><a href="#cb2945-264" aria-hidden="true" tabindex="-1"></a>               <span class="at">VC =</span> TVVC,</span>
+<span id="cb2945-265"><a href="#cb2945-265" aria-hidden="true" tabindex="-1"></a>               <span class="at">KA =</span> TVKA,</span>
+<span id="cb2945-266"><a href="#cb2945-266" aria-hidden="true" tabindex="-1"></a>               <span class="at">F1 =</span> <span class="dv">1</span>,</span>
+<span id="cb2945-267"><a href="#cb2945-267" aria-hidden="true" tabindex="-1"></a>               <span class="at">LAGTIME =</span> <span class="dv">0</span>)) <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-268"><a href="#cb2945-268" aria-hidden="true" tabindex="-1"></a>  <span class="fu">data_set</span>(dosing_data) <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-269"><a href="#cb2945-269" aria-hidden="true" tabindex="-1"></a>  <span class="fu">mrgsim_df</span>(<span class="at">tgrid =</span> times_to_simulate) <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-270"><a href="#cb2945-270" aria-hidden="true" tabindex="-1"></a>  <span class="fu">as_tibble</span>() <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-271"><a href="#cb2945-271" aria-hidden="true" tabindex="-1"></a>  <span class="fu">mutate</span>(<span class="at">solver =</span> <span class="st">&quot;mrgsolve&quot;</span>)</span>
+<span id="cb2945-272"><a href="#cb2945-272" aria-hidden="true" tabindex="-1"></a><span class="in">```</span></span>
+<span id="cb2945-273"><a href="#cb2945-273" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-274"><a href="#cb2945-274" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-277"><a href="#cb2945-277" aria-hidden="true" tabindex="-1"></a><span class="in">```{r}</span></span>
+<span id="cb2945-278"><a href="#cb2945-278" aria-hidden="true" tabindex="-1"></a><span class="co">#| fig-align: center</span></span>
+<span id="cb2945-279"><a href="#cb2945-279" aria-hidden="true" tabindex="-1"></a><span class="co">#| </span></span>
+<span id="cb2945-280"><a href="#cb2945-280" aria-hidden="true" tabindex="-1"></a><span class="fu">mget</span>(<span class="fu">str_subset</span>(<span class="fu">ls</span>(), <span class="st">&quot;^data_&quot;</span>)) <span class="sc">%&gt;%</span></span>
+<span id="cb2945-281"><a href="#cb2945-281" aria-hidden="true" tabindex="-1"></a>  <span class="fu">bind_rows</span>() <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-282"><a href="#cb2945-282" aria-hidden="true" tabindex="-1"></a>  <span class="fu">ggplot</span>(<span class="fu">aes</span>(<span class="at">x =</span> TIME, <span class="at">y =</span> IPRED, <span class="at">color =</span> solver)) <span class="sc">+</span></span>
+<span id="cb2945-283"><a href="#cb2945-283" aria-hidden="true" tabindex="-1"></a>  <span class="fu">geom_line</span>(<span class="fu">aes</span>(<span class="at">linetype =</span> solver)) <span class="sc">+</span></span>
+<span id="cb2945-284"><a href="#cb2945-284" aria-hidden="true" tabindex="-1"></a>  <span class="fu">theme_bw</span>() <span class="sc">+</span></span>
+<span id="cb2945-285"><a href="#cb2945-285" aria-hidden="true" tabindex="-1"></a>  <span class="fu">scale_x_continuous</span>(<span class="at">name =</span> <span class="st">&quot;Time (h)&quot;</span>,</span>
+<span id="cb2945-286"><a href="#cb2945-286" aria-hidden="true" tabindex="-1"></a>                     <span class="at">breaks =</span> <span class="fu">seq</span>(<span class="dv">0</span>, <span class="dv">168</span>, <span class="at">by =</span> <span class="dv">24</span>),</span>
+<span id="cb2945-287"><a href="#cb2945-287" aria-hidden="true" tabindex="-1"></a>                     <span class="at">labels =</span> <span class="fu">seq</span>(<span class="dv">0</span>, <span class="dv">168</span>, <span class="at">by =</span> <span class="dv">24</span>)) <span class="sc">+</span></span>
+<span id="cb2945-288"><a href="#cb2945-288" aria-hidden="true" tabindex="-1"></a>  <span class="fu">scale_y_continuous</span>(<span class="at">name =</span> <span class="st">&quot;Drug Conc. (ug/mL)&quot;</span>)</span>
+<span id="cb2945-289"><a href="#cb2945-289" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-290"><a href="#cb2945-290" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-291"><a href="#cb2945-291" aria-hidden="true" tabindex="-1"></a><span class="in">```</span></span>
+<span id="cb2945-292"><a href="#cb2945-292" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-293"><a href="#cb2945-293" aria-hidden="true" tabindex="-1"></a>So you can see for the M2, the analytical soultion, linear ODE, general ODE, </span>
+<span id="cb2945-294"><a href="#cb2945-294" aria-hidden="true" tabindex="-1"></a>and mrgsolve simulations are all the same, in contrast with the M3 where the </span>
+<span id="cb2945-295"><a href="#cb2945-295" aria-hidden="true" tabindex="-1"></a>analytical solution was a vector of zeros.</span>
+<span id="cb2945-296"><a href="#cb2945-296" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-297"><a href="#cb2945-297" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-298"><a href="#cb2945-298" aria-hidden="true" tabindex="-1"></a><span class="fu">### Two-Compartment IV with Proportional Error</span></span>
+<span id="cb2945-299"><a href="#cb2945-299" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-300"><a href="#cb2945-300" aria-hidden="true" tabindex="-1"></a>The following code simulates with Stan + Torsten with an analytical solution, </span>
+<span id="cb2945-301"><a href="#cb2945-301" aria-hidden="true" tabindex="-1"></a>linear ODE solution, and general ODE solution using code I&#39;ve written in the </span>
+<span id="cb2945-302"><a href="#cb2945-302" aria-hidden="true" tabindex="-1"></a>past, and then also a simulation with mrgsolve as a comparison.</span>
+<span id="cb2945-303"><a href="#cb2945-303" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-304"><a href="#cb2945-304" aria-hidden="true" tabindex="-1"></a>:::{.scrolling_500}</span>
+<span id="cb2945-305"><a href="#cb2945-305" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-308"><a href="#cb2945-308" aria-hidden="true" tabindex="-1"></a><span class="in">```{r}</span></span>
+<span id="cb2945-309"><a href="#cb2945-309" aria-hidden="true" tabindex="-1"></a><span class="co">#| cache: true</span></span>
+<span id="cb2945-310"><a href="#cb2945-310" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-311"><a href="#cb2945-311" aria-hidden="true" tabindex="-1"></a>TVCL <span class="ot">&lt;-</span> <span class="fl">0.25</span>  <span class="co"># L/d</span></span>
+<span id="cb2945-312"><a href="#cb2945-312" aria-hidden="true" tabindex="-1"></a>TVVC <span class="ot">&lt;-</span> <span class="dv">3</span>     <span class="co"># L</span></span>
+<span id="cb2945-313"><a href="#cb2945-313" aria-hidden="true" tabindex="-1"></a>TVQ <span class="ot">&lt;-</span> <span class="dv">1</span>      <span class="co"># L/d</span></span>
+<span id="cb2945-314"><a href="#cb2945-314" aria-hidden="true" tabindex="-1"></a>TVVP <span class="ot">&lt;-</span> <span class="dv">4</span>     <span class="co"># L</span></span>
+<span id="cb2945-315"><a href="#cb2945-315" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-316"><a href="#cb2945-316" aria-hidden="true" tabindex="-1"></a>omega_cl <span class="ot">&lt;-</span> <span class="dv">0</span></span>
+<span id="cb2945-317"><a href="#cb2945-317" aria-hidden="true" tabindex="-1"></a>omega_vc <span class="ot">&lt;-</span> <span class="dv">0</span></span>
+<span id="cb2945-318"><a href="#cb2945-318" aria-hidden="true" tabindex="-1"></a>omega_q <span class="ot">&lt;-</span> <span class="dv">0</span></span>
+<span id="cb2945-319"><a href="#cb2945-319" aria-hidden="true" tabindex="-1"></a>omega_vp <span class="ot">&lt;-</span> <span class="dv">0</span></span>
+<span id="cb2945-320"><a href="#cb2945-320" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-321"><a href="#cb2945-321" aria-hidden="true" tabindex="-1"></a>R <span class="ot">&lt;-</span> <span class="fu">diag</span>(<span class="fu">rep</span>(<span class="dv">1</span>, <span class="at">times =</span> <span class="dv">4</span>))</span>
+<span id="cb2945-322"><a href="#cb2945-322" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-323"><a href="#cb2945-323" aria-hidden="true" tabindex="-1"></a>sigma_p <span class="ot">&lt;-</span> <span class="fl">0.2</span></span>
+<span id="cb2945-324"><a href="#cb2945-324" aria-hidden="true" tabindex="-1"></a>sigma_a <span class="ot">&lt;-</span> <span class="fl">0.05</span></span>
+<span id="cb2945-325"><a href="#cb2945-325" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-326"><a href="#cb2945-326" aria-hidden="true" tabindex="-1"></a>cor_p_a <span class="ot">&lt;-</span> <span class="dv">0</span></span>
+<span id="cb2945-327"><a href="#cb2945-327" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-328"><a href="#cb2945-328" aria-hidden="true" tabindex="-1"></a>solver <span class="ot">&lt;-</span> <span class="dv">1</span> <span class="co"># analytical = 1, mat exp = 2, rk45 = 3</span></span>
+<span id="cb2945-329"><a href="#cb2945-329" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-330"><a href="#cb2945-330" aria-hidden="true" tabindex="-1"></a><span class="co"># If using Torsten&#39;s analytical solver, dose into the second compartment </span></span>
+<span id="cb2945-331"><a href="#cb2945-331" aria-hidden="true" tabindex="-1"></a><span class="co"># (cmt = 2). If using matrix-exponential or ODE, then dose into the first</span></span>
+<span id="cb2945-332"><a href="#cb2945-332" aria-hidden="true" tabindex="-1"></a><span class="co"># compartment (cmt = 1)</span></span>
+<span id="cb2945-333"><a href="#cb2945-333" aria-hidden="true" tabindex="-1"></a>dosing_data <span class="ot">&lt;-</span> <span class="fu">expand.ev</span>(<span class="at">ID =</span> <span class="dv">1</span>, <span class="at">addl =</span> <span class="dv">5</span>, <span class="at">ii =</span> <span class="dv">14</span>, </span>
+<span id="cb2945-334"><a href="#cb2945-334" aria-hidden="true" tabindex="-1"></a>                         <span class="at">cmt =</span> <span class="dv">2</span>, <span class="at">amt =</span> <span class="dv">400</span>, <span class="at">ss =</span> <span class="dv">0</span>, </span>
+<span id="cb2945-335"><a href="#cb2945-335" aria-hidden="true" tabindex="-1"></a>                         <span class="at">tinf =</span> <span class="dv">1</span><span class="sc">/</span><span class="dv">24</span>, <span class="at">evid =</span> <span class="dv">1</span>) <span class="sc">%&gt;%</span></span>
+<span id="cb2945-336"><a href="#cb2945-336" aria-hidden="true" tabindex="-1"></a>  <span class="fu">as_tibble</span>() <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-337"><a href="#cb2945-337" aria-hidden="true" tabindex="-1"></a>  <span class="fu">mutate</span>(<span class="at">cmt =</span> <span class="fu">if_else</span>(solver <span class="sc">==</span> <span class="dv">1</span>, <span class="dv">2</span>, <span class="dv">1</span>)) <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-338"><a href="#cb2945-338" aria-hidden="true" tabindex="-1"></a>  <span class="fu">rename_all</span>(toupper) <span class="sc">%&gt;%</span></span>
+<span id="cb2945-339"><a href="#cb2945-339" aria-hidden="true" tabindex="-1"></a>  <span class="fu">select</span>(ID, TIME, <span class="fu">everything</span>()) </span>
+<span id="cb2945-340"><a href="#cb2945-340" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-341"><a href="#cb2945-341" aria-hidden="true" tabindex="-1"></a>times_to_simulate <span class="ot">&lt;-</span> <span class="fu">seq</span>(<span class="dv">0</span>, <span class="dv">84</span><span class="sc">*</span><span class="dv">24</span>, <span class="at">by =</span> <span class="dv">1</span>)<span class="sc">/</span><span class="dv">24</span></span>
+<span id="cb2945-342"><a href="#cb2945-342" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-343"><a href="#cb2945-343" aria-hidden="true" tabindex="-1"></a>nonmem_data_simulate <span class="ot">&lt;-</span> dosing_data <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-344"><a href="#cb2945-344" aria-hidden="true" tabindex="-1"></a>  <span class="fu">group_by</span>(ID) <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-345"><a href="#cb2945-345" aria-hidden="true" tabindex="-1"></a>  <span class="fu">slice</span>(<span class="fu">rep</span>(<span class="dv">1</span>, <span class="at">times =</span> <span class="fu">length</span>(times_to_simulate))) <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-346"><a href="#cb2945-346" aria-hidden="true" tabindex="-1"></a>  <span class="fu">mutate</span>(<span class="at">AMT =</span> <span class="dv">0</span>,</span>
+<span id="cb2945-347"><a href="#cb2945-347" aria-hidden="true" tabindex="-1"></a>         <span class="at">ADDL =</span> <span class="dv">0</span>,</span>
+<span id="cb2945-348"><a href="#cb2945-348" aria-hidden="true" tabindex="-1"></a>         <span class="at">II =</span> <span class="dv">0</span>,</span>
+<span id="cb2945-349"><a href="#cb2945-349" aria-hidden="true" tabindex="-1"></a>         <span class="at">CMT =</span> <span class="fu">if_else</span>(solver <span class="sc">==</span> <span class="dv">1</span>, <span class="dv">2</span>, <span class="dv">1</span>),</span>
+<span id="cb2945-350"><a href="#cb2945-350" aria-hidden="true" tabindex="-1"></a>         <span class="at">EVID =</span> <span class="dv">0</span>,</span>
+<span id="cb2945-351"><a href="#cb2945-351" aria-hidden="true" tabindex="-1"></a>         <span class="at">RATE =</span> <span class="dv">0</span>,</span>
+<span id="cb2945-352"><a href="#cb2945-352" aria-hidden="true" tabindex="-1"></a>         <span class="at">TIME =</span> times_to_simulate) <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-353"><a href="#cb2945-353" aria-hidden="true" tabindex="-1"></a>  <span class="fu">ungroup</span>() <span class="sc">%&gt;%</span></span>
+<span id="cb2945-354"><a href="#cb2945-354" aria-hidden="true" tabindex="-1"></a>  <span class="fu">bind_rows</span>(dosing_data) <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-355"><a href="#cb2945-355" aria-hidden="true" tabindex="-1"></a>  <span class="fu">arrange</span>(ID, TIME, AMT)</span>
+<span id="cb2945-356"><a href="#cb2945-356" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-357"><a href="#cb2945-357" aria-hidden="true" tabindex="-1"></a>n_subjects <span class="ot">&lt;-</span> nonmem_data_simulate <span class="sc">%&gt;%</span>  <span class="co"># number of individuals to simulate</span></span>
+<span id="cb2945-358"><a href="#cb2945-358" aria-hidden="true" tabindex="-1"></a>  <span class="fu">distinct</span>(ID) <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-359"><a href="#cb2945-359" aria-hidden="true" tabindex="-1"></a>  <span class="fu">count</span>() <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-360"><a href="#cb2945-360" aria-hidden="true" tabindex="-1"></a>  <span class="fu">deframe</span>()</span>
+<span id="cb2945-361"><a href="#cb2945-361" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-362"><a href="#cb2945-362" aria-hidden="true" tabindex="-1"></a>n_total <span class="ot">&lt;-</span> <span class="fu">nrow</span>(nonmem_data_simulate) <span class="co"># total number of time points at which to predict</span></span>
+<span id="cb2945-363"><a href="#cb2945-363" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-364"><a href="#cb2945-364" aria-hidden="true" tabindex="-1"></a>subj_start <span class="ot">&lt;-</span> nonmem_data_simulate <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-365"><a href="#cb2945-365" aria-hidden="true" tabindex="-1"></a>  <span class="fu">mutate</span>(<span class="at">row_num =</span> <span class="dv">1</span><span class="sc">:</span><span class="fu">n</span>()) <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-366"><a href="#cb2945-366" aria-hidden="true" tabindex="-1"></a>  <span class="fu">group_by</span>(ID) <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-367"><a href="#cb2945-367" aria-hidden="true" tabindex="-1"></a>  <span class="fu">slice_head</span>(<span class="at">n =</span> <span class="dv">1</span>) <span class="sc">%&gt;%</span></span>
+<span id="cb2945-368"><a href="#cb2945-368" aria-hidden="true" tabindex="-1"></a>  <span class="fu">ungroup</span>() <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-369"><a href="#cb2945-369" aria-hidden="true" tabindex="-1"></a>  <span class="fu">select</span>(row_num) <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-370"><a href="#cb2945-370" aria-hidden="true" tabindex="-1"></a>  <span class="fu">deframe</span>()</span>
+<span id="cb2945-371"><a href="#cb2945-371" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-372"><a href="#cb2945-372" aria-hidden="true" tabindex="-1"></a>subj_end <span class="ot">&lt;-</span> <span class="fu">c</span>(subj_start[<span class="sc">-</span><span class="dv">1</span>] <span class="sc">-</span> <span class="dv">1</span>, n_total) </span>
+<span id="cb2945-373"><a href="#cb2945-373" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-374"><a href="#cb2945-374" aria-hidden="true" tabindex="-1"></a>stan_data <span class="ot">&lt;-</span> <span class="fu">list</span>(<span class="at">n_subjects =</span> n_subjects,</span>
+<span id="cb2945-375"><a href="#cb2945-375" aria-hidden="true" tabindex="-1"></a>                  <span class="at">n_total =</span> n_total,</span>
+<span id="cb2945-376"><a href="#cb2945-376" aria-hidden="true" tabindex="-1"></a>                  <span class="at">time =</span> nonmem_data_simulate<span class="sc">$</span>TIME,</span>
+<span id="cb2945-377"><a href="#cb2945-377" aria-hidden="true" tabindex="-1"></a>                  <span class="at">amt =</span> nonmem_data_simulate<span class="sc">$</span>AMT,</span>
+<span id="cb2945-378"><a href="#cb2945-378" aria-hidden="true" tabindex="-1"></a>                  <span class="at">cmt =</span> nonmem_data_simulate<span class="sc">$</span>CMT,</span>
+<span id="cb2945-379"><a href="#cb2945-379" aria-hidden="true" tabindex="-1"></a>                  <span class="at">evid =</span> nonmem_data_simulate<span class="sc">$</span>EVID,</span>
+<span id="cb2945-380"><a href="#cb2945-380" aria-hidden="true" tabindex="-1"></a>                  <span class="at">rate =</span> nonmem_data_simulate<span class="sc">$</span>RATE,</span>
+<span id="cb2945-381"><a href="#cb2945-381" aria-hidden="true" tabindex="-1"></a>                  <span class="at">ii =</span> nonmem_data_simulate<span class="sc">$</span>II,</span>
+<span id="cb2945-382"><a href="#cb2945-382" aria-hidden="true" tabindex="-1"></a>                  <span class="at">addl =</span> nonmem_data_simulate<span class="sc">$</span>ADDL,</span>
+<span id="cb2945-383"><a href="#cb2945-383" aria-hidden="true" tabindex="-1"></a>                  <span class="at">ss =</span> nonmem_data_simulate<span class="sc">$</span>SS,</span>
+<span id="cb2945-384"><a href="#cb2945-384" aria-hidden="true" tabindex="-1"></a>                  <span class="at">subj_start =</span> subj_start,</span>
+<span id="cb2945-385"><a href="#cb2945-385" aria-hidden="true" tabindex="-1"></a>                  <span class="at">subj_end =</span> subj_end,</span>
+<span id="cb2945-386"><a href="#cb2945-386" aria-hidden="true" tabindex="-1"></a>                  <span class="at">TVCL =</span> TVCL,</span>
+<span id="cb2945-387"><a href="#cb2945-387" aria-hidden="true" tabindex="-1"></a>                  <span class="at">TVVC =</span> TVVC,</span>
+<span id="cb2945-388"><a href="#cb2945-388" aria-hidden="true" tabindex="-1"></a>                  <span class="at">TVQ =</span> TVQ,</span>
+<span id="cb2945-389"><a href="#cb2945-389" aria-hidden="true" tabindex="-1"></a>                  <span class="at">TVVP =</span> TVVP,</span>
+<span id="cb2945-390"><a href="#cb2945-390" aria-hidden="true" tabindex="-1"></a>                  <span class="at">omega_cl =</span> omega_cl,</span>
+<span id="cb2945-391"><a href="#cb2945-391" aria-hidden="true" tabindex="-1"></a>                  <span class="at">omega_vc =</span> omega_vc,</span>
+<span id="cb2945-392"><a href="#cb2945-392" aria-hidden="true" tabindex="-1"></a>                  <span class="at">omega_q =</span> omega_q,</span>
+<span id="cb2945-393"><a href="#cb2945-393" aria-hidden="true" tabindex="-1"></a>                  <span class="at">omega_vp =</span> omega_vp,</span>
+<span id="cb2945-394"><a href="#cb2945-394" aria-hidden="true" tabindex="-1"></a>                  <span class="at">R =</span> R,</span>
+<span id="cb2945-395"><a href="#cb2945-395" aria-hidden="true" tabindex="-1"></a>                  <span class="at">sigma_p =</span> sigma_p,</span>
+<span id="cb2945-396"><a href="#cb2945-396" aria-hidden="true" tabindex="-1"></a>                  <span class="at">sigma_a =</span> sigma_a,</span>
+<span id="cb2945-397"><a href="#cb2945-397" aria-hidden="true" tabindex="-1"></a>                  <span class="at">cor_p_a =</span> cor_p_a,</span>
+<span id="cb2945-398"><a href="#cb2945-398" aria-hidden="true" tabindex="-1"></a>                  <span class="at">solver =</span> solver) <span class="co"># analytical = 1, mat exp = 2, rk45 = 3</span></span>
+<span id="cb2945-399"><a href="#cb2945-399" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-400"><a href="#cb2945-400" aria-hidden="true" tabindex="-1"></a>model <span class="ot">&lt;-</span> <span class="fu">cmdstan_model</span>(</span>
+<span id="cb2945-401"><a href="#cb2945-401" aria-hidden="true" tabindex="-1"></a>  here<span class="sc">::</span><span class="fu">here</span>(<span class="st">&quot;M3/iv_2cmt_linear/Stan/Simulate/iv_2cmt_ppa.stan&quot;</span>))</span>
+<span id="cb2945-402"><a href="#cb2945-402" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-403"><a href="#cb2945-403" aria-hidden="true" tabindex="-1"></a>model<span class="sc">$</span><span class="fu">print</span>()</span>
+<span id="cb2945-404"><a href="#cb2945-404" aria-hidden="true" tabindex="-1"></a><span class="in">```</span></span>
+<span id="cb2945-405"><a href="#cb2945-405" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-406"><a href="#cb2945-406" aria-hidden="true" tabindex="-1"></a>:::</span>
+<span id="cb2945-407"><a href="#cb2945-407" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-410"><a href="#cb2945-410" aria-hidden="true" tabindex="-1"></a><span class="in">```{r}</span></span>
+<span id="cb2945-411"><a href="#cb2945-411" aria-hidden="true" tabindex="-1"></a><span class="co">#| cache: true</span></span>
+<span id="cb2945-412"><a href="#cb2945-412" aria-hidden="true" tabindex="-1"></a><span class="co">#| output: false</span></span>
+<span id="cb2945-413"><a href="#cb2945-413" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-414"><a href="#cb2945-414" aria-hidden="true" tabindex="-1"></a>simulated_data <span class="ot">&lt;-</span> model<span class="sc">$</span><span class="fu">sample</span>(<span class="at">data =</span> stan_data,</span>
+<span id="cb2945-415"><a href="#cb2945-415" aria-hidden="true" tabindex="-1"></a>                               <span class="at">fixed_param =</span> <span class="cn">TRUE</span>,</span>
+<span id="cb2945-416"><a href="#cb2945-416" aria-hidden="true" tabindex="-1"></a>                               <span class="at">seed =</span> <span class="dv">112358</span>,</span>
+<span id="cb2945-417"><a href="#cb2945-417" aria-hidden="true" tabindex="-1"></a>                               <span class="at">iter_warmup =</span> <span class="dv">0</span>,</span>
+<span id="cb2945-418"><a href="#cb2945-418" aria-hidden="true" tabindex="-1"></a>                               <span class="at">iter_sampling =</span> <span class="dv">1</span>,</span>
+<span id="cb2945-419"><a href="#cb2945-419" aria-hidden="true" tabindex="-1"></a>                               <span class="at">chains =</span> <span class="dv">1</span>,</span>
+<span id="cb2945-420"><a href="#cb2945-420" aria-hidden="true" tabindex="-1"></a>                               <span class="at">parallel_chains =</span> <span class="dv">1</span>)</span>
+<span id="cb2945-421"><a href="#cb2945-421" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-422"><a href="#cb2945-422" aria-hidden="true" tabindex="-1"></a>data_analytical <span class="ot">&lt;-</span> simulated_data<span class="sc">$</span><span class="fu">draws</span>(<span class="fu">c</span>(<span class="st">&quot;dv&quot;</span>, <span class="st">&quot;ipred&quot;</span>)) <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-423"><a href="#cb2945-423" aria-hidden="true" tabindex="-1"></a>  <span class="fu">spread_draws</span>(dv[i], ipred[i]) <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-424"><a href="#cb2945-424" aria-hidden="true" tabindex="-1"></a>  <span class="fu">ungroup</span>() <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-425"><a href="#cb2945-425" aria-hidden="true" tabindex="-1"></a>  <span class="fu">inner_join</span>(nonmem_data_simulate <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-426"><a href="#cb2945-426" aria-hidden="true" tabindex="-1"></a>               <span class="fu">mutate</span>(<span class="at">i =</span> <span class="dv">1</span><span class="sc">:</span><span class="fu">n</span>()),</span>
+<span id="cb2945-427"><a href="#cb2945-427" aria-hidden="true" tabindex="-1"></a>             <span class="at">by =</span> <span class="st">&quot;i&quot;</span>) <span class="sc">%&gt;%</span></span>
+<span id="cb2945-428"><a href="#cb2945-428" aria-hidden="true" tabindex="-1"></a>  <span class="fu">select</span>(ID, AMT, II, ADDL, RATE, CMT, EVID, SS, TIME, </span>
+<span id="cb2945-429"><a href="#cb2945-429" aria-hidden="true" tabindex="-1"></a>         <span class="at">DV =</span> <span class="st">&quot;dv&quot;</span>, <span class="at">IPRED =</span> <span class="st">&quot;ipred&quot;</span>) <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-430"><a href="#cb2945-430" aria-hidden="true" tabindex="-1"></a>  <span class="fu">mutate</span>(<span class="at">LLOQ =</span> <span class="fl">1e-6</span>, </span>
+<span id="cb2945-431"><a href="#cb2945-431" aria-hidden="true" tabindex="-1"></a>         <span class="at">BLOQ =</span> <span class="fu">case_when</span>(EVID <span class="sc">==</span> <span class="dv">1</span> <span class="sc">~</span> <span class="cn">NA_real_</span>,</span>
+<span id="cb2945-432"><a href="#cb2945-432" aria-hidden="true" tabindex="-1"></a>                          DV <span class="sc">&lt;=</span> LLOQ <span class="sc">~</span> <span class="dv">1</span>,</span>
+<span id="cb2945-433"><a href="#cb2945-433" aria-hidden="true" tabindex="-1"></a>                          DV <span class="sc">&gt;</span> LLOQ <span class="sc">~</span> <span class="dv">0</span>,</span>
+<span id="cb2945-434"><a href="#cb2945-434" aria-hidden="true" tabindex="-1"></a>                          <span class="cn">TRUE</span> <span class="sc">~</span> <span class="cn">NA_real_</span>),</span>
+<span id="cb2945-435"><a href="#cb2945-435" aria-hidden="true" tabindex="-1"></a>         <span class="at">DV =</span> <span class="fu">if_else</span>(EVID <span class="sc">==</span> <span class="dv">1</span> <span class="sc">|</span> BLOQ <span class="sc">==</span> <span class="dv">1</span>, <span class="cn">NA_real_</span>, DV),</span>
+<span id="cb2945-436"><a href="#cb2945-436" aria-hidden="true" tabindex="-1"></a>         <span class="at">MDV =</span> <span class="fu">if_else</span>(<span class="fu">is.na</span>(DV), <span class="dv">1</span>, <span class="dv">0</span>)) <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-437"><a href="#cb2945-437" aria-hidden="true" tabindex="-1"></a>  <span class="fu">relocate</span>(DV, <span class="at">.after =</span> <span class="fu">last_col</span>()) <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-438"><a href="#cb2945-438" aria-hidden="true" tabindex="-1"></a>  <span class="fu">relocate</span>(TIME, <span class="at">.before =</span> DV) <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-439"><a href="#cb2945-439" aria-hidden="true" tabindex="-1"></a>  <span class="fu">mutate</span>(<span class="at">solver =</span> <span class="st">&quot;analytical&quot;</span>)</span>
+<span id="cb2945-440"><a href="#cb2945-440" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-441"><a href="#cb2945-441" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-442"><a href="#cb2945-442" aria-hidden="true" tabindex="-1"></a>solver <span class="ot">&lt;-</span> <span class="dv">2</span></span>
+<span id="cb2945-443"><a href="#cb2945-443" aria-hidden="true" tabindex="-1"></a>dosing_data <span class="ot">&lt;-</span> dosing_data <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-444"><a href="#cb2945-444" aria-hidden="true" tabindex="-1"></a>  <span class="fu">mutate</span>(<span class="at">CMT =</span> <span class="fu">if_else</span>(solver <span class="sc">==</span> <span class="dv">1</span>, <span class="dv">2</span>, <span class="dv">1</span>)) </span>
+<span id="cb2945-445"><a href="#cb2945-445" aria-hidden="true" tabindex="-1"></a>  </span>
+<span id="cb2945-446"><a href="#cb2945-446" aria-hidden="true" tabindex="-1"></a>nonmem_data_simulate <span class="ot">&lt;-</span> dosing_data <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-447"><a href="#cb2945-447" aria-hidden="true" tabindex="-1"></a>  <span class="fu">group_by</span>(ID) <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-448"><a href="#cb2945-448" aria-hidden="true" tabindex="-1"></a>  <span class="fu">slice</span>(<span class="fu">rep</span>(<span class="dv">1</span>, <span class="at">times =</span> <span class="fu">length</span>(times_to_simulate))) <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-449"><a href="#cb2945-449" aria-hidden="true" tabindex="-1"></a>  <span class="fu">mutate</span>(<span class="at">AMT =</span> <span class="dv">0</span>,</span>
+<span id="cb2945-450"><a href="#cb2945-450" aria-hidden="true" tabindex="-1"></a>         <span class="at">ADDL =</span> <span class="dv">0</span>,</span>
+<span id="cb2945-451"><a href="#cb2945-451" aria-hidden="true" tabindex="-1"></a>         <span class="at">II =</span> <span class="dv">0</span>,</span>
+<span id="cb2945-452"><a href="#cb2945-452" aria-hidden="true" tabindex="-1"></a>         <span class="at">CMT =</span> <span class="fu">if_else</span>(solver <span class="sc">==</span> <span class="dv">1</span>, <span class="dv">2</span>, <span class="dv">1</span>),</span>
+<span id="cb2945-453"><a href="#cb2945-453" aria-hidden="true" tabindex="-1"></a>         <span class="at">EVID =</span> <span class="dv">0</span>,</span>
+<span id="cb2945-454"><a href="#cb2945-454" aria-hidden="true" tabindex="-1"></a>         <span class="at">RATE =</span> <span class="dv">0</span>,</span>
+<span id="cb2945-455"><a href="#cb2945-455" aria-hidden="true" tabindex="-1"></a>         <span class="at">TIME =</span> times_to_simulate) <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-456"><a href="#cb2945-456" aria-hidden="true" tabindex="-1"></a>  <span class="fu">ungroup</span>() <span class="sc">%&gt;%</span></span>
+<span id="cb2945-457"><a href="#cb2945-457" aria-hidden="true" tabindex="-1"></a>  <span class="fu">bind_rows</span>(dosing_data) <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-458"><a href="#cb2945-458" aria-hidden="true" tabindex="-1"></a>  <span class="fu">arrange</span>(ID, TIME, AMT) </span>
+<span id="cb2945-459"><a href="#cb2945-459" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-460"><a href="#cb2945-460" aria-hidden="true" tabindex="-1"></a>stan_data <span class="ot">&lt;-</span> <span class="fu">list</span>(<span class="at">n_subjects =</span> n_subjects,</span>
+<span id="cb2945-461"><a href="#cb2945-461" aria-hidden="true" tabindex="-1"></a>                  <span class="at">n_total =</span> n_total,</span>
+<span id="cb2945-462"><a href="#cb2945-462" aria-hidden="true" tabindex="-1"></a>                  <span class="at">time =</span> nonmem_data_simulate<span class="sc">$</span>TIME,</span>
+<span id="cb2945-463"><a href="#cb2945-463" aria-hidden="true" tabindex="-1"></a>                  <span class="at">amt =</span> nonmem_data_simulate<span class="sc">$</span>AMT,</span>
+<span id="cb2945-464"><a href="#cb2945-464" aria-hidden="true" tabindex="-1"></a>                  <span class="at">cmt =</span> nonmem_data_simulate<span class="sc">$</span>CMT,</span>
+<span id="cb2945-465"><a href="#cb2945-465" aria-hidden="true" tabindex="-1"></a>                  <span class="at">evid =</span> nonmem_data_simulate<span class="sc">$</span>EVID,</span>
+<span id="cb2945-466"><a href="#cb2945-466" aria-hidden="true" tabindex="-1"></a>                  <span class="at">rate =</span> nonmem_data_simulate<span class="sc">$</span>RATE,</span>
+<span id="cb2945-467"><a href="#cb2945-467" aria-hidden="true" tabindex="-1"></a>                  <span class="at">ii =</span> nonmem_data_simulate<span class="sc">$</span>II,</span>
+<span id="cb2945-468"><a href="#cb2945-468" aria-hidden="true" tabindex="-1"></a>                  <span class="at">addl =</span> nonmem_data_simulate<span class="sc">$</span>ADDL,</span>
+<span id="cb2945-469"><a href="#cb2945-469" aria-hidden="true" tabindex="-1"></a>                  <span class="at">ss =</span> nonmem_data_simulate<span class="sc">$</span>SS,</span>
+<span id="cb2945-470"><a href="#cb2945-470" aria-hidden="true" tabindex="-1"></a>                  <span class="at">subj_start =</span> subj_start,</span>
+<span id="cb2945-471"><a href="#cb2945-471" aria-hidden="true" tabindex="-1"></a>                  <span class="at">subj_end =</span> subj_end,</span>
+<span id="cb2945-472"><a href="#cb2945-472" aria-hidden="true" tabindex="-1"></a>                  <span class="at">TVCL =</span> TVCL,</span>
+<span id="cb2945-473"><a href="#cb2945-473" aria-hidden="true" tabindex="-1"></a>                  <span class="at">TVVC =</span> TVVC,</span>
+<span id="cb2945-474"><a href="#cb2945-474" aria-hidden="true" tabindex="-1"></a>                  <span class="at">TVQ =</span> TVQ,</span>
+<span id="cb2945-475"><a href="#cb2945-475" aria-hidden="true" tabindex="-1"></a>                  <span class="at">TVVP =</span> TVVP,</span>
+<span id="cb2945-476"><a href="#cb2945-476" aria-hidden="true" tabindex="-1"></a>                  <span class="at">omega_cl =</span> omega_cl,</span>
+<span id="cb2945-477"><a href="#cb2945-477" aria-hidden="true" tabindex="-1"></a>                  <span class="at">omega_vc =</span> omega_vc,</span>
+<span id="cb2945-478"><a href="#cb2945-478" aria-hidden="true" tabindex="-1"></a>                  <span class="at">omega_q =</span> omega_q,</span>
+<span id="cb2945-479"><a href="#cb2945-479" aria-hidden="true" tabindex="-1"></a>                  <span class="at">omega_vp =</span> omega_vp,</span>
+<span id="cb2945-480"><a href="#cb2945-480" aria-hidden="true" tabindex="-1"></a>                  <span class="at">R =</span> R,</span>
+<span id="cb2945-481"><a href="#cb2945-481" aria-hidden="true" tabindex="-1"></a>                  <span class="at">sigma_p =</span> sigma_p,</span>
+<span id="cb2945-482"><a href="#cb2945-482" aria-hidden="true" tabindex="-1"></a>                  <span class="at">sigma_a =</span> sigma_a,</span>
+<span id="cb2945-483"><a href="#cb2945-483" aria-hidden="true" tabindex="-1"></a>                  <span class="at">cor_p_a =</span> cor_p_a,</span>
+<span id="cb2945-484"><a href="#cb2945-484" aria-hidden="true" tabindex="-1"></a>                  <span class="at">solver =</span> solver) </span>
+<span id="cb2945-485"><a href="#cb2945-485" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-486"><a href="#cb2945-486" aria-hidden="true" tabindex="-1"></a>simulated_data <span class="ot">&lt;-</span> model<span class="sc">$</span><span class="fu">sample</span>(<span class="at">data =</span> stan_data,</span>
+<span id="cb2945-487"><a href="#cb2945-487" aria-hidden="true" tabindex="-1"></a>                               <span class="at">fixed_param =</span> <span class="cn">TRUE</span>,</span>
+<span id="cb2945-488"><a href="#cb2945-488" aria-hidden="true" tabindex="-1"></a>                               <span class="at">seed =</span> <span class="dv">112358</span>,</span>
+<span id="cb2945-489"><a href="#cb2945-489" aria-hidden="true" tabindex="-1"></a>                               <span class="at">iter_warmup =</span> <span class="dv">0</span>,</span>
+<span id="cb2945-490"><a href="#cb2945-490" aria-hidden="true" tabindex="-1"></a>                               <span class="at">iter_sampling =</span> <span class="dv">1</span>,</span>
+<span id="cb2945-491"><a href="#cb2945-491" aria-hidden="true" tabindex="-1"></a>                               <span class="at">chains =</span> <span class="dv">1</span>,</span>
+<span id="cb2945-492"><a href="#cb2945-492" aria-hidden="true" tabindex="-1"></a>                               <span class="at">parallel_chains =</span> <span class="dv">1</span>)</span>
+<span id="cb2945-493"><a href="#cb2945-493" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-494"><a href="#cb2945-494" aria-hidden="true" tabindex="-1"></a>data_mat_exp <span class="ot">&lt;-</span> simulated_data<span class="sc">$</span><span class="fu">draws</span>(<span class="fu">c</span>(<span class="st">&quot;dv&quot;</span>, <span class="st">&quot;ipred&quot;</span>)) <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-495"><a href="#cb2945-495" aria-hidden="true" tabindex="-1"></a>  <span class="fu">spread_draws</span>(dv[i], ipred[i]) <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-496"><a href="#cb2945-496" aria-hidden="true" tabindex="-1"></a>  <span class="fu">ungroup</span>() <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-497"><a href="#cb2945-497" aria-hidden="true" tabindex="-1"></a>  <span class="fu">inner_join</span>(nonmem_data_simulate <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-498"><a href="#cb2945-498" aria-hidden="true" tabindex="-1"></a>               <span class="fu">mutate</span>(<span class="at">i =</span> <span class="dv">1</span><span class="sc">:</span><span class="fu">n</span>()),</span>
+<span id="cb2945-499"><a href="#cb2945-499" aria-hidden="true" tabindex="-1"></a>             <span class="at">by =</span> <span class="st">&quot;i&quot;</span>) <span class="sc">%&gt;%</span></span>
+<span id="cb2945-500"><a href="#cb2945-500" aria-hidden="true" tabindex="-1"></a>  <span class="fu">select</span>(ID, AMT, II, ADDL, RATE, CMT, EVID, SS, TIME, </span>
+<span id="cb2945-501"><a href="#cb2945-501" aria-hidden="true" tabindex="-1"></a>         <span class="at">DV =</span> <span class="st">&quot;dv&quot;</span>, <span class="at">IPRED =</span> <span class="st">&quot;ipred&quot;</span>) <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-502"><a href="#cb2945-502" aria-hidden="true" tabindex="-1"></a>  <span class="fu">mutate</span>(<span class="at">LLOQ =</span> <span class="fl">1e-6</span>, </span>
+<span id="cb2945-503"><a href="#cb2945-503" aria-hidden="true" tabindex="-1"></a>         <span class="at">BLOQ =</span> <span class="fu">case_when</span>(EVID <span class="sc">==</span> <span class="dv">1</span> <span class="sc">~</span> <span class="cn">NA_real_</span>,</span>
+<span id="cb2945-504"><a href="#cb2945-504" aria-hidden="true" tabindex="-1"></a>                          DV <span class="sc">&lt;=</span> LLOQ <span class="sc">~</span> <span class="dv">1</span>,</span>
+<span id="cb2945-505"><a href="#cb2945-505" aria-hidden="true" tabindex="-1"></a>                          DV <span class="sc">&gt;</span> LLOQ <span class="sc">~</span> <span class="dv">0</span>,</span>
+<span id="cb2945-506"><a href="#cb2945-506" aria-hidden="true" tabindex="-1"></a>                          <span class="cn">TRUE</span> <span class="sc">~</span> <span class="cn">NA_real_</span>),</span>
+<span id="cb2945-507"><a href="#cb2945-507" aria-hidden="true" tabindex="-1"></a>         <span class="at">DV =</span> <span class="fu">if_else</span>(EVID <span class="sc">==</span> <span class="dv">1</span> <span class="sc">|</span> BLOQ <span class="sc">==</span> <span class="dv">1</span>, <span class="cn">NA_real_</span>, DV),</span>
+<span id="cb2945-508"><a href="#cb2945-508" aria-hidden="true" tabindex="-1"></a>         <span class="at">MDV =</span> <span class="fu">if_else</span>(<span class="fu">is.na</span>(DV), <span class="dv">1</span>, <span class="dv">0</span>)) <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-509"><a href="#cb2945-509" aria-hidden="true" tabindex="-1"></a>  <span class="fu">relocate</span>(DV, <span class="at">.after =</span> <span class="fu">last_col</span>()) <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-510"><a href="#cb2945-510" aria-hidden="true" tabindex="-1"></a>  <span class="fu">relocate</span>(TIME, <span class="at">.before =</span> DV) <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-511"><a href="#cb2945-511" aria-hidden="true" tabindex="-1"></a>  <span class="fu">mutate</span>(<span class="at">solver =</span> <span class="st">&quot;mat_exp&quot;</span>)</span>
+<span id="cb2945-512"><a href="#cb2945-512" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-513"><a href="#cb2945-513" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-514"><a href="#cb2945-514" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-515"><a href="#cb2945-515" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-516"><a href="#cb2945-516" aria-hidden="true" tabindex="-1"></a>solver <span class="ot">&lt;-</span> <span class="dv">3</span></span>
+<span id="cb2945-517"><a href="#cb2945-517" aria-hidden="true" tabindex="-1"></a>stan_data<span class="sc">$</span>solver <span class="ot">&lt;-</span> solver</span>
+<span id="cb2945-518"><a href="#cb2945-518" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-519"><a href="#cb2945-519" aria-hidden="true" tabindex="-1"></a>simulated_data <span class="ot">&lt;-</span> model<span class="sc">$</span><span class="fu">sample</span>(<span class="at">data =</span> stan_data,</span>
+<span id="cb2945-520"><a href="#cb2945-520" aria-hidden="true" tabindex="-1"></a>                               <span class="at">fixed_param =</span> <span class="cn">TRUE</span>,</span>
+<span id="cb2945-521"><a href="#cb2945-521" aria-hidden="true" tabindex="-1"></a>                               <span class="at">seed =</span> <span class="dv">112358</span>,</span>
+<span id="cb2945-522"><a href="#cb2945-522" aria-hidden="true" tabindex="-1"></a>                               <span class="at">iter_warmup =</span> <span class="dv">0</span>,</span>
+<span id="cb2945-523"><a href="#cb2945-523" aria-hidden="true" tabindex="-1"></a>                               <span class="at">iter_sampling =</span> <span class="dv">1</span>,</span>
+<span id="cb2945-524"><a href="#cb2945-524" aria-hidden="true" tabindex="-1"></a>                               <span class="at">chains =</span> <span class="dv">1</span>,</span>
+<span id="cb2945-525"><a href="#cb2945-525" aria-hidden="true" tabindex="-1"></a>                               <span class="at">parallel_chains =</span> <span class="dv">1</span>)</span>
+<span id="cb2945-526"><a href="#cb2945-526" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-527"><a href="#cb2945-527" aria-hidden="true" tabindex="-1"></a>data_rk45 <span class="ot">&lt;-</span> simulated_data<span class="sc">$</span><span class="fu">draws</span>(<span class="fu">c</span>(<span class="st">&quot;dv&quot;</span>, <span class="st">&quot;ipred&quot;</span>)) <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-528"><a href="#cb2945-528" aria-hidden="true" tabindex="-1"></a>  <span class="fu">spread_draws</span>(dv[i], ipred[i]) <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-529"><a href="#cb2945-529" aria-hidden="true" tabindex="-1"></a>  <span class="fu">ungroup</span>() <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-530"><a href="#cb2945-530" aria-hidden="true" tabindex="-1"></a>  <span class="fu">inner_join</span>(nonmem_data_simulate <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-531"><a href="#cb2945-531" aria-hidden="true" tabindex="-1"></a>               <span class="fu">mutate</span>(<span class="at">i =</span> <span class="dv">1</span><span class="sc">:</span><span class="fu">n</span>()),</span>
+<span id="cb2945-532"><a href="#cb2945-532" aria-hidden="true" tabindex="-1"></a>             <span class="at">by =</span> <span class="st">&quot;i&quot;</span>) <span class="sc">%&gt;%</span></span>
+<span id="cb2945-533"><a href="#cb2945-533" aria-hidden="true" tabindex="-1"></a>  <span class="fu">select</span>(ID, AMT, II, ADDL, RATE, CMT, EVID, SS, TIME, </span>
+<span id="cb2945-534"><a href="#cb2945-534" aria-hidden="true" tabindex="-1"></a>         <span class="at">DV =</span> <span class="st">&quot;dv&quot;</span>, <span class="at">IPRED =</span> <span class="st">&quot;ipred&quot;</span>) <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-535"><a href="#cb2945-535" aria-hidden="true" tabindex="-1"></a>  <span class="fu">mutate</span>(<span class="at">LLOQ =</span> <span class="fl">1e-6</span>, </span>
+<span id="cb2945-536"><a href="#cb2945-536" aria-hidden="true" tabindex="-1"></a>         <span class="at">BLOQ =</span> <span class="fu">case_when</span>(EVID <span class="sc">==</span> <span class="dv">1</span> <span class="sc">~</span> <span class="cn">NA_real_</span>,</span>
+<span id="cb2945-537"><a href="#cb2945-537" aria-hidden="true" tabindex="-1"></a>                          DV <span class="sc">&lt;=</span> LLOQ <span class="sc">~</span> <span class="dv">1</span>,</span>
+<span id="cb2945-538"><a href="#cb2945-538" aria-hidden="true" tabindex="-1"></a>                          DV <span class="sc">&gt;</span> LLOQ <span class="sc">~</span> <span class="dv">0</span>,</span>
+<span id="cb2945-539"><a href="#cb2945-539" aria-hidden="true" tabindex="-1"></a>                          <span class="cn">TRUE</span> <span class="sc">~</span> <span class="cn">NA_real_</span>),</span>
+<span id="cb2945-540"><a href="#cb2945-540" aria-hidden="true" tabindex="-1"></a>         <span class="at">DV =</span> <span class="fu">if_else</span>(EVID <span class="sc">==</span> <span class="dv">1</span> <span class="sc">|</span> BLOQ <span class="sc">==</span> <span class="dv">1</span>, <span class="cn">NA_real_</span>, DV),</span>
+<span id="cb2945-541"><a href="#cb2945-541" aria-hidden="true" tabindex="-1"></a>         <span class="at">MDV =</span> <span class="fu">if_else</span>(<span class="fu">is.na</span>(DV), <span class="dv">1</span>, <span class="dv">0</span>)) <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-542"><a href="#cb2945-542" aria-hidden="true" tabindex="-1"></a>  <span class="fu">relocate</span>(DV, <span class="at">.after =</span> <span class="fu">last_col</span>()) <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-543"><a href="#cb2945-543" aria-hidden="true" tabindex="-1"></a>  <span class="fu">relocate</span>(TIME, <span class="at">.before =</span> DV) <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-544"><a href="#cb2945-544" aria-hidden="true" tabindex="-1"></a>  <span class="fu">mutate</span>(<span class="at">solver =</span> <span class="st">&quot;rk45&quot;</span>)</span>
+<span id="cb2945-545"><a href="#cb2945-545" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-546"><a href="#cb2945-546" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-547"><a href="#cb2945-547" aria-hidden="true" tabindex="-1"></a><span class="do">## Now do it with mrgsolve to check</span></span>
+<span id="cb2945-548"><a href="#cb2945-548" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-549"><a href="#cb2945-549" aria-hidden="true" tabindex="-1"></a>mod <span class="ot">&lt;-</span> <span class="fu">mread</span>(here<span class="sc">::</span><span class="fu">here</span>(<span class="st">&quot;M3/iv_2cmt_linear/mrgsolve/iv_2cmt_ppa.cpp&quot;</span>))</span>
+<span id="cb2945-550"><a href="#cb2945-550" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-551"><a href="#cb2945-551" aria-hidden="true" tabindex="-1"></a>data_mrgsolve <span class="ot">&lt;-</span> mod <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-552"><a href="#cb2945-552" aria-hidden="true" tabindex="-1"></a>  <span class="fu">param</span>(<span class="fu">tibble</span>(<span class="at">TVCL =</span> TVCL,</span>
+<span id="cb2945-553"><a href="#cb2945-553" aria-hidden="true" tabindex="-1"></a>               <span class="at">TVVC =</span> TVVC,</span>
+<span id="cb2945-554"><a href="#cb2945-554" aria-hidden="true" tabindex="-1"></a>               <span class="at">TVQ =</span> TVQ,</span>
+<span id="cb2945-555"><a href="#cb2945-555" aria-hidden="true" tabindex="-1"></a>               <span class="at">TVVP =</span> TVVP)) <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-556"><a href="#cb2945-556" aria-hidden="true" tabindex="-1"></a>  <span class="fu">data_set</span>(dosing_data) <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-557"><a href="#cb2945-557" aria-hidden="true" tabindex="-1"></a>  <span class="fu">mrgsim_df</span>(<span class="at">tgrid =</span> times_to_simulate) <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-558"><a href="#cb2945-558" aria-hidden="true" tabindex="-1"></a>  <span class="fu">as_tibble</span>() <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-559"><a href="#cb2945-559" aria-hidden="true" tabindex="-1"></a>  <span class="fu">mutate</span>(<span class="at">solver =</span> <span class="st">&quot;mrgsolve&quot;</span>)</span>
+<span id="cb2945-560"><a href="#cb2945-560" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-561"><a href="#cb2945-561" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-562"><a href="#cb2945-562" aria-hidden="true" tabindex="-1"></a><span class="in">```</span></span>
+<span id="cb2945-563"><a href="#cb2945-563" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-564"><a href="#cb2945-564" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-567"><a href="#cb2945-567" aria-hidden="true" tabindex="-1"></a><span class="in">```{r}</span></span>
+<span id="cb2945-568"><a href="#cb2945-568" aria-hidden="true" tabindex="-1"></a><span class="co">#| fig-align: center</span></span>
+<span id="cb2945-569"><a href="#cb2945-569" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-570"><a href="#cb2945-570" aria-hidden="true" tabindex="-1"></a><span class="fu">mget</span>(<span class="fu">str_subset</span>(<span class="fu">ls</span>(), <span class="st">&quot;^data_&quot;</span>)) <span class="sc">%&gt;%</span></span>
+<span id="cb2945-571"><a href="#cb2945-571" aria-hidden="true" tabindex="-1"></a>  <span class="fu">bind_rows</span>() <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-572"><a href="#cb2945-572" aria-hidden="true" tabindex="-1"></a>  <span class="fu">ggplot</span>(<span class="fu">aes</span>(<span class="at">x =</span> TIME, <span class="at">y =</span> IPRED, <span class="at">color =</span> solver)) <span class="sc">+</span></span>
+<span id="cb2945-573"><a href="#cb2945-573" aria-hidden="true" tabindex="-1"></a>  <span class="fu">geom_line</span>(<span class="fu">aes</span>(<span class="at">linetype =</span> solver)) <span class="sc">+</span></span>
+<span id="cb2945-574"><a href="#cb2945-574" aria-hidden="true" tabindex="-1"></a>  <span class="fu">theme_bw</span>() <span class="sc">+</span></span>
+<span id="cb2945-575"><a href="#cb2945-575" aria-hidden="true" tabindex="-1"></a>  <span class="fu">scale_x_continuous</span>(<span class="at">name =</span> <span class="st">&quot;Time (h)&quot;</span>,</span>
+<span id="cb2945-576"><a href="#cb2945-576" aria-hidden="true" tabindex="-1"></a>                     <span class="at">breaks =</span> <span class="fu">seq</span>(<span class="dv">0</span>, <span class="dv">168</span>, <span class="at">by =</span> <span class="dv">24</span>),</span>
+<span id="cb2945-577"><a href="#cb2945-577" aria-hidden="true" tabindex="-1"></a>                     <span class="at">labels =</span> <span class="fu">seq</span>(<span class="dv">0</span>, <span class="dv">168</span>, <span class="at">by =</span> <span class="dv">24</span>)) <span class="sc">+</span></span>
+<span id="cb2945-578"><a href="#cb2945-578" aria-hidden="true" tabindex="-1"></a>  <span class="fu">scale_y_continuous</span>(<span class="at">name =</span> <span class="st">&quot;Drug Conc. (ug/mL)&quot;</span>)</span>
+<span id="cb2945-579"><a href="#cb2945-579" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-580"><a href="#cb2945-580" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-581"><a href="#cb2945-581" aria-hidden="true" tabindex="-1"></a><span class="in">```</span></span>
+<span id="cb2945-582"><a href="#cb2945-582" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-583"><a href="#cb2945-583" aria-hidden="true" tabindex="-1"></a>So you can see for the M2, the analytical soultion, linear ODE, general ODE, </span>
+<span id="cb2945-584"><a href="#cb2945-584" aria-hidden="true" tabindex="-1"></a>and mrgsolve simulations are all the same, in contrast with the M3 where the </span>
+<span id="cb2945-585"><a href="#cb2945-585" aria-hidden="true" tabindex="-1"></a>analytical solution was a vector of zeros.</span>
+<span id="cb2945-586"><a href="#cb2945-586" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-587"><a href="#cb2945-587" aria-hidden="true" tabindex="-1"></a><span class="fu">## Fitting ```pk2cpt```, ```pk2cpt_linode```, ```pk2cpt_ode``` from ```example-models/```</span></span>
+<span id="cb2945-588"><a href="#cb2945-588" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-589"><a href="#cb2945-589" aria-hidden="true" tabindex="-1"></a>I made a few modifications in the R script to fit the project and a couple </span>
+<span id="cb2945-590"><a href="#cb2945-590" aria-hidden="true" tabindex="-1"></a>small changes in the general ODE model while trying to debug it, but no changes </span>
+<span id="cb2945-591"><a href="#cb2945-591" aria-hidden="true" tabindex="-1"></a>of any major substance.</span>
+<span id="cb2945-592"><a href="#cb2945-592" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-593"><a href="#cb2945-593" aria-hidden="true" tabindex="-1"></a><span class="fu">### ```pk2cpt```</span></span>
+<span id="cb2945-594"><a href="#cb2945-594" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-595"><a href="#cb2945-595" aria-hidden="true" tabindex="-1"></a>:::{.scrolling_500}</span>
+<span id="cb2945-596"><a href="#cb2945-596" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-599"><a href="#cb2945-599" aria-hidden="true" tabindex="-1"></a><span class="in">```{r}</span></span>
+<span id="cb2945-600"><a href="#cb2945-600" aria-hidden="true" tabindex="-1"></a>model_analytical <span class="ot">&lt;-</span> <span class="fu">cmdstan_model</span>(</span>
+<span id="cb2945-601"><a href="#cb2945-601" aria-hidden="true" tabindex="-1"></a>  here<span class="sc">::</span><span class="fu">here</span>(<span class="st">&quot;M3/example_models_metrum/pk2cpt/pk2cpt.stan&quot;</span>))</span>
+<span id="cb2945-602"><a href="#cb2945-602" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-603"><a href="#cb2945-603" aria-hidden="true" tabindex="-1"></a>fit_analytical <span class="ot">&lt;-</span> model_analytical<span class="sc">$</span><span class="fu">sample</span>(</span>
+<span id="cb2945-604"><a href="#cb2945-604" aria-hidden="true" tabindex="-1"></a>  <span class="at">data =</span> here<span class="sc">::</span><span class="fu">here</span>(<span class="st">&quot;M3/example_models_metrum/pk2cpt/pk2cpt.data.R&quot;</span>), </span>
+<span id="cb2945-605"><a href="#cb2945-605" aria-hidden="true" tabindex="-1"></a>  <span class="at">init =</span> here<span class="sc">::</span><span class="fu">here</span>(<span class="st">&quot;M3/example_models_metrum/pk2cpt/pk2cpt.init.R&quot;</span>), </span>
+<span id="cb2945-606"><a href="#cb2945-606" aria-hidden="true" tabindex="-1"></a>  <span class="at">seed =</span> <span class="dv">3191951</span>,</span>
+<span id="cb2945-607"><a href="#cb2945-607" aria-hidden="true" tabindex="-1"></a>  <span class="at">chains =</span> <span class="dv">1</span>,</span>
+<span id="cb2945-608"><a href="#cb2945-608" aria-hidden="true" tabindex="-1"></a>  <span class="at">parallel_chains =</span> <span class="dv">1</span>,</span>
+<span id="cb2945-609"><a href="#cb2945-609" aria-hidden="true" tabindex="-1"></a>  <span class="at">iter_warmup =</span> <span class="dv">500</span>,</span>
+<span id="cb2945-610"><a href="#cb2945-610" aria-hidden="true" tabindex="-1"></a>  <span class="at">iter_sampling =</span> <span class="dv">1000</span>,</span>
+<span id="cb2945-611"><a href="#cb2945-611" aria-hidden="true" tabindex="-1"></a>  <span class="at">adapt_delta =</span> <span class="fl">0.80</span>)</span>
+<span id="cb2945-612"><a href="#cb2945-612" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-613"><a href="#cb2945-613" aria-hidden="true" tabindex="-1"></a><span class="in">```</span></span>
+<span id="cb2945-614"><a href="#cb2945-614" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-615"><a href="#cb2945-615" aria-hidden="true" tabindex="-1"></a>:::</span>
+<span id="cb2945-616"><a href="#cb2945-616" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-617"><a href="#cb2945-617" aria-hidden="true" tabindex="-1"></a>This seems to work, in contrast to the M3 where we had a vector of zeros.</span>
+<span id="cb2945-618"><a href="#cb2945-618" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-619"><a href="#cb2945-619" aria-hidden="true" tabindex="-1"></a><span class="fu">### ```pk2cpt_linode```</span></span>
+<span id="cb2945-620"><a href="#cb2945-620" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-621"><a href="#cb2945-621" aria-hidden="true" tabindex="-1"></a>:::{.scrolling_500}</span>
+<span id="cb2945-622"><a href="#cb2945-622" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-625"><a href="#cb2945-625" aria-hidden="true" tabindex="-1"></a><span class="in">```{r}</span></span>
+<span id="cb2945-626"><a href="#cb2945-626" aria-hidden="true" tabindex="-1"></a><span class="co">#| cache: true</span></span>
+<span id="cb2945-627"><a href="#cb2945-627" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-628"><a href="#cb2945-628" aria-hidden="true" tabindex="-1"></a>model_mat_exp <span class="ot">&lt;-</span> <span class="fu">cmdstan_model</span>(</span>
+<span id="cb2945-629"><a href="#cb2945-629" aria-hidden="true" tabindex="-1"></a>  here<span class="sc">::</span><span class="fu">here</span>(<span class="st">&quot;M3/example_models_metrum/pk2cpt_linode/pk2cpt_linode.stan&quot;</span>))</span>
+<span id="cb2945-630"><a href="#cb2945-630" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-631"><a href="#cb2945-631" aria-hidden="true" tabindex="-1"></a>fit_mat_exp <span class="ot">&lt;-</span> model_mat_exp<span class="sc">$</span><span class="fu">sample</span>(</span>
+<span id="cb2945-632"><a href="#cb2945-632" aria-hidden="true" tabindex="-1"></a>  <span class="at">data =</span> here<span class="sc">::</span><span class="fu">here</span>(<span class="st">&quot;M3/example_models_metrum/pk2cpt_linode/pk2cpt_linode.data.R&quot;</span>), </span>
+<span id="cb2945-633"><a href="#cb2945-633" aria-hidden="true" tabindex="-1"></a>  <span class="at">init =</span> here<span class="sc">::</span><span class="fu">here</span>(<span class="st">&quot;M3/example_models_metrum/pk2cpt_linode/pk2cpt_linode.init.R&quot;</span>), </span>
+<span id="cb2945-634"><a href="#cb2945-634" aria-hidden="true" tabindex="-1"></a>  <span class="at">seed =</span> <span class="dv">3191951</span>,</span>
+<span id="cb2945-635"><a href="#cb2945-635" aria-hidden="true" tabindex="-1"></a>  <span class="at">chains =</span> <span class="dv">4</span>,</span>
+<span id="cb2945-636"><a href="#cb2945-636" aria-hidden="true" tabindex="-1"></a>  <span class="at">parallel_chains =</span> <span class="dv">4</span>,</span>
+<span id="cb2945-637"><a href="#cb2945-637" aria-hidden="true" tabindex="-1"></a>  <span class="at">iter_warmup =</span> <span class="dv">500</span>,</span>
+<span id="cb2945-638"><a href="#cb2945-638" aria-hidden="true" tabindex="-1"></a>  <span class="at">iter_sampling =</span> <span class="dv">1000</span>,</span>
+<span id="cb2945-639"><a href="#cb2945-639" aria-hidden="true" tabindex="-1"></a>  <span class="at">refresh =</span> <span class="dv">0</span>,</span>
+<span id="cb2945-640"><a href="#cb2945-640" aria-hidden="true" tabindex="-1"></a>  <span class="at">adapt_delta =</span> <span class="fl">0.80</span>)</span>
+<span id="cb2945-641"><a href="#cb2945-641" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-642"><a href="#cb2945-642" aria-hidden="true" tabindex="-1"></a><span class="in">```</span></span>
+<span id="cb2945-643"><a href="#cb2945-643" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-644"><a href="#cb2945-644" aria-hidden="true" tabindex="-1"></a>:::</span>
+<span id="cb2945-645"><a href="#cb2945-645" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-646"><a href="#cb2945-646" aria-hidden="true" tabindex="-1"></a>Works fine.</span>
+<span id="cb2945-647"><a href="#cb2945-647" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-648"><a href="#cb2945-648" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-649"><a href="#cb2945-649" aria-hidden="true" tabindex="-1"></a><span class="fu">### ```pk2cpt_ode```</span></span>
+<span id="cb2945-650"><a href="#cb2945-650" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-651"><a href="#cb2945-651" aria-hidden="true" tabindex="-1"></a>:::{.scrolling_500}</span>
+<span id="cb2945-652"><a href="#cb2945-652" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-655"><a href="#cb2945-655" aria-hidden="true" tabindex="-1"></a><span class="in">```{r}</span></span>
+<span id="cb2945-656"><a href="#cb2945-656" aria-hidden="true" tabindex="-1"></a><span class="co">#| cache: true</span></span>
+<span id="cb2945-657"><a href="#cb2945-657" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-658"><a href="#cb2945-658" aria-hidden="true" tabindex="-1"></a>model_rk45 <span class="ot">&lt;-</span> <span class="fu">cmdstan_model</span>(</span>
+<span id="cb2945-659"><a href="#cb2945-659" aria-hidden="true" tabindex="-1"></a>  here<span class="sc">::</span><span class="fu">here</span>(<span class="st">&quot;M3/example_models_metrum/pk2cpt_ode/pk2cpt_ode.stan&quot;</span>))</span>
+<span id="cb2945-660"><a href="#cb2945-660" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-661"><a href="#cb2945-661" aria-hidden="true" tabindex="-1"></a>stan_data_rk45 <span class="ot">&lt;-</span> rstan<span class="sc">::</span><span class="fu">read_rdump</span>(</span>
+<span id="cb2945-662"><a href="#cb2945-662" aria-hidden="true" tabindex="-1"></a>  here<span class="sc">::</span><span class="fu">here</span>(<span class="st">&quot;M3/example_models_metrum/pk2cpt_ode/pk2cpt_ode.data.R&quot;</span>))</span>
+<span id="cb2945-663"><a href="#cb2945-663" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-664"><a href="#cb2945-664" aria-hidden="true" tabindex="-1"></a>stan_data_rk45<span class="sc">$</span>prior_only <span class="ot">&lt;-</span> <span class="dv">1</span></span>
+<span id="cb2945-665"><a href="#cb2945-665" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-666"><a href="#cb2945-666" aria-hidden="true" tabindex="-1"></a>fit_rk45 <span class="ot">&lt;-</span> model_rk45<span class="sc">$</span><span class="fu">sample</span>(</span>
+<span id="cb2945-667"><a href="#cb2945-667" aria-hidden="true" tabindex="-1"></a>  <span class="at">data =</span> stan_data_rk45, </span>
+<span id="cb2945-668"><a href="#cb2945-668" aria-hidden="true" tabindex="-1"></a>  <span class="at">init =</span> here<span class="sc">::</span><span class="fu">here</span>(<span class="st">&quot;M3/example_models_metrum/pk2cpt_ode/pk2cpt_ode.init.R&quot;</span>), </span>
+<span id="cb2945-669"><a href="#cb2945-669" aria-hidden="true" tabindex="-1"></a>  <span class="at">seed =</span> <span class="dv">3191951</span>,</span>
+<span id="cb2945-670"><a href="#cb2945-670" aria-hidden="true" tabindex="-1"></a>  <span class="at">chains =</span> <span class="dv">1</span>,</span>
+<span id="cb2945-671"><a href="#cb2945-671" aria-hidden="true" tabindex="-1"></a>  <span class="at">parallel_chains =</span> <span class="dv">1</span>,</span>
+<span id="cb2945-672"><a href="#cb2945-672" aria-hidden="true" tabindex="-1"></a>  <span class="at">iter_warmup =</span> <span class="dv">1</span>,</span>
+<span id="cb2945-673"><a href="#cb2945-673" aria-hidden="true" tabindex="-1"></a>  <span class="at">iter_sampling =</span> <span class="dv">1</span>,</span>
+<span id="cb2945-674"><a href="#cb2945-674" aria-hidden="true" tabindex="-1"></a>  <span class="at">adapt_delta =</span> <span class="fl">0.80</span>)</span>
+<span id="cb2945-675"><a href="#cb2945-675" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-676"><a href="#cb2945-676" aria-hidden="true" tabindex="-1"></a><span class="in">```</span></span>
+<span id="cb2945-677"><a href="#cb2945-677" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-678"><a href="#cb2945-678" aria-hidden="true" tabindex="-1"></a>:::</span>
+<span id="cb2945-679"><a href="#cb2945-679" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-680"><a href="#cb2945-680" aria-hidden="true" tabindex="-1"></a>Works fine, in contrast to the one from the M3, where it was returning a vector</span>
+<span id="cb2945-681"><a href="#cb2945-681" aria-hidden="true" tabindex="-1"></a>of zeros.</span>
+<span id="cb2945-682"><a href="#cb2945-682" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-683"><a href="#cb2945-683" aria-hidden="true" tabindex="-1"></a><span class="fu">## Fitting ```poppk2cpt``` from ```example-models/```</span></span>
+<span id="cb2945-684"><a href="#cb2945-684" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-685"><a href="#cb2945-685" aria-hidden="true" tabindex="-1"></a>I made a couple adjustments in ```poppk2cpt.stan``` so that it can be fit with</span>
+<span id="cb2945-686"><a href="#cb2945-686" aria-hidden="true" tabindex="-1"></a>an analytical solver, the linear ODE, or the general ODE.</span>
+<span id="cb2945-687"><a href="#cb2945-687" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-688"><a href="#cb2945-688" aria-hidden="true" tabindex="-1"></a><span class="fu">### Analytical Solution</span></span>
+<span id="cb2945-689"><a href="#cb2945-689" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-690"><a href="#cb2945-690" aria-hidden="true" tabindex="-1"></a>:::{.scrolling_500}</span>
+<span id="cb2945-691"><a href="#cb2945-691" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-694"><a href="#cb2945-694" aria-hidden="true" tabindex="-1"></a><span class="in">```{r}</span></span>
+<span id="cb2945-695"><a href="#cb2945-695" aria-hidden="true" tabindex="-1"></a><span class="co">#| cache: true</span></span>
+<span id="cb2945-696"><a href="#cb2945-696" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-697"><a href="#cb2945-697" aria-hidden="true" tabindex="-1"></a>model <span class="ot">&lt;-</span> <span class="fu">cmdstan_model</span>(</span>
+<span id="cb2945-698"><a href="#cb2945-698" aria-hidden="true" tabindex="-1"></a>  here<span class="sc">::</span><span class="fu">here</span>(<span class="st">&quot;M3/example_models_metrum/poppk2cpt/poppk2cpt.stan&quot;</span>))</span>
+<span id="cb2945-699"><a href="#cb2945-699" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-700"><a href="#cb2945-700" aria-hidden="true" tabindex="-1"></a>stan_data <span class="ot">&lt;-</span> rstan<span class="sc">::</span><span class="fu">read_rdump</span>(</span>
+<span id="cb2945-701"><a href="#cb2945-701" aria-hidden="true" tabindex="-1"></a>  here<span class="sc">::</span><span class="fu">here</span>(<span class="st">&quot;M3/example_models_metrum/poppk2cpt/poppk2cpt.data.R&quot;</span>))</span>
+<span id="cb2945-702"><a href="#cb2945-702" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-703"><a href="#cb2945-703" aria-hidden="true" tabindex="-1"></a>stan_data<span class="sc">$</span>solver <span class="ot">&lt;-</span> <span class="dv">1</span></span>
+<span id="cb2945-704"><a href="#cb2945-704" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-705"><a href="#cb2945-705" aria-hidden="true" tabindex="-1"></a>fit_analytical <span class="ot">&lt;-</span> model<span class="sc">$</span><span class="fu">sample</span>(</span>
+<span id="cb2945-706"><a href="#cb2945-706" aria-hidden="true" tabindex="-1"></a>  <span class="at">data =</span> stan_data, </span>
+<span id="cb2945-707"><a href="#cb2945-707" aria-hidden="true" tabindex="-1"></a>  <span class="at">init =</span> here<span class="sc">::</span><span class="fu">here</span>(<span class="st">&quot;M3/example_models_metrum/poppk2cpt/poppk2cpt.init.R&quot;</span>), </span>
+<span id="cb2945-708"><a href="#cb2945-708" aria-hidden="true" tabindex="-1"></a>  <span class="at">seed =</span> <span class="dv">3191951</span>,</span>
+<span id="cb2945-709"><a href="#cb2945-709" aria-hidden="true" tabindex="-1"></a>  <span class="at">chains =</span> <span class="dv">4</span>,</span>
+<span id="cb2945-710"><a href="#cb2945-710" aria-hidden="true" tabindex="-1"></a>  <span class="at">parallel_chains =</span> <span class="dv">4</span>,</span>
+<span id="cb2945-711"><a href="#cb2945-711" aria-hidden="true" tabindex="-1"></a>  <span class="at">iter_warmup =</span> <span class="dv">500</span>,</span>
+<span id="cb2945-712"><a href="#cb2945-712" aria-hidden="true" tabindex="-1"></a>  <span class="at">iter_sampling =</span> <span class="dv">500</span>,</span>
+<span id="cb2945-713"><a href="#cb2945-713" aria-hidden="true" tabindex="-1"></a>  <span class="at">adapt_delta =</span> <span class="fl">0.80</span>)</span>
+<span id="cb2945-714"><a href="#cb2945-714" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-715"><a href="#cb2945-715" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-716"><a href="#cb2945-716" aria-hidden="true" tabindex="-1"></a><span class="in">```</span></span>
+<span id="cb2945-717"><a href="#cb2945-717" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-718"><a href="#cb2945-718" aria-hidden="true" tabindex="-1"></a>:::</span>
+<span id="cb2945-719"><a href="#cb2945-719" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-720"><a href="#cb2945-720" aria-hidden="true" tabindex="-1"></a>This one fits fine.</span>
+<span id="cb2945-721"><a href="#cb2945-721" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-722"><a href="#cb2945-722" aria-hidden="true" tabindex="-1"></a><span class="fu">### Linear ODE Solution</span></span>
+<span id="cb2945-723"><a href="#cb2945-723" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-724"><a href="#cb2945-724" aria-hidden="true" tabindex="-1"></a>:::{.scrolling_500}</span>
+<span id="cb2945-725"><a href="#cb2945-725" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-728"><a href="#cb2945-728" aria-hidden="true" tabindex="-1"></a><span class="in">```{r}</span></span>
+<span id="cb2945-729"><a href="#cb2945-729" aria-hidden="true" tabindex="-1"></a><span class="co">#| cache: true</span></span>
+<span id="cb2945-730"><a href="#cb2945-730" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-731"><a href="#cb2945-731" aria-hidden="true" tabindex="-1"></a>stan_data<span class="sc">$</span>solver <span class="ot">&lt;-</span> <span class="dv">2</span></span>
+<span id="cb2945-732"><a href="#cb2945-732" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-733"><a href="#cb2945-733" aria-hidden="true" tabindex="-1"></a>fit_mat_exp <span class="ot">&lt;-</span> model<span class="sc">$</span><span class="fu">sample</span>(</span>
+<span id="cb2945-734"><a href="#cb2945-734" aria-hidden="true" tabindex="-1"></a>  <span class="at">data =</span> stan_data, </span>
+<span id="cb2945-735"><a href="#cb2945-735" aria-hidden="true" tabindex="-1"></a>  <span class="at">init =</span> here<span class="sc">::</span><span class="fu">here</span>(<span class="st">&quot;M3/example_models_metrum/poppk2cpt/poppk2cpt.init.R&quot;</span>), </span>
+<span id="cb2945-736"><a href="#cb2945-736" aria-hidden="true" tabindex="-1"></a>  <span class="at">seed =</span> <span class="dv">3191951</span>,</span>
+<span id="cb2945-737"><a href="#cb2945-737" aria-hidden="true" tabindex="-1"></a>  <span class="at">chains =</span> <span class="dv">4</span>,</span>
+<span id="cb2945-738"><a href="#cb2945-738" aria-hidden="true" tabindex="-1"></a>  <span class="at">parallel_chains =</span> <span class="dv">4</span>,</span>
+<span id="cb2945-739"><a href="#cb2945-739" aria-hidden="true" tabindex="-1"></a>  <span class="at">iter_warmup =</span> <span class="dv">300</span>,</span>
+<span id="cb2945-740"><a href="#cb2945-740" aria-hidden="true" tabindex="-1"></a>  <span class="at">iter_sampling =</span> <span class="dv">100</span>,</span>
+<span id="cb2945-741"><a href="#cb2945-741" aria-hidden="true" tabindex="-1"></a>  <span class="at">adapt_delta =</span> <span class="fl">0.80</span>)</span>
+<span id="cb2945-742"><a href="#cb2945-742" aria-hidden="true" tabindex="-1"></a><span class="in">```</span></span>
+<span id="cb2945-743"><a href="#cb2945-743" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-744"><a href="#cb2945-744" aria-hidden="true" tabindex="-1"></a>:::</span>
+<span id="cb2945-745"><a href="#cb2945-745" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-746"><a href="#cb2945-746" aria-hidden="true" tabindex="-1"></a><span class="co">&lt;!-- This one doesn&#39;t work. --&gt;</span></span>
+<span id="cb2945-747"><a href="#cb2945-747" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-748"><a href="#cb2945-748" aria-hidden="true" tabindex="-1"></a><span class="fu">### General ODE Solution</span></span>
+<span id="cb2945-749"><a href="#cb2945-749" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-750"><a href="#cb2945-750" aria-hidden="true" tabindex="-1"></a>:::{.scrolling_500}</span>
+<span id="cb2945-751"><a href="#cb2945-751" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-754"><a href="#cb2945-754" aria-hidden="true" tabindex="-1"></a><span class="in">```{r}</span></span>
+<span id="cb2945-755"><a href="#cb2945-755" aria-hidden="true" tabindex="-1"></a><span class="co">#| cache: true</span></span>
+<span id="cb2945-756"><a href="#cb2945-756" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-757"><a href="#cb2945-757" aria-hidden="true" tabindex="-1"></a>stan_data<span class="sc">$</span>solver <span class="ot">&lt;-</span> <span class="dv">3</span></span>
+<span id="cb2945-758"><a href="#cb2945-758" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-759"><a href="#cb2945-759" aria-hidden="true" tabindex="-1"></a>fit_rk45 <span class="ot">&lt;-</span> model<span class="sc">$</span><span class="fu">sample</span>(</span>
+<span id="cb2945-760"><a href="#cb2945-760" aria-hidden="true" tabindex="-1"></a>  <span class="at">data =</span> stan_data, </span>
+<span id="cb2945-761"><a href="#cb2945-761" aria-hidden="true" tabindex="-1"></a>  <span class="at">init =</span> here<span class="sc">::</span><span class="fu">here</span>(<span class="st">&quot;M3/example_models_metrum/poppk2cpt/poppk2cpt.init.R&quot;</span>), </span>
+<span id="cb2945-762"><a href="#cb2945-762" aria-hidden="true" tabindex="-1"></a>  <span class="at">seed =</span> <span class="dv">3191951</span>,</span>
+<span id="cb2945-763"><a href="#cb2945-763" aria-hidden="true" tabindex="-1"></a>  <span class="at">chains =</span> <span class="dv">4</span>,</span>
+<span id="cb2945-764"><a href="#cb2945-764" aria-hidden="true" tabindex="-1"></a>  <span class="at">parallel_chains =</span> <span class="dv">4</span>,</span>
+<span id="cb2945-765"><a href="#cb2945-765" aria-hidden="true" tabindex="-1"></a>  <span class="at">iter_warmup =</span> <span class="dv">300</span>,</span>
+<span id="cb2945-766"><a href="#cb2945-766" aria-hidden="true" tabindex="-1"></a>  <span class="at">iter_sampling =</span> <span class="dv">100</span>,</span>
+<span id="cb2945-767"><a href="#cb2945-767" aria-hidden="true" tabindex="-1"></a>  <span class="at">adapt_delta =</span> <span class="fl">0.80</span>)</span>
+<span id="cb2945-768"><a href="#cb2945-768" aria-hidden="true" tabindex="-1"></a><span class="in">```</span></span>
+<span id="cb2945-769"><a href="#cb2945-769" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-770"><a href="#cb2945-770" aria-hidden="true" tabindex="-1"></a>:::</span>
+<span id="cb2945-771"><a href="#cb2945-771" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-772"><a href="#cb2945-772" aria-hidden="true" tabindex="-1"></a>This one works.</span>
+<span id="cb2945-773"><a href="#cb2945-773" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-774"><a href="#cb2945-774" aria-hidden="true" tabindex="-1"></a><span class="fu">## Fitting ```poppk2cpt``` from ```example-models/``` With My Own Models</span></span>
+<span id="cb2945-775"><a href="#cb2945-775" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-776"><a href="#cb2945-776" aria-hidden="true" tabindex="-1"></a>I&#39;ve previously written this model to fit with the analytical, linear ODE, and</span>
+<span id="cb2945-777"><a href="#cb2945-777" aria-hidden="true" tabindex="-1"></a>general ODE solutions with proportional error, so I&#39;m just going to use that, </span>
+<span id="cb2945-778"><a href="#cb2945-778" aria-hidden="true" tabindex="-1"></a>but it shouldn&#39;t make a difference.</span>
+<span id="cb2945-779"><a href="#cb2945-779" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-780"><a href="#cb2945-780" aria-hidden="true" tabindex="-1"></a><span class="fu">### Data Wrangling</span></span>
+<span id="cb2945-781"><a href="#cb2945-781" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-782"><a href="#cb2945-782" aria-hidden="true" tabindex="-1"></a>My models should work from a NONMEM dataset in .csv format, so I&#39;ll wrangle the</span>
+<span id="cb2945-783"><a href="#cb2945-783" aria-hidden="true" tabindex="-1"></a>data into something like that first.</span>
+<span id="cb2945-784"><a href="#cb2945-784" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-785"><a href="#cb2945-785" aria-hidden="true" tabindex="-1"></a>:::{.scrolling_500}</span>
+<span id="cb2945-786"><a href="#cb2945-786" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-789"><a href="#cb2945-789" aria-hidden="true" tabindex="-1"></a><span class="in">```{r}</span></span>
+<span id="cb2945-790"><a href="#cb2945-790" aria-hidden="true" tabindex="-1"></a>dv <span class="ot">&lt;-</span> <span class="fu">rep</span>(<span class="cn">NA</span>, stan_data<span class="sc">$</span>nt)</span>
+<span id="cb2945-791"><a href="#cb2945-791" aria-hidden="true" tabindex="-1"></a>dv[stan_data<span class="sc">$</span>iObs] <span class="ot">&lt;-</span> stan_data<span class="sc">$</span>cObs</span>
+<span id="cb2945-792"><a href="#cb2945-792" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-793"><a href="#cb2945-793" aria-hidden="true" tabindex="-1"></a>nonmem_data <span class="ot">&lt;-</span> <span class="fu">with</span>(stan_data, </span>
+<span id="cb2945-794"><a href="#cb2945-794" aria-hidden="true" tabindex="-1"></a>                    <span class="fu">tibble</span>(<span class="at">ID =</span> <span class="fu">rep</span>(<span class="dv">1</span><span class="sc">:</span>stan_data<span class="sc">$</span>nSubj, <span class="at">each =</span> <span class="dv">54</span>),</span>
+<span id="cb2945-795"><a href="#cb2945-795" aria-hidden="true" tabindex="-1"></a>                           <span class="at">amt =</span> amt, </span>
+<span id="cb2945-796"><a href="#cb2945-796" aria-hidden="true" tabindex="-1"></a>                           <span class="at">ii =</span> ii,</span>
+<span id="cb2945-797"><a href="#cb2945-797" aria-hidden="true" tabindex="-1"></a>                           <span class="at">addl =</span> addl,</span>
+<span id="cb2945-798"><a href="#cb2945-798" aria-hidden="true" tabindex="-1"></a>                           <span class="at">rate =</span> rate,</span>
+<span id="cb2945-799"><a href="#cb2945-799" aria-hidden="true" tabindex="-1"></a>                           <span class="at">cmt =</span> cmt,</span>
+<span id="cb2945-800"><a href="#cb2945-800" aria-hidden="true" tabindex="-1"></a>                           <span class="at">evid =</span> evid, </span>
+<span id="cb2945-801"><a href="#cb2945-801" aria-hidden="true" tabindex="-1"></a>                           <span class="at">ss =</span> ss,</span>
+<span id="cb2945-802"><a href="#cb2945-802" aria-hidden="true" tabindex="-1"></a>                           <span class="at">lloq =</span> <span class="dv">0</span>,</span>
+<span id="cb2945-803"><a href="#cb2945-803" aria-hidden="true" tabindex="-1"></a>                           <span class="at">bloq =</span> <span class="dv">0</span>,</span>
+<span id="cb2945-804"><a href="#cb2945-804" aria-hidden="true" tabindex="-1"></a>                           <span class="at">time =</span> time,</span>
+<span id="cb2945-805"><a href="#cb2945-805" aria-hidden="true" tabindex="-1"></a>                           <span class="at">DV =</span> dv)) <span class="sc">%&gt;%</span> </span>
+<span id="cb2945-806"><a href="#cb2945-806" aria-hidden="true" tabindex="-1"></a>  <span class="fu">mutate</span>(<span class="at">DV =</span> <span class="fu">if_else</span>(<span class="fu">is.na</span>(DV), <span class="dv">5555555</span>, DV),    <span class="co"># This value can be anything except NA. It&#39;ll be indexed away </span></span>
+<span id="cb2945-807"><a href="#cb2945-807" aria-hidden="true" tabindex="-1"></a>         <span class="at">bloq =</span> <span class="fu">if_else</span>(<span class="fu">is.na</span>(bloq), <span class="sc">-</span><span class="dv">999</span>, bloq)) <span class="co"># This value can be anything except NA. It&#39;ll be indexed away </span></span>
+<span id="cb2945-808"><a href="#cb2945-808" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-809"><a href="#cb2945-809" aria-hidden="true" tabindex="-1"></a>n_subjects <span class="ot">&lt;-</span> nonmem_data <span class="sc">%&gt;%</span>  <span class="co"># number of individuals</span></span>
+<span id="cb2945-810"><a href="#cb2945-810" aria-hidden="true" tabindex="-1"></a>  <span class="fu">distinct</span>(ID) <span class="sc">%&gt;%</span></span>
+<span id="cb2945-811"><a href="#cb2945-811" aria-hidden="true" tabindex="-1"></a>  <span class="fu">count</span>() <span class="sc">%&gt;%</span></span>
+<span id="cb2945-812"><a href="#cb2945-812" aria-hidden="true" tabindex="-1"></a>  <span class="fu">deframe</span>()</span>
+<span id="cb2945-813"><a href="#cb2945-813" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-814"><a href="#cb2945-814" aria-hidden="true" tabindex="-1"></a>n_total <span class="ot">&lt;-</span> <span class="fu">nrow</span>(nonmem_data)   <span class="co"># total number of records</span></span>
+<span id="cb2945-815"><a href="#cb2945-815" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-816"><a href="#cb2945-816" aria-hidden="true" tabindex="-1"></a>i_obs <span class="ot">&lt;-</span> nonmem_data <span class="sc">%&gt;%</span></span>
+<span id="cb2945-817"><a href="#cb2945-817" aria-hidden="true" tabindex="-1"></a>  <span class="fu">mutate</span>(<span class="at">row_num =</span> <span class="dv">1</span><span class="sc">:</span><span class="fu">n</span>()) <span class="sc">%&gt;%</span></span>
+<span id="cb2945-818"><a href="#cb2945-818" aria-hidden="true" tabindex="-1"></a>  <span class="fu">filter</span>(evid <span class="sc">==</span> <span class="dv">0</span>) <span class="sc">%&gt;%</span></span>
+<span id="cb2945-819"><a href="#cb2945-819" aria-hidden="true" tabindex="-1"></a>  <span class="fu">select</span>(row_num) <span class="sc">%&gt;%</span></span>
+<span id="cb2945-820"><a href="#cb2945-820" aria-hidden="true" tabindex="-1"></a>  <span class="fu">deframe</span>()</span>
+<span id="cb2945-821"><a href="#cb2945-821" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-822"><a href="#cb2945-822" aria-hidden="true" tabindex="-1"></a>n_obs <span class="ot">&lt;-</span> <span class="fu">length</span>(i_obs)</span>
+<span id="cb2945-823"><a href="#cb2945-823" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-824"><a href="#cb2945-824" aria-hidden="true" tabindex="-1"></a>subj_start <span class="ot">&lt;-</span> nonmem_data <span class="sc">%&gt;%</span></span>
+<span id="cb2945-825"><a href="#cb2945-825" aria-hidden="true" tabindex="-1"></a>  <span class="fu">mutate</span>(<span class="at">row_num =</span> <span class="dv">1</span><span class="sc">:</span><span class="fu">n</span>()) <span class="sc">%&gt;%</span></span>
+<span id="cb2945-826"><a href="#cb2945-826" aria-hidden="true" tabindex="-1"></a>  <span class="fu">group_by</span>(ID) <span class="sc">%&gt;%</span></span>
+<span id="cb2945-827"><a href="#cb2945-827" aria-hidden="true" tabindex="-1"></a>  <span class="fu">slice_head</span>(<span class="at">n =</span> <span class="dv">1</span>) <span class="sc">%&gt;%</span></span>
+<span id="cb2945-828"><a href="#cb2945-828" aria-hidden="true" tabindex="-1"></a>  <span class="fu">ungroup</span>() <span class="sc">%&gt;%</span></span>
+<span id="cb2945-829"><a href="#cb2945-829" aria-hidden="true" tabindex="-1"></a>  <span class="fu">select</span>(row_num) <span class="sc">%&gt;%</span></span>
+<span id="cb2945-830"><a href="#cb2945-830" aria-hidden="true" tabindex="-1"></a>  <span class="fu">deframe</span>()</span>
+<span id="cb2945-831"><a href="#cb2945-831" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-832"><a href="#cb2945-832" aria-hidden="true" tabindex="-1"></a>subj_end <span class="ot">&lt;-</span> <span class="fu">c</span>(subj_start[<span class="sc">-</span><span class="dv">1</span>] <span class="sc">-</span> <span class="dv">1</span>, n_total)</span>
+<span id="cb2945-833"><a href="#cb2945-833" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-834"><a href="#cb2945-834" aria-hidden="true" tabindex="-1"></a>stan_data <span class="ot">&lt;-</span> <span class="fu">list</span>(<span class="at">n_subjects =</span> n_subjects,</span>
+<span id="cb2945-835"><a href="#cb2945-835" aria-hidden="true" tabindex="-1"></a>                  <span class="at">n_total =</span> n_total,</span>
+<span id="cb2945-836"><a href="#cb2945-836" aria-hidden="true" tabindex="-1"></a>                  <span class="at">n_obs =</span> n_obs,</span>
+<span id="cb2945-837"><a href="#cb2945-837" aria-hidden="true" tabindex="-1"></a>                  <span class="at">i_obs =</span> i_obs,</span>
+<span id="cb2945-838"><a href="#cb2945-838" aria-hidden="true" tabindex="-1"></a>                  <span class="at">ID =</span> nonmem_data<span class="sc">$</span>ID,</span>
+<span id="cb2945-839"><a href="#cb2945-839" aria-hidden="true" tabindex="-1"></a>                  <span class="at">amt =</span> nonmem_data<span class="sc">$</span>amt,</span>
+<span id="cb2945-840"><a href="#cb2945-840" aria-hidden="true" tabindex="-1"></a>                  <span class="at">cmt =</span> nonmem_data<span class="sc">$</span>cmt,</span>
+<span id="cb2945-841"><a href="#cb2945-841" aria-hidden="true" tabindex="-1"></a>                  <span class="at">evid =</span> nonmem_data<span class="sc">$</span>evid,</span>
+<span id="cb2945-842"><a href="#cb2945-842" aria-hidden="true" tabindex="-1"></a>                  <span class="at">rate =</span> nonmem_data<span class="sc">$</span>rate,</span>
+<span id="cb2945-843"><a href="#cb2945-843" aria-hidden="true" tabindex="-1"></a>                  <span class="at">ii =</span> nonmem_data<span class="sc">$</span>ii,</span>
+<span id="cb2945-844"><a href="#cb2945-844" aria-hidden="true" tabindex="-1"></a>                  <span class="at">addl =</span> nonmem_data<span class="sc">$</span>addl,</span>
+<span id="cb2945-845"><a href="#cb2945-845" aria-hidden="true" tabindex="-1"></a>                  <span class="at">ss =</span> nonmem_data<span class="sc">$</span>ss,</span>
+<span id="cb2945-846"><a href="#cb2945-846" aria-hidden="true" tabindex="-1"></a>                  <span class="at">time =</span> nonmem_data<span class="sc">$</span>time,</span>
+<span id="cb2945-847"><a href="#cb2945-847" aria-hidden="true" tabindex="-1"></a>                  <span class="at">dv =</span> nonmem_data<span class="sc">$</span>DV,</span>
+<span id="cb2945-848"><a href="#cb2945-848" aria-hidden="true" tabindex="-1"></a>                  <span class="at">subj_start =</span> subj_start,</span>
+<span id="cb2945-849"><a href="#cb2945-849" aria-hidden="true" tabindex="-1"></a>                  <span class="at">subj_end =</span> subj_end,</span>
+<span id="cb2945-850"><a href="#cb2945-850" aria-hidden="true" tabindex="-1"></a>                  <span class="at">lloq =</span> nonmem_data<span class="sc">$</span>lloq,</span>
+<span id="cb2945-851"><a href="#cb2945-851" aria-hidden="true" tabindex="-1"></a>                  <span class="at">bloq =</span> nonmem_data<span class="sc">$</span>bloq,</span>
+<span id="cb2945-852"><a href="#cb2945-852" aria-hidden="true" tabindex="-1"></a>                  <span class="at">location_tvcl =</span> <span class="fl">0.75</span>,</span>
+<span id="cb2945-853"><a href="#cb2945-853" aria-hidden="true" tabindex="-1"></a>                  <span class="at">location_tvvc =</span> <span class="dv">18</span>,</span>
+<span id="cb2945-854"><a href="#cb2945-854" aria-hidden="true" tabindex="-1"></a>                  <span class="at">location_tvq =</span> <span class="dv">3</span>,</span>
+<span id="cb2945-855"><a href="#cb2945-855" aria-hidden="true" tabindex="-1"></a>                  <span class="at">location_tvvp =</span> <span class="dv">35</span>,</span>
+<span id="cb2945-856"><a href="#cb2945-856" aria-hidden="true" tabindex="-1"></a>                  <span class="at">location_tvka =</span> <span class="fl">0.8</span>,</span>
+<span id="cb2945-857"><a href="#cb2945-857" aria-hidden="true" tabindex="-1"></a>                  <span class="at">scale_tvcl =</span> <span class="dv">1</span>,</span>
+<span id="cb2945-858"><a href="#cb2945-858" aria-hidden="true" tabindex="-1"></a>                  <span class="at">scale_tvvc =</span> <span class="dv">1</span>,</span>
+<span id="cb2945-859"><a href="#cb2945-859" aria-hidden="true" tabindex="-1"></a>                  <span class="at">scale_tvq =</span> <span class="dv">1</span>,</span>
+<span id="cb2945-860"><a href="#cb2945-860" aria-hidden="true" tabindex="-1"></a>                  <span class="at">scale_tvvp =</span> <span class="dv">1</span>,</span>
+<span id="cb2945-861"><a href="#cb2945-861" aria-hidden="true" tabindex="-1"></a>                  <span class="at">scale_tvka =</span> <span class="dv">1</span>,</span>
+<span id="cb2945-862"><a href="#cb2945-862" aria-hidden="true" tabindex="-1"></a>                  <span class="at">scale_omega_cl =</span> <span class="fl">0.4</span>,</span>
+<span id="cb2945-863"><a href="#cb2945-863" aria-hidden="true" tabindex="-1"></a>                  <span class="at">scale_omega_vc =</span> <span class="fl">0.4</span>,</span>
+<span id="cb2945-864"><a href="#cb2945-864" aria-hidden="true" tabindex="-1"></a>                  <span class="at">scale_omega_q =</span> <span class="fl">0.4</span>,</span>
+<span id="cb2945-865"><a href="#cb2945-865" aria-hidden="true" tabindex="-1"></a>                  <span class="at">scale_omega_vp =</span> <span class="fl">0.4</span>,</span>
+<span id="cb2945-866"><a href="#cb2945-866" aria-hidden="true" tabindex="-1"></a>                  <span class="at">scale_omega_ka =</span> <span class="fl">0.4</span>,</span>
+<span id="cb2945-867"><a href="#cb2945-867" aria-hidden="true" tabindex="-1"></a>                  <span class="at">lkj_df_omega =</span> <span class="dv">2</span>,</span>
+<span id="cb2945-868"><a href="#cb2945-868" aria-hidden="true" tabindex="-1"></a>                  <span class="at">scale_sigma_p =</span> <span class="fl">0.5</span>,</span>
+<span id="cb2945-869"><a href="#cb2945-869" aria-hidden="true" tabindex="-1"></a>                  <span class="at">prior_only =</span> <span class="dv">0</span>)</span>
+<span id="cb2945-870"><a href="#cb2945-870" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-871"><a href="#cb2945-871" aria-hidden="true" tabindex="-1"></a>model <span class="ot">&lt;-</span> <span class="fu">cmdstan_model</span>(</span>
+<span id="cb2945-872"><a href="#cb2945-872" aria-hidden="true" tabindex="-1"></a>  here<span class="sc">::</span><span class="fu">here</span>(<span class="st">&quot;M3/depot_2cmt_linear/Stan/Fit/depot_2cmt_prop_all_solvers.stan&quot;</span>),</span>
+<span id="cb2945-873"><a href="#cb2945-873" aria-hidden="true" tabindex="-1"></a>  <span class="at">cpp_options =</span> <span class="fu">list</span>(<span class="at">stan_threads =</span> <span class="cn">TRUE</span>))</span>
+<span id="cb2945-874"><a href="#cb2945-874" aria-hidden="true" tabindex="-1"></a><span class="in">```</span></span>
+<span id="cb2945-875"><a href="#cb2945-875" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-876"><a href="#cb2945-876" aria-hidden="true" tabindex="-1"></a>:::</span>
+<span id="cb2945-877"><a href="#cb2945-877" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-878"><a href="#cb2945-878" aria-hidden="true" tabindex="-1"></a><span class="fu">### Analytical Solution</span></span>
+<span id="cb2945-879"><a href="#cb2945-879" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-880"><a href="#cb2945-880" aria-hidden="true" tabindex="-1"></a>:::{.scrolling_500}</span>
+<span id="cb2945-881"><a href="#cb2945-881" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-884"><a href="#cb2945-884" aria-hidden="true" tabindex="-1"></a><span class="in">```{r}</span></span>
+<span id="cb2945-885"><a href="#cb2945-885" aria-hidden="true" tabindex="-1"></a><span class="co">#| cache: true</span></span>
+<span id="cb2945-886"><a href="#cb2945-886" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-887"><a href="#cb2945-887" aria-hidden="true" tabindex="-1"></a>stan_data<span class="sc">$</span>solver <span class="ot">&lt;-</span> <span class="dv">1</span></span>
+<span id="cb2945-888"><a href="#cb2945-888" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-889"><a href="#cb2945-889" aria-hidden="true" tabindex="-1"></a>fit <span class="ot">&lt;-</span> model<span class="sc">$</span><span class="fu">sample</span>(<span class="at">data =</span> stan_data,</span>
+<span id="cb2945-890"><a href="#cb2945-890" aria-hidden="true" tabindex="-1"></a>                    <span class="at">seed =</span> <span class="dv">11235</span>,</span>
+<span id="cb2945-891"><a href="#cb2945-891" aria-hidden="true" tabindex="-1"></a>                    <span class="at">chains =</span> <span class="dv">4</span>,</span>
+<span id="cb2945-892"><a href="#cb2945-892" aria-hidden="true" tabindex="-1"></a>                    <span class="at">parallel_chains =</span> <span class="dv">4</span>,</span>
+<span id="cb2945-893"><a href="#cb2945-893" aria-hidden="true" tabindex="-1"></a>                    <span class="at">threads_per_chain =</span> parallel<span class="sc">::</span><span class="fu">detectCores</span>()<span class="sc">/</span><span class="dv">4</span>,</span>
+<span id="cb2945-894"><a href="#cb2945-894" aria-hidden="true" tabindex="-1"></a>                    <span class="at">iter_warmup =</span> <span class="dv">500</span>,</span>
+<span id="cb2945-895"><a href="#cb2945-895" aria-hidden="true" tabindex="-1"></a>                    <span class="at">iter_sampling =</span> <span class="dv">1000</span>,</span>
+<span id="cb2945-896"><a href="#cb2945-896" aria-hidden="true" tabindex="-1"></a>                    <span class="at">adapt_delta =</span> <span class="fl">0.8</span>,</span>
+<span id="cb2945-897"><a href="#cb2945-897" aria-hidden="true" tabindex="-1"></a>                    <span class="at">refresh =</span> <span class="dv">500</span>,</span>
+<span id="cb2945-898"><a href="#cb2945-898" aria-hidden="true" tabindex="-1"></a>                    <span class="at">max_treedepth =</span> <span class="dv">10</span>,</span>
+<span id="cb2945-899"><a href="#cb2945-899" aria-hidden="true" tabindex="-1"></a>                    <span class="at">init =</span> <span class="cf">function</span>() <span class="fu">list</span>(<span class="at">TVCL =</span> <span class="fu">rlnorm</span>(<span class="dv">1</span>, <span class="fu">log</span>(<span class="dv">5</span>), <span class="fl">0.1</span>),</span>
+<span id="cb2945-900"><a href="#cb2945-900" aria-hidden="true" tabindex="-1"></a>                                           <span class="at">TVVC =</span> <span class="fu">rlnorm</span>(<span class="dv">1</span>, <span class="fu">log</span>(<span class="dv">20</span>), <span class="fl">0.1</span>),</span>
+<span id="cb2945-901"><a href="#cb2945-901" aria-hidden="true" tabindex="-1"></a>                                           <span class="at">TVQ =</span> <span class="fu">rlnorm</span>(<span class="dv">1</span>, <span class="fu">log</span>(<span class="dv">7</span>), <span class="fl">0.1</span>),</span>
+<span id="cb2945-902"><a href="#cb2945-902" aria-hidden="true" tabindex="-1"></a>                                           <span class="at">TVVP =</span> <span class="fu">rlnorm</span>(<span class="dv">1</span>, <span class="fu">log</span>(<span class="dv">70</span>), <span class="fl">0.1</span>),</span>
+<span id="cb2945-903"><a href="#cb2945-903" aria-hidden="true" tabindex="-1"></a>                                           <span class="at">TVKA =</span> <span class="fu">rlnorm</span>(<span class="dv">1</span>, <span class="fu">log</span>(<span class="fl">1.2</span>), <span class="fl">0.1</span>),</span>
+<span id="cb2945-904"><a href="#cb2945-904" aria-hidden="true" tabindex="-1"></a>                                           <span class="at">omega =</span> <span class="fu">rlnorm</span>(<span class="dv">5</span>, <span class="fu">log</span>(<span class="fl">0.1</span>), <span class="fl">0.1</span>),</span>
+<span id="cb2945-905"><a href="#cb2945-905" aria-hidden="true" tabindex="-1"></a>                                           <span class="at">sigma_p =</span> <span class="fu">rlnorm</span>(<span class="dv">1</span>, <span class="fu">log</span>(<span class="fl">0.1</span>), <span class="fl">0.1</span>)))</span>
+<span id="cb2945-906"><a href="#cb2945-906" aria-hidden="true" tabindex="-1"></a><span class="in">```</span></span>
+<span id="cb2945-907"><a href="#cb2945-907" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-908"><a href="#cb2945-908" aria-hidden="true" tabindex="-1"></a>:::</span>
+<span id="cb2945-909"><a href="#cb2945-909" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-910"><a href="#cb2945-910" aria-hidden="true" tabindex="-1"></a>Seems to work fine.</span>
+<span id="cb2945-911"><a href="#cb2945-911" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-912"><a href="#cb2945-912" aria-hidden="true" tabindex="-1"></a><span class="fu">### Linear ODE</span></span>
+<span id="cb2945-913"><a href="#cb2945-913" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-914"><a href="#cb2945-914" aria-hidden="true" tabindex="-1"></a>:::{.scrolling_500}</span>
+<span id="cb2945-915"><a href="#cb2945-915" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-918"><a href="#cb2945-918" aria-hidden="true" tabindex="-1"></a><span class="in">```{r}</span></span>
+<span id="cb2945-919"><a href="#cb2945-919" aria-hidden="true" tabindex="-1"></a><span class="co">#| cache: true</span></span>
+<span id="cb2945-920"><a href="#cb2945-920" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-921"><a href="#cb2945-921" aria-hidden="true" tabindex="-1"></a>stan_data<span class="sc">$</span>solver <span class="ot">&lt;-</span> <span class="dv">2</span></span>
+<span id="cb2945-922"><a href="#cb2945-922" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-923"><a href="#cb2945-923" aria-hidden="true" tabindex="-1"></a>fit_mat_exp_cd <span class="ot">&lt;-</span> model<span class="sc">$</span><span class="fu">sample</span>(</span>
+<span id="cb2945-924"><a href="#cb2945-924" aria-hidden="true" tabindex="-1"></a>  <span class="at">data =</span> stan_data,</span>
+<span id="cb2945-925"><a href="#cb2945-925" aria-hidden="true" tabindex="-1"></a>  <span class="at">seed =</span> <span class="dv">11235</span>,</span>
+<span id="cb2945-926"><a href="#cb2945-926" aria-hidden="true" tabindex="-1"></a>  <span class="at">chains =</span> <span class="dv">4</span>,</span>
+<span id="cb2945-927"><a href="#cb2945-927" aria-hidden="true" tabindex="-1"></a>  <span class="at">parallel_chains =</span> <span class="dv">4</span>,</span>
+<span id="cb2945-928"><a href="#cb2945-928" aria-hidden="true" tabindex="-1"></a>  <span class="at">threads_per_chain =</span> parallel<span class="sc">::</span><span class="fu">detectCores</span>()<span class="sc">/</span><span class="dv">4</span>,</span>
+<span id="cb2945-929"><a href="#cb2945-929" aria-hidden="true" tabindex="-1"></a>  <span class="at">iter_warmup =</span> <span class="dv">500</span>,</span>
+<span id="cb2945-930"><a href="#cb2945-930" aria-hidden="true" tabindex="-1"></a>  <span class="at">iter_sampling =</span> <span class="dv">1000</span>,</span>
+<span id="cb2945-931"><a href="#cb2945-931" aria-hidden="true" tabindex="-1"></a>  <span class="at">adapt_delta =</span> <span class="fl">0.8</span>,</span>
+<span id="cb2945-932"><a href="#cb2945-932" aria-hidden="true" tabindex="-1"></a>  <span class="at">refresh =</span> <span class="dv">500</span>,</span>
+<span id="cb2945-933"><a href="#cb2945-933" aria-hidden="true" tabindex="-1"></a>  <span class="at">max_treedepth =</span> <span class="dv">10</span>,</span>
+<span id="cb2945-934"><a href="#cb2945-934" aria-hidden="true" tabindex="-1"></a>  <span class="at">init =</span> <span class="cf">function</span>() <span class="fu">list</span>(<span class="at">TVCL =</span> <span class="fu">rlnorm</span>(<span class="dv">1</span>, <span class="fu">log</span>(<span class="dv">5</span>), <span class="fl">0.1</span>),</span>
+<span id="cb2945-935"><a href="#cb2945-935" aria-hidden="true" tabindex="-1"></a>                         <span class="at">TVVC =</span> <span class="fu">rlnorm</span>(<span class="dv">1</span>, <span class="fu">log</span>(<span class="dv">20</span>), <span class="fl">0.1</span>),</span>
+<span id="cb2945-936"><a href="#cb2945-936" aria-hidden="true" tabindex="-1"></a>                         <span class="at">TVQ =</span> <span class="fu">rlnorm</span>(<span class="dv">1</span>, <span class="fu">log</span>(<span class="dv">7</span>), <span class="fl">0.1</span>),</span>
+<span id="cb2945-937"><a href="#cb2945-937" aria-hidden="true" tabindex="-1"></a>                         <span class="at">TVVP =</span> <span class="fu">rlnorm</span>(<span class="dv">1</span>, <span class="fu">log</span>(<span class="dv">70</span>), <span class="fl">0.1</span>),</span>
+<span id="cb2945-938"><a href="#cb2945-938" aria-hidden="true" tabindex="-1"></a>                         <span class="at">TVKA =</span> <span class="fu">rlnorm</span>(<span class="dv">1</span>, <span class="fu">log</span>(<span class="fl">1.2</span>), <span class="fl">0.1</span>),</span>
+<span id="cb2945-939"><a href="#cb2945-939" aria-hidden="true" tabindex="-1"></a>                         <span class="at">omega =</span> <span class="fu">rlnorm</span>(<span class="dv">5</span>, <span class="fu">log</span>(<span class="fl">0.1</span>), <span class="fl">0.1</span>),</span>
+<span id="cb2945-940"><a href="#cb2945-940" aria-hidden="true" tabindex="-1"></a>                         <span class="at">sigma_p =</span> <span class="fu">rlnorm</span>(<span class="dv">1</span>, <span class="fu">log</span>(<span class="fl">0.1</span>), <span class="fl">0.1</span>)))</span>
+<span id="cb2945-941"><a href="#cb2945-941" aria-hidden="true" tabindex="-1"></a><span class="in">```</span></span>
+<span id="cb2945-942"><a href="#cb2945-942" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-943"><a href="#cb2945-943" aria-hidden="true" tabindex="-1"></a>:::</span>
+<span id="cb2945-944"><a href="#cb2945-944" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-945"><a href="#cb2945-945" aria-hidden="true" tabindex="-1"></a>This one works fine.</span>
+<span id="cb2945-946"><a href="#cb2945-946" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-947"><a href="#cb2945-947" aria-hidden="true" tabindex="-1"></a><span class="fu">### General ODE</span></span>
+<span id="cb2945-948"><a href="#cb2945-948" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-949"><a href="#cb2945-949" aria-hidden="true" tabindex="-1"></a>:::{.scrolling_500}</span>
+<span id="cb2945-950"><a href="#cb2945-950" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-953"><a href="#cb2945-953" aria-hidden="true" tabindex="-1"></a><span class="in">```{r}</span></span>
+<span id="cb2945-954"><a href="#cb2945-954" aria-hidden="true" tabindex="-1"></a><span class="co">#| cache: true</span></span>
+<span id="cb2945-955"><a href="#cb2945-955" aria-hidden="true" tabindex="-1"></a> </span>
+<span id="cb2945-956"><a href="#cb2945-956" aria-hidden="true" tabindex="-1"></a>stan_data<span class="sc">$</span>solver <span class="ot">&lt;-</span> <span class="dv">3</span></span>
+<span id="cb2945-957"><a href="#cb2945-957" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-958"><a href="#cb2945-958" aria-hidden="true" tabindex="-1"></a>fit_rk45_cd <span class="ot">&lt;-</span> model<span class="sc">$</span><span class="fu">sample</span>(</span>
+<span id="cb2945-959"><a href="#cb2945-959" aria-hidden="true" tabindex="-1"></a>  <span class="at">data =</span> stan_data,</span>
+<span id="cb2945-960"><a href="#cb2945-960" aria-hidden="true" tabindex="-1"></a>  <span class="at">seed =</span> <span class="dv">11235</span>,</span>
+<span id="cb2945-961"><a href="#cb2945-961" aria-hidden="true" tabindex="-1"></a>  <span class="at">chains =</span> <span class="dv">4</span>,</span>
+<span id="cb2945-962"><a href="#cb2945-962" aria-hidden="true" tabindex="-1"></a>  <span class="at">parallel_chains =</span> <span class="dv">4</span>,</span>
+<span id="cb2945-963"><a href="#cb2945-963" aria-hidden="true" tabindex="-1"></a>  <span class="at">threads_per_chain =</span> parallel<span class="sc">::</span><span class="fu">detectCores</span>()<span class="sc">/</span><span class="dv">4</span>,</span>
+<span id="cb2945-964"><a href="#cb2945-964" aria-hidden="true" tabindex="-1"></a>  <span class="at">iter_warmup =</span> <span class="dv">300</span>,</span>
+<span id="cb2945-965"><a href="#cb2945-965" aria-hidden="true" tabindex="-1"></a>  <span class="at">iter_sampling =</span> <span class="dv">100</span>,</span>
+<span id="cb2945-966"><a href="#cb2945-966" aria-hidden="true" tabindex="-1"></a>  <span class="at">adapt_delta =</span> <span class="fl">0.8</span>,</span>
+<span id="cb2945-967"><a href="#cb2945-967" aria-hidden="true" tabindex="-1"></a>  <span class="at">refresh =</span> <span class="dv">0</span>,</span>
+<span id="cb2945-968"><a href="#cb2945-968" aria-hidden="true" tabindex="-1"></a>  <span class="at">max_treedepth =</span> <span class="dv">10</span>,</span>
+<span id="cb2945-969"><a href="#cb2945-969" aria-hidden="true" tabindex="-1"></a>  <span class="at">init =</span> <span class="cf">function</span>() <span class="fu">list</span>(<span class="at">TVCL =</span> <span class="fu">rlnorm</span>(<span class="dv">1</span>, <span class="fu">log</span>(<span class="dv">5</span>), <span class="fl">0.1</span>),</span>
+<span id="cb2945-970"><a href="#cb2945-970" aria-hidden="true" tabindex="-1"></a>                         <span class="at">TVVC =</span> <span class="fu">rlnorm</span>(<span class="dv">1</span>, <span class="fu">log</span>(<span class="dv">20</span>), <span class="fl">0.1</span>),</span>
+<span id="cb2945-971"><a href="#cb2945-971" aria-hidden="true" tabindex="-1"></a>                         <span class="at">TVQ =</span> <span class="fu">rlnorm</span>(<span class="dv">1</span>, <span class="fu">log</span>(<span class="dv">7</span>), <span class="fl">0.1</span>),</span>
+<span id="cb2945-972"><a href="#cb2945-972" aria-hidden="true" tabindex="-1"></a>                         <span class="at">TVVP =</span> <span class="fu">rlnorm</span>(<span class="dv">1</span>, <span class="fu">log</span>(<span class="dv">70</span>), <span class="fl">0.1</span>),</span>
+<span id="cb2945-973"><a href="#cb2945-973" aria-hidden="true" tabindex="-1"></a>                         <span class="at">TVKA =</span> <span class="fu">rlnorm</span>(<span class="dv">1</span>, <span class="fu">log</span>(<span class="fl">1.2</span>), <span class="fl">0.1</span>),</span>
+<span id="cb2945-974"><a href="#cb2945-974" aria-hidden="true" tabindex="-1"></a>                         <span class="at">omega =</span> <span class="fu">rlnorm</span>(<span class="dv">5</span>, <span class="fu">log</span>(<span class="fl">0.1</span>), <span class="fl">0.1</span>),</span>
+<span id="cb2945-975"><a href="#cb2945-975" aria-hidden="true" tabindex="-1"></a>                         <span class="at">sigma_p =</span> <span class="fu">rlnorm</span>(<span class="dv">1</span>, <span class="fu">log</span>(<span class="fl">0.1</span>), <span class="fl">0.1</span>)))</span>
+<span id="cb2945-976"><a href="#cb2945-976" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-977"><a href="#cb2945-977" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-978"><a href="#cb2945-978" aria-hidden="true" tabindex="-1"></a><span class="in">```</span></span>
+<span id="cb2945-979"><a href="#cb2945-979" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-980"><a href="#cb2945-980" aria-hidden="true" tabindex="-1"></a>:::</span>
+<span id="cb2945-981"><a href="#cb2945-981" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-982"><a href="#cb2945-982" aria-hidden="true" tabindex="-1"></a>This one works fine.</span>
+<span id="cb2945-983"><a href="#cb2945-983" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-984"><a href="#cb2945-984" aria-hidden="true" tabindex="-1"></a><span class="fu"># Summary</span></span>
+<span id="cb2945-985"><a href="#cb2945-985" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-986"><a href="#cb2945-986" aria-hidden="true" tabindex="-1"></a><span class="co">&lt;!-- Basically, I haven&#39;t figured out if there&#39;s any rhyme or reason to when the  --&gt;</span></span>
+<span id="cb2945-987"><a href="#cb2945-987" aria-hidden="true" tabindex="-1"></a><span class="co">&lt;!-- analytical, linear ODE, or general ODE solution works or not.  --&gt;</span></span>
+<span id="cb2945-988"><a href="#cb2945-988" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-989"><a href="#cb2945-989" aria-hidden="true" tabindex="-1"></a><span class="fu"># Session Info</span></span>
+<span id="cb2945-990"><a href="#cb2945-990" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-993"><a href="#cb2945-993" aria-hidden="true" tabindex="-1"></a><span class="in">```{r}</span></span>
+<span id="cb2945-994"><a href="#cb2945-994" aria-hidden="true" tabindex="-1"></a><span class="fu">sessionInfo</span>()</span>
+<span id="cb2945-995"><a href="#cb2945-995" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2945-996"><a href="#cb2945-996" aria-hidden="true" tabindex="-1"></a><span class="in">```</span></span>
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