From e6840bc07bb961fb7c098ab0b1d3f64b2fceba6f Mon Sep 17 00:00:00 2001 From: Bill Denney Date: Tue, 22 Jul 2025 10:58:14 -0400 Subject: [PATCH 1/5] Rebuild docs (no code changes) --- DESCRIPTION | 2 +- man/dgr_table.Rd | 5 ++++- man/gm.Rd | 6 +++++- man/pcv.Rd | 2 +- man/plot_scm.Rd | 2 +- man/read_nm_all.Rd | 2 +- man/read_nm_multi_table.Rd | 2 +- man/read_nmcov.Rd | 2 +- man/read_nmext.Rd | 2 +- man/read_nmtables.Rd | 2 +- man/read_scm.Rd | 4 ++-- 11 files changed, 19 insertions(+), 12 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 4e58f69..1e09179 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -22,7 +22,7 @@ License: GPL-2 URL: https://github.com/kestrel99/pmxTools, https://kestrel99.github.io/pmxTools/ BugReports: https://github.com/kestrel99/pmxTools/issues -RoxygenNote: 7.2.3 +RoxygenNote: 7.3.2 Imports: ggplot2, chron, diff --git a/man/dgr_table.Rd b/man/dgr_table.Rd index 5e6ed5f..2ce4984 100644 --- a/man/dgr_table.Rd +++ b/man/dgr_table.Rd @@ -12,7 +12,8 @@ dgr_table( sig = 3, by = NULL, idvar = "ID", - navars = c("-99", "-999") + navars = c("-99", "-999"), + mtype = "geomean" ) } \arguments{ @@ -31,6 +32,8 @@ dgr_table( \item{idvar}{The field in the dataset identifying each unique individual (defaults to "ID").} \item{navars}{A vector containing values that are to be interpreted as missing (defaults to "-99" and "-999"). `NA` values are always considered to be missing.} + +\item{mtype}{The type of mean to apply; `geomean`, the geometric mean (default) or `mean`, the arithmetic mean.} } \value{ A data frame containing a summary of all the fields listed in \code{fields}, for each individual in the dataset (the dataset should not contain duplicated individuals), conditioned on the field in \code{by}. Continuous values are summarized as median, mean, range and number of missing values. Categorical values are summarized as count and relative percentage. diff --git a/man/gm.Rd b/man/gm.Rd index 2e4c8c1..5bf35d4 100644 --- a/man/gm.Rd +++ b/man/gm.Rd @@ -4,10 +4,14 @@ \alias{gm} \title{Calculate geometric mean} \usage{ -gm(x) +gm(x, na.rm = FALSE, neg.rm = FALSE) } \arguments{ \item{x}{Numeric vector.} + +\item{na.rm}{Flag for removing \code{NA} values (defaults to \code{FALSE}).} + +\item{neg.rm}{Flag for removing negative or zero values (defaults to \code{FALSE}).} } \value{ The geometric mean. \code{NA} is returned if there are any non-positive elements in \code{x}. diff --git a/man/pcv.Rd b/man/pcv.Rd index fd0927e..ccc59eb 100644 --- a/man/pcv.Rd +++ b/man/pcv.Rd @@ -9,7 +9,7 @@ pcv(x, na.rm = FALSE) \arguments{ \item{x}{Numeric vector.} -\item{na.rm}{A logical value indicating whether NA values should be stripped before the computation proceeds.} +\item{na.rm}{A logical value indicating whether `NA` values should be stripped before the computation proceeds.} } \value{ The percentage coefficient of variation. diff --git a/man/plot_scm.Rd b/man/plot_scm.Rd index d0008e1..d22fe71 100644 --- a/man/plot_scm.Rd +++ b/man/plot_scm.Rd @@ -134,12 +134,12 @@ Lindbom L, Ribbing J & Jonsson EN (2004). Perl-speaks-NONMEM (PsN) - A Perl modu Lindbom L, Pihlgren P & Jonsson N (2005). PsN-Toolkit - A collection of computer intensive statistical methods for non-linear mixed effect modeling using NONMEM. Computer Methods and Programs in Biomedicine, 79(3), 241-257. \doi{10.1016/j.cmpb.2005.04.005} Other NONMEM reading: +\code{\link{read_nm}()}, \code{\link{read_nm_all}()}, \code{\link{read_nm_multi_table}()}, \code{\link{read_nmcov}()}, \code{\link{read_nmext}()}, \code{\link{read_nmtables}()}, -\code{\link{read_nm}()}, \code{\link{read_scm}()} } \author{ diff --git a/man/read_nm_all.Rd b/man/read_nm_all.Rd index 77ac9fd..8533419 100644 --- a/man/read_nm_all.Rd +++ b/man/read_nm_all.Rd @@ -29,11 +29,11 @@ The filename for loading is constructed as \code{paste(run_prefix, \seealso{ Other NONMEM reading: \code{\link{plot_scm}()}, +\code{\link{read_nm}()}, \code{\link{read_nm_multi_table}()}, \code{\link{read_nmcov}()}, \code{\link{read_nmext}()}, \code{\link{read_nmtables}()}, -\code{\link{read_nm}()}, \code{\link{read_scm}()} } \concept{NONMEM reading} diff --git a/man/read_nm_multi_table.Rd b/man/read_nm_multi_table.Rd index e7a9874..51c719a 100644 --- a/man/read_nm_multi_table.Rd +++ b/man/read_nm_multi_table.Rd @@ -37,11 +37,11 @@ read_nm_multi_table("run1.cov", row.names=1) \seealso{ Other NONMEM reading: \code{\link{plot_scm}()}, +\code{\link{read_nm}()}, \code{\link{read_nm_all}()}, \code{\link{read_nmcov}()}, \code{\link{read_nmext}()}, \code{\link{read_nmtables}()}, -\code{\link{read_nm}()}, \code{\link{read_scm}()} } \author{ diff --git a/man/read_nmcov.Rd b/man/read_nmcov.Rd index b8af476..473d60f 100644 --- a/man/read_nmcov.Rd +++ b/man/read_nmcov.Rd @@ -35,11 +35,11 @@ NONMEM (\url{https://www.iconplc.com/innovation/nonmem/}) Other NONMEM reading: \code{\link{plot_scm}()}, +\code{\link{read_nm}()}, \code{\link{read_nm_all}()}, \code{\link{read_nm_multi_table}()}, \code{\link{read_nmext}()}, \code{\link{read_nmtables}()}, -\code{\link{read_nm}()}, \code{\link{read_scm}()} } \author{ diff --git a/man/read_nmext.Rd b/man/read_nmext.Rd index 19a70df..c4e01e0 100644 --- a/man/read_nmext.Rd +++ b/man/read_nmext.Rd @@ -57,11 +57,11 @@ NONMEM (\url{https://www.iconplc.com/innovation/nonmem/}) Other NONMEM reading: \code{\link{plot_scm}()}, +\code{\link{read_nm}()}, \code{\link{read_nm_all}()}, \code{\link{read_nm_multi_table}()}, \code{\link{read_nmcov}()}, \code{\link{read_nmtables}()}, -\code{\link{read_nm}()}, \code{\link{read_scm}()} } \author{ diff --git a/man/read_nmtables.Rd b/man/read_nmtables.Rd index a81af30..a054ff2 100644 --- a/man/read_nmtables.Rd +++ b/man/read_nmtables.Rd @@ -61,11 +61,11 @@ Jonsson EN, Karlsson MO. Xpose--an S-PLUS based population \seealso{ Other NONMEM reading: \code{\link{plot_scm}()}, +\code{\link{read_nm}()}, \code{\link{read_nm_all}()}, \code{\link{read_nm_multi_table}()}, \code{\link{read_nmcov}()}, \code{\link{read_nmext}()}, -\code{\link{read_nm}()}, \code{\link{read_scm}()} } \author{ diff --git a/man/read_scm.Rd b/man/read_scm.Rd index 4c4467b..14c1731 100644 --- a/man/read_scm.Rd +++ b/man/read_scm.Rd @@ -43,12 +43,12 @@ Lindbom L, Pihlgren P & Jonsson N (2005). PsN-Toolkit - A collection of computer Other NONMEM reading: \code{\link{plot_scm}()}, +\code{\link{read_nm}()}, \code{\link{read_nm_all}()}, \code{\link{read_nm_multi_table}()}, \code{\link{read_nmcov}()}, \code{\link{read_nmext}()}, -\code{\link{read_nmtables}()}, -\code{\link{read_nm}()} +\code{\link{read_nmtables}()} } \author{ Justin Wilkins, \email{justin.wilkins@occams.com} From 9478013e342a2523739981f9892adf04e812e4c5 Mon Sep 17 00:00:00 2001 From: Bill Denney Date: Tue, 22 Jul 2025 11:02:59 -0400 Subject: [PATCH 2/5] Update continuous integration --- .github/workflows/R-CMD-check.yaml | 51 +++++++++++++++++++++++ .github/workflows/blank.yml | 17 -------- .github/workflows/pkgdown.yaml | 11 +++-- .github/workflows/test-coverage.yaml | 62 ++++++++++++++++++++++++++++ .travis.yml | 1 - README.md | 7 +++- _pkgdown.yml | 2 - 7 files changed, 125 insertions(+), 26 deletions(-) create mode 100644 .github/workflows/R-CMD-check.yaml delete mode 100644 .github/workflows/blank.yml create mode 100644 .github/workflows/test-coverage.yaml delete mode 100644 .travis.yml diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml new file mode 100644 index 0000000..562fe0f --- /dev/null +++ b/.github/workflows/R-CMD-check.yaml @@ -0,0 +1,51 @@ +# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples +# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help +on: + push: + branches: [main, master] + pull_request: + +name: R-CMD-check.yaml + +permissions: read-all + +jobs: + R-CMD-check: + runs-on: ${{ matrix.config.os }} + + name: ${{ matrix.config.os }} (${{ matrix.config.r }}) + + strategy: + fail-fast: false + matrix: + config: + - {os: macos-latest, r: 'release'} + - {os: windows-latest, r: 'release'} + - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'} + - {os: ubuntu-latest, r: 'release'} + - {os: ubuntu-latest, r: 'oldrel-1'} + + env: + GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + R_KEEP_PKG_SOURCE: yes + + steps: + - uses: actions/checkout@v4 + + - uses: r-lib/actions/setup-pandoc@v2 + + - uses: r-lib/actions/setup-r@v2 + with: + r-version: ${{ matrix.config.r }} + http-user-agent: ${{ matrix.config.http-user-agent }} + use-public-rspm: true + + - uses: r-lib/actions/setup-r-dependencies@v2 + with: + extra-packages: any::rcmdcheck + needs: check + + - uses: r-lib/actions/check-r-package@v2 + with: + upload-snapshots: true + build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")' diff --git a/.github/workflows/blank.yml b/.github/workflows/blank.yml deleted file mode 100644 index b2340b2..0000000 --- a/.github/workflows/blank.yml +++ /dev/null @@ -1,17 +0,0 @@ -name: CI - -on: [push] - -jobs: - build: - - runs-on: ubuntu-latest - - steps: - - uses: actions/checkout@v1 - - name: Run a one-line script - run: echo Hello, world! - - name: Run a multi-line script - run: | - echo Add other actions to build, - echo test, and deploy your project. diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml index 087f0b0..bfc9f4d 100644 --- a/.github/workflows/pkgdown.yaml +++ b/.github/workflows/pkgdown.yaml @@ -4,12 +4,13 @@ on: push: branches: [main, master] pull_request: - branches: [main, master] release: types: [published] workflow_dispatch: -name: pkgdown +name: pkgdown.yaml + +permissions: read-all jobs: pkgdown: @@ -19,8 +20,10 @@ jobs: group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }} env: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + permissions: + contents: write steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - uses: r-lib/actions/setup-pandoc@v2 @@ -39,7 +42,7 @@ jobs: - name: Deploy to GitHub pages 🚀 if: github.event_name != 'pull_request' - uses: JamesIves/github-pages-deploy-action@v4.4.1 + uses: JamesIves/github-pages-deploy-action@v4.5.0 with: clean: false branch: gh-pages diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml new file mode 100644 index 0000000..0ab748d --- /dev/null +++ b/.github/workflows/test-coverage.yaml @@ -0,0 +1,62 @@ +# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples +# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help +on: + push: + branches: [main, master] + pull_request: + +name: test-coverage.yaml + +permissions: read-all + +jobs: + test-coverage: + runs-on: ubuntu-latest + env: + GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + + steps: + - uses: actions/checkout@v4 + + - uses: r-lib/actions/setup-r@v2 + with: + use-public-rspm: true + + - uses: r-lib/actions/setup-r-dependencies@v2 + with: + extra-packages: any::covr, any::xml2 + needs: coverage + + - name: Test coverage + run: | + cov <- covr::package_coverage( + quiet = FALSE, + clean = FALSE, + install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package") + ) + print(cov) + covr::to_cobertura(cov) + shell: Rscript {0} + + - uses: codecov/codecov-action@v5 + with: + # Fail if error if not on PR, or if on PR and token is given + fail_ci_if_error: ${{ github.event_name != 'pull_request' || secrets.CODECOV_TOKEN }} + files: ./cobertura.xml + plugins: noop + disable_search: true + token: ${{ secrets.CODECOV_TOKEN }} + + - name: Show testthat output + if: always() + run: | + ## -------------------------------------------------------------------- + find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true + shell: bash + + - name: Upload test results + if: failure() + uses: actions/upload-artifact@v4 + with: + name: coverage-test-failures + path: ${{ runner.temp }}/package diff --git a/.travis.yml b/.travis.yml deleted file mode 100644 index e837f5d..0000000 --- a/.travis.yml +++ /dev/null @@ -1 +0,0 @@ -language: r diff --git a/README.md b/README.md index 1a2806d..6de83f4 100644 --- a/README.md +++ b/README.md @@ -1,10 +1,13 @@ # pmxTools Pharmacometric Tools for Modeling & Simulation -[![Build Status](https://travis-ci.org/kestrel99/pmxTools.png?branch=master)](https://travis-ci.org/kestrel99/pmxTools) + +[![R-CMD-check](https://github.com/kestrel99/pmxTools/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/kestrel99/pmxTools/actions/workflows/R-CMD-check.yaml) [![contributions welcome](https://img.shields.io/badge/contributions-welcome-brightgreen.svg?style=flat)](https://github.com/kestrel99/pmxTools/issues) -[![](https://www.r-pkg.org/badges/version/pmxTools?color=green)](https://cran.r-project.org/package=pmxTools) [![](http://cranlogs.r-pkg.org/badges/grand-total/pmxTools?color=blue)](https://cran.r-project.org/package=pmxTools) +[![Codecov test coverage](https://codecov.io/gh/kestrel99/pmxTools/graph/badge.svg)](https://app.codecov.io/gh/kestrel99/pmxTools) +[![CRAN status](https://www.r-pkg.org/badges/version/pmxTools)](https://CRAN.R-project.org/package=pmxTools) + diff --git a/_pkgdown.yml b/_pkgdown.yml index 87bddcc..2a0b389 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -2,5 +2,3 @@ url: https://kestrel99.github.io/pmxTools/ template: bootstrap: 5 -development: - mode: auto \ No newline at end of file From bfe387901bba603b0374dff9786117f0eb804960 Mon Sep 17 00:00:00 2001 From: Bill Denney Date: Tue, 22 Jul 2025 11:05:17 -0400 Subject: [PATCH 3/5] Update testthat template code --- DESCRIPTION | 2 +- tests/testthat.R | 8 ++++++++ 2 files changed, 9 insertions(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 1e09179..bf329ed 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -41,7 +41,7 @@ Depends: R (>= 3.50), patchwork Suggests: - testthat, + testthat (>= 3.0.0), vdiffr, knitr, rmarkdown diff --git a/tests/testthat.R b/tests/testthat.R index d0e820d..855e380 100644 --- a/tests/testthat.R +++ b/tests/testthat.R @@ -1,3 +1,11 @@ +# This file is part of the standard setup for testthat. +# It is recommended that you do not modify it. +# +# Where should you do additional test configuration? +# Learn more about the roles of various files in: +# * https://r-pkgs.org/testing-design.html#sec-tests-files-overview +# * https://testthat.r-lib.org/articles/special-files.html + library(testthat) library(pmxTools) From ec0ec08963bb7fd182c99197af9153e9150b630a Mon Sep 17 00:00:00 2001 From: Bill Denney Date: Tue, 22 Jul 2025 11:58:26 -0400 Subject: [PATCH 4/5] Convert snapshot tests to data tests --- DESCRIPTION | 3 +- tests/testthat/_snaps/nm.md | 2029 --------------------- tests/testthat/_snaps/plot/est.svg | 18 - tests/testthat/_snaps/plot/perc.svg | 18 - tests/testthat/test-nm.R | 45 +- tests/testthat/test-plot.R | 29 +- tests/testthat/testData/nmcov.RDS | Bin 0 -> 297 bytes tests/testthat/testData/nmext.RDS | Bin 0 -> 838 bytes tests/testthat/testData/read_nm.RDS | Bin 0 -> 6883 bytes tests/testthat/testData/rnm.RDS | Bin 0 -> 1421 bytes tests/testthat/testData/sample_omega.RDS | Bin 0 -> 964 bytes tests/testthat/testData/sample_sigma.RDS | Bin 0 -> 547 bytes tests/testthat/testData/sample_uncert.RDS | Bin 0 -> 2124 bytes 13 files changed, 47 insertions(+), 2095 deletions(-) delete mode 100644 tests/testthat/_snaps/nm.md create mode 100644 tests/testthat/testData/nmcov.RDS create mode 100644 tests/testthat/testData/nmext.RDS create mode 100644 tests/testthat/testData/read_nm.RDS create mode 100644 tests/testthat/testData/rnm.RDS create mode 100644 tests/testthat/testData/sample_omega.RDS create mode 100644 tests/testthat/testData/sample_sigma.RDS create mode 100644 tests/testthat/testData/sample_uncert.RDS diff --git a/DESCRIPTION b/DESCRIPTION index bf329ed..b8152c8 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -44,7 +44,8 @@ Suggests: testthat (>= 3.0.0), vdiffr, knitr, - rmarkdown + rmarkdown, + withr Encoding: UTF-8 VignetteBuilder: knitr Config/testthat/edition: 3 diff --git a/tests/testthat/_snaps/nm.md b/tests/testthat/_snaps/nm.md deleted file mode 100644 index 4cedad8..0000000 --- a/tests/testthat/_snaps/nm.md +++ /dev/null @@ -1,2029 +0,0 @@ -# read_nm - - Code - read_nm("testData/runR001.xml") - Message - Reading testData/runR001.xml - Output - $start_datetime - $start_datetime[[1]] - [1] "2021-02-04T17:29:28.815" - - - $control_stream - $control_stream[[1]] - [1] "\n$PROB BOLUS_1CPT_VCL SINGLE DOSE FOCE INTER (120 Ind/2276 Obs) runR001\n$INPUT ID TIME DV=DROP LNDV=DV MDV AMT EVID DOSE VI CLI SSX IIX SD CMT\n$DATA BOLUS_1CPT.csv IGNORE=@ IGNORE (SD.EQ.0)\n$SUBR ADVAN1,TRANS2\n$PK\n CL=THETA(1)*EXP(ETA(1))\n V=THETA(2)*EXP(ETA(2))\n S1=V\n$ERROR (ONLY OBSERVATIONS)\n IPRED=LOG(0.0025)\n W=THETA(3)\n IF (F.GT.0) IPRED=LOG(F)\n IRES=IPRED-DV\n IWRES=IRES/W\n Y=IPRED+W*ERR(1)\n$THETA (0,5,15) (0,90,200) (0,0.3,1)\n;# CL V RSV\n$OMEGA 0.15 0.15\n;# IIV_CL IIV_V\n$SIGMA 1 FIX\n;# RSV_FIX\n$EST NSIG=3 PRINT=5 MAX=9999 NOABORT POSTHOC METHOD=COND INTER NOOBT\n$COV\n$TABLE ID TIME LNDV MDV AMT EVID DOSE VI CLI CL V ETA1 ETA2\n IPRED IRES IWRES CWRESI\n ONEHEADER NOPRINT FILE=runR001.csv\n" - - - $nmtran - $nmtran[[1]] - [1] "\n\n WARNINGS AND ERRORS (IF ANY) FOR PROBLEM 1\n\n (WARNING 2) NM-TRAN INFERS THAT THE DATA ARE POPULATION.\n" - - - $nonmem - $nonmem$license_information - $nonmem$license_information[[1]] - [1] "\nLicense Registered to: Occams\nExpiration Date: 14 JUN 2021\nCurrent Date: 4 FEB 2021\nDays until program expires : 130\n" - - - $nonmem$program_information - $nonmem$program_information[[1]] - [1] "\n1NONLINEAR MIXED EFFECTS MODEL PROGRAM (NONMEM) VERSION 7.5.0\n ORIGINALLY DEVELOPED BY STUART BEAL, LEWIS SHEINER, AND ALISON BOECKMANN\n CURRENT DEVELOPERS ARE ROBERT BAUER, ICON DEVELOPMENT SOLUTIONS,\n AND ALISON BOECKMANN. IMPLEMENTATION, EFFICIENCY, AND STANDARDIZATION\n PERFORMED BY NOUS INFOSYSTEMS.\n" - - - $nonmem$problem - $nonmem$problem$problem_title - $nonmem$problem$problem_title[[1]] - [1] "BOLUS_1CPT_VCL SINGLE DOSE FOCE INTER (120 Ind/2276 Obs) runR001" - - - $nonmem$problem$problem_information - $nonmem$problem$problem_information[[1]] - [1] "\n\n PROBLEM NO.: 1\n BOLUS_1CPT_VCL SINGLE DOSE FOCE INTER (120 Ind/2276 Obs) runR001\n0DATA CHECKOUT RUN: NO\n DATA SET LOCATED ON UNIT NO.: 2\n THIS UNIT TO BE REWOUND: NO\n NO. OF DATA RECS IN DATA SET: 2400\n NO. OF DATA ITEMS IN DATA SET: 13\n ID DATA ITEM IS DATA ITEM NO.: 1\n DEP VARIABLE IS DATA ITEM NO.: 3\n MDV DATA ITEM IS DATA ITEM NO.: 4\n0INDICES PASSED TO SUBROUTINE PRED:\n 6 2 5 0 0 0 13 0 0 0 0\n0LABELS FOR DATA ITEMS:\n ID TIME LNDV MDV AMT EVID DOSE VI CLI SSX IIX SD CMT\n0(NONBLANK) LABELS FOR PRED-DEFINED ITEMS:\n CL V IPRED IRES IWRES\n0FORMAT FOR DATA:\n (E4.0,2E7.0,E2.0,E7.0,E2.0,E7.0,E6.0,E5.0,2E3.0,2E2.0)\n\n TOT. NO. OF OBS RECS: 2276\n TOT. NO. OF INDIVIDUALS: 120\n0LENGTH OF THETA: 3\n0DEFAULT THETA BOUNDARY TEST OMITTED: NO\n0OMEGA HAS SIMPLE DIAGONAL FORM WITH DIMENSION: 2\n0DEFAULT OMEGA BOUNDARY TEST OMITTED: YES\n0SIGMA HAS SIMPLE DIAGONAL FORM WITH DIMENSION: 1\n0DEFAULT SIGMA BOUNDARY TEST OMITTED: NO\n0INITIAL ESTIMATE OF THETA:\n LOWER BOUND INITIAL EST UPPER BOUND\n 0.0000E+00 0.5000E+01 0.1500E+02\n 0.0000E+00 0.9000E+02 0.2000E+03\n 0.0000E+00 0.3000E+00 0.1000E+01\n0INITIAL ESTIMATE OF OMEGA:\n 0.1500E+00\n 0.0000E+00 0.1500E+00\n0INITIAL ESTIMATE OF SIGMA:\n 0.1000E+01\n0SIGMA CONSTRAINED TO BE THIS INITIAL ESTIMATE\n0COVARIANCE STEP OMITTED: NO\n EIGENVLS. PRINTED: NO\n SPECIAL COMPUTATION: NO\n COMPRESSED FORMAT: NO\n GRADIENT METHOD USED: NOSLOW\n SIGDIGITS ETAHAT (SIGLO): -1\n SIGDIGITS GRADIENTS (SIGL): -1\n EXCLUDE COV FOR FOCE (NOFCOV): NO\n Cholesky Transposition of R Matrix (CHOLROFF):0\n KNUTHSUMOFF: -1\n RESUME COV ANALYSIS (RESUME): NO\n SIR SAMPLE SIZE (SIRSAMPLE):\n NON-LINEARLY TRANSFORM THETAS DURING COV (THBND): 1\n PRECONDTIONING CYCLES (PRECOND): 0\n PRECONDTIONING TYPES (PRECONDS): TOS\n FORCED PRECONDTIONING CYCLES (PFCOND):0\n PRECONDTIONING TYPE (PRETYPE): 0\n FORCED POS. DEFINITE SETTING DURING PRECONDITIONING: (FPOSDEF):0\n SIMPLE POS. DEFINITE SETTING: (POSDEF):-1\n0TABLES STEP OMITTED: NO\n NO. OF TABLES: 1\n SEED NUMBER (SEED): 11456\n RANMETHOD: 3U\n MC SAMPLES (ESAMPLE): 300\n WRES SQUARE ROOT TYPE (WRESCHOL): EIGENVALUE\n0-- TABLE 1 --\n0RECORDS ONLY: ALL\n04 COLUMNS APPENDED: YES\n PRINTED: NO\n HEADERS: ONE\n FILE TO BE FORWARDED: NO\n FORMAT: S1PE11.4\n IDFORMAT:\n LFORMAT:\n RFORMAT:\n FIXED_EFFECT_ETAS:\n0USER-CHOSEN ITEMS:\n ID TIME LNDV MDV AMT EVID DOSE VI CLI CL V ETA1 ETA2 IPRED IRES IWRES CWRESI\n1DOUBLE PRECISION PREDPP VERSION 7.5.0\n\n ONE COMPARTMENT MODEL (ADVAN1)\n0MAXIMUM NO. OF BASIC PK PARAMETERS: 2\n0BASIC PK PARAMETERS (AFTER TRANSLATION):\n ELIMINATION RATE (K) IS BASIC PK PARAMETER NO.: 1\n\n TRANSLATOR WILL CONVERT PARAMETERS\n CLEARANCE (CL) AND VOLUME (V) TO K (TRANS2)\n0COMPARTMENT ATTRIBUTES\n COMPT. NO. FUNCTION INITIAL ON/OFF DOSE DEFAULT DEFAULT\n STATUS ALLOWED ALLOWED FOR DOSE FOR OBS.\n 1 CENTRAL ON NO YES YES YES\n 2 OUTPUT OFF YES NO NO NO\n1\n ADDITIONAL PK PARAMETERS - ASSIGNMENT OF ROWS IN GG\n COMPT. NO. INDICES\n SCALE BIOAVAIL. 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- $nonmem$problem$estimation$invcovariance$row$col - $nonmem$problem$estimation$invcovariance$row$col[[1]] - [1] "6825.27392229574" - - attr(,"cname") - [1] "OMEGA(2,2)" - - attr(,"rname") - [1] "OMEGA(2,2)" - - $nonmem$problem$estimation$invcovariance$row - $nonmem$problem$estimation$invcovariance$row$col - $nonmem$problem$estimation$invcovariance$row$col[[1]] - [1] "0.000000000000000E+000" - - attr(,"cname") - [1] "THETA1" - - $nonmem$problem$estimation$invcovariance$row$col - $nonmem$problem$estimation$invcovariance$row$col[[1]] - [1] "0.000000000000000E+000" - - attr(,"cname") - [1] "THETA2" - - $nonmem$problem$estimation$invcovariance$row$col - $nonmem$problem$estimation$invcovariance$row$col[[1]] - [1] "0.000000000000000E+000" - - attr(,"cname") - [1] "THETA3" - - $nonmem$problem$estimation$invcovariance$row$col - $nonmem$problem$estimation$invcovariance$row$col[[1]] - [1] "0.000000000000000E+000" - - attr(,"cname") - [1] "OMEGA(1,1)" - - $nonmem$problem$estimation$invcovariance$row$col - $nonmem$problem$estimation$invcovariance$row$col[[1]] - [1] "0.000000000000000E+000" - - attr(,"cname") - [1] "OMEGA(1,2)" - - $nonmem$problem$estimation$invcovariance$row$col - $nonmem$problem$estimation$invcovariance$row$col[[1]] - [1] "0.000000000000000E+000" - - attr(,"cname") - [1] "OMEGA(2,2)" - - $nonmem$problem$estimation$invcovariance$row$col - $nonmem$problem$estimation$invcovariance$row$col[[1]] - [1] "0.000000000000000E+000" - - attr(,"cname") - [1] "SIGMA(1,1)" - - attr(,"rname") - [1] "SIGMA(1,1)" - - - attr(,"number") - [1] "1" - attr(,"type") - [1] "0" - - $nonmem$problem$post_process_times - $nonmem$problem$post_process_times$post_elapsed_time - $nonmem$problem$post_process_times$post_elapsed_time[[1]] - [1] "0.08" - - - $nonmem$problem$post_process_times$finaloutput_elapsed_time - $nonmem$problem$post_process_times$finaloutput_elapsed_time[[1]] - [1] "0.20" - - - - attr(,"number") - [1] "1" - attr(,"subproblem") - [1] "0" - attr(,"superproblem1") - [1] "0" - attr(,"iteration1") - [1] "0" - attr(,"superproblem2") - [1] "0" - attr(,"iteration2") - [1] "0" - - attr(,"version") - [1] "7.5.0" - - $stop_datetime - $stop_datetime[[1]] - [1] "2021-02-04T17:29:31.574" - - - $total_cputime - $total_cputime[[1]] - [1] "7.266" - - - attr(,"schemaLocation") - [1] "http://namespaces.oreilly.com/xmlnut/address output.xsd" - attr(,"xmlns:xsi") - [1] "http://www.w3.org/2001/XMLSchema-instance" - attr(,"xmlns:nm") - [1] "http://namespaces.oreilly.com/xmlnut/address" - -# rnm - - Code - rnm(index = "001", prefix = "runR", pathNM = "testData", ext = ".res", extmod = ".ctl") - Output - $Theta - Parameter Estimate SE CV CIL CIU P - 1 THETA1 3.980130 0.09897590 2.486750 3.7861408 4.1741192 0 - 2 THETA2 68.219400 1.92949000 2.828360 64.4376691 72.0011309 0 - 3 THETA3 0.199472 0.00280475 1.406087 0.1939748 0.2049692 0 - - $Eta - Eta Estimate SE CV EtaCV Shrinkage - 1 1 0.0715555 0.00912817 12.75677 26.74986 1.37216 - 2 2 0.0921585 0.01220090 13.23904 30.35762 1.46175 - - $Epsilon - Epsilon Estimate SE CV EpsCV Shrinkage - 1 1 1 0 0 100 5.22027 - - $CorTheta - THETA1 THETA2 THETA3 - 1 1.00000000 0.109072 0.00138964 - 2 0.10907200 1.000000 0.12310700 - 3 0.00138964 0.123107 1.00000000 - - $CorOmega - Eta1 Eta2 - Eta1 1.000 0.000 - Eta2 0.000 1.000 - - $CorSigma - Eps1 - Eps1 1.000 - - $OmegaMatrix - [,1] [,2] - [1,] 0.0715555 0.0000000 - [2,] 0.0000000 0.0921585 - - $SigmaMatrix - [,1] - [1,] 1 - - $CovMatrixTheta - THETA1 THETA2 THETA3 - 1 9.79623e-03 0.020829800 3.85768e-07 - 2 2.08298e-02 3.722920000 6.66221e-04 - 3 3.85768e-07 0.000666221 7.86662e-06 - - $CovMatrix - THETA1 THETA2 THETA3 SIGMA.1.1. OMEGA.1.1. OMEGA.2.1. - 1 9.79623e-03 0.020829800 3.85768e-07 0 1.81304e-05 0 - 2 2.08298e-02 3.722920000 6.66221e-04 0 5.51038e-04 0 - 3 3.85768e-07 0.000666221 7.86662e-06 0 1.67878e-06 0 - 4 0.00000e+00 0.000000000 0.00000e+00 0 0.00000e+00 0 - 5 1.81304e-05 0.000551038 1.67878e-06 0 8.33235e-05 0 - 6 0.00000e+00 0.000000000 0.00000e+00 0 0.00000e+00 0 - 7 -9.96425e-05 0.000811546 -2.60664e-06 0 -2.55098e-06 0 - OMEGA.2.2. - 1 -9.96425e-05 - 2 8.11546e-04 - 3 -2.60664e-06 - 4 0.00000e+00 - 5 -2.55098e-06 - 6 0.00000e+00 - 7 1.48861e-04 - - $OFV - [1] -4126.115 - - $ThetaString - Parameter Estimate SE CV Estimate (95% CI) P - 1 THETA1 3.98 0.0990 2.5% 3.98 (3.79/4.17) < 0.00001 - 2 THETA2 68.2 1.93 2.8% 68.2 (64.4/72.0) < 0.00001 - 3 THETA3 0.199 0.00280 1.4% 0.199 (0.194/0.205) < 0.00001 - - $EtaString - Eta Estimate SE CV 100*sqrt(Omega) Shrinkage - 1 1 0.0716 0.00913 12.8% 26.7% 1.4% - 2 2 0.0922 0.0122 13.2% 30.4% 1.5% - - $EpsString - Epsilon Estimate SE CV 100*sqrt(Omega) Shrinkage - 1 1 1.00 (Fixed) 5.2% - - $RunTime - [1] 17.35 - - $conditionN - NULL - - -# read_nmcov - - Code - read_nmcov("testData/runR001.cov") - Message - Reading testData/runR001.cov - Output - THETA1 THETA2 THETA3 SIGMA.1.1. OMEGA.1.1. OMEGA.2.1. - [1,] 9.79623e-03 0.020829800 3.85768e-07 0 1.81304e-05 0 - [2,] 2.08298e-02 3.722920000 6.66221e-04 0 5.51038e-04 0 - [3,] 3.85768e-07 0.000666221 7.86662e-06 0 1.67878e-06 0 - [4,] 0.00000e+00 0.000000000 0.00000e+00 0 0.00000e+00 0 - [5,] 1.81304e-05 0.000551038 1.67878e-06 0 8.33235e-05 0 - [6,] 0.00000e+00 0.000000000 0.00000e+00 0 0.00000e+00 0 - [7,] -9.96425e-05 0.000811546 -2.60664e-06 0 -2.55098e-06 0 - OMEGA.2.2. - [1,] -9.96425e-05 - [2,] 8.11546e-04 - [3,] -2.60664e-06 - [4,] 0.00000e+00 - [5,] -2.55098e-06 - [6,] 0.00000e+00 - [7,] 1.48861e-04 - -# read_nmext - - Code - read_nmext("testData/runR001.ext") - Message - Reading testData/runR001.ext - Output - $Termination - NULL - - $OFV - [1] -4126.115 - - $Thetas - [1] 3.980130 68.219400 0.199472 - - $Omega - $Omega[[1]] - [1] 0.0715555 - - $Omega[[2]] - [1] 0.0000000 0.0921585 - - - $Sigma - $Sigma[[1]] - [1] 1 - - - $seThetas - [1] 0.09897590 1.92949000 0.00280475 - - $seOmega - $seOmega[[1]] - [1] 0.00912817 - - $seOmega[[2]] - [1] NA 0.0122009 - - - $seSigma - $seSigma[[1]] - [1] NA - - - $raw_lst - [1] "TABLE NO. 1: First Order Conditional Estimation with Interaction: Goal Function=MINIMUM VALUE OF OBJECTIVE FUNCTION: Problem=1 Subproblem=0 Superproblem1=0 Iteration1=0 Superproblem2=0 Iteration2=0" - [2] " ITERATION THETA1 THETA2 THETA3 SIGMA(1,1) OMEGA(1,1) OMEGA(2,1) OMEGA(2,2) OBJ" - [3] " 0 5.00000E+00 9.00000E+01 3.00000E-01 1.00000E+00 1.50000E-01 0.00000E+00 1.50000E-01 -3465.72885682371" - [4] " 5 3.83588E+00 6.72641E+01 1.91725E-01 1.00000E+00 7.13261E-02 0.00000E+00 1.29166E-01 -4111.52222574939" - [5] " 10 3.94172E+00 6.73826E+01 1.99381E-01 1.00000E+00 7.15277E-02 0.00000E+00 9.19553E-02 -4125.77900367604" - [6] " 14 3.98013E+00 6.82194E+01 1.99472E-01 1.00000E+00 7.15555E-02 0.00000E+00 9.21585E-02 -4126.11481640313" - [7] " -1000000000 3.98013E+00 6.82194E+01 1.99472E-01 1.00000E+00 7.15555E-02 0.00000E+00 9.21585E-02 -4126.11481640313" - [8] " -1000000001 9.89759E-02 1.92949E+00 2.80475E-03 1.00000E+10 9.12817E-03 1.00000E+10 1.22009E-02 0.000000000000000E+000" - [9] " -1000000004 0.00000E+00 0.00000E+00 0.00000E+00 1.00000E+00 2.67499E-01 0.00000E+00 3.03576E-01 0.000000000000000E+000" - [10] " -1000000005 0.00000E+00 0.00000E+00 0.00000E+00 1.00000E+10 1.70621E-02 1.00000E+10 2.00952E-02 0.000000000000000E+000" - [11] " -1000000006 0.00000E+00 0.00000E+00 0.00000E+00 1.00000E+00 0.00000E+00 1.00000E+00 0.00000E+00 0.000000000000000E+000" - [12] " -1000000007 0.00000E+00 3.70000E+01 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.000000000000000E+000" - [13] " -1000000008 3.88104E-02 -2.92122E-03 -4.33821E-01 0.00000E+00 -4.03024E-01 0.00000E+00 1.44149E-01 0.000000000000000E+000" - - -# get_est_table - - Code - get_est_table(nm1, thetaLabels = c("CL", "V", "KA"), omegaLabels = c("CL", "V"), - sigmaLabels = "Residual") - Output - Parameter Estimate RSE CI95 Shrinkage - 1 CL 3.9800 2.49 3.79-4.17 - - 2 V 68.2000 2.83 64.4-72.0 - - 3 KA 0.1990 1.41 0.194-0.205 - - 4 CL 0.0716 12.80 0.0537-0.0894 1.37 - 5 OM2,1 0.0000 NA - - 6 V 0.0922 13.20 0.0682-0.116 1.46 - 7 Residual 1.0000 NA --- 5.22 - -# get_probinfo - - Code - get_probinfo(nm1) - Output - $prob_title - [1] "BOLUS_1CPT_VCL SINGLE DOSE FOCE INTER (120 Ind/2276 Obs) runR001" - - $prog_info - [1] "\n1NONLINEAR MIXED EFFECTS MODEL PROGRAM (NONMEM) VERSION 7.5.0\n ORIGINALLY DEVELOPED BY STUART BEAL, LEWIS SHEINER, AND ALISON BOECKMANN\n CURRENT DEVELOPERS ARE ROBERT BAUER, ICON DEVELOPMENT SOLUTIONS,\n AND ALISON BOECKMANN. IMPLEMENTATION, EFFICIENCY, AND STANDARDIZATION\n PERFORMED BY NOUS INFOSYSTEMS.\n" - - $lic_info - [1] "\nLicense Registered to: Occams\nExpiration Date: 14 JUN 2021\nCurrent Date: 4 FEB 2021\nDays until program expires : 130\n" - - $prob_times - startTime stopTime elapsedTime - 1 2021-02-04T17:29:31.574 2021-02-04T17:29:31.574 7.266 - - $prob_info - nRecords nOBS nIND nTHETA nOMEGA nSIGMA COV_STEP_OMITTED COV_MATRIX - 1 2400 2276 120 3 NA 1 NO rsr - - $est_info - final_objective_function estimation_method - 1 -4126.11 focei - estimation_title estimation_elapsed_time - 1 First Order Conditional Estimation with Interaction 0.83 - termination_status condition_number - 1 SUCCESSFUL NA - - -# sample_uncertainty - - Code - sample_uncert("testData/runR001.xml", n = 50, seed = 740727) - Message - Reading testData/runR001.xml - Reading testData/runR001.cov - Output - V1 V2 V3 V4 V5 V6 V7 - 1 4.165433 69.39547 0.2027448 1 0.06848604 0 0.09347681 - 2 3.980225 69.50231 0.1994999 1 0.07953186 0 0.08515790 - 3 4.008908 67.31330 0.2020217 1 0.04367090 0 0.08225640 - 4 4.001296 68.48560 0.2047266 1 0.07295125 0 0.09326988 - 5 3.978739 67.59651 0.1971732 1 0.08556432 0 0.08930405 - 6 4.042743 71.34557 0.1996294 1 0.05363680 0 0.10454367 - 7 3.969076 69.34515 0.1982914 1 0.07396419 0 0.09076399 - 8 3.869667 69.34122 0.1993334 1 0.06957219 0 0.08570421 - 9 4.083545 68.47258 0.2010389 1 0.07686870 0 0.08509724 - 10 4.153517 68.51932 0.2009742 1 0.06672599 0 0.11383226 - 11 4.028990 67.55515 0.2025752 1 0.06291851 0 0.08666884 - 12 4.095689 67.97826 0.2024989 1 0.07236835 0 0.09128803 - 13 4.028240 71.82350 0.2024290 1 0.07231574 0 0.09965155 - 14 3.983857 65.11927 0.1980753 1 0.07718695 0 0.09164850 - 15 3.942173 67.80190 0.2045056 1 0.06681079 0 0.08288682 - 16 3.945592 68.78126 0.1997871 1 0.06646189 0 0.10900627 - 17 3.842798 68.74961 0.2024411 1 0.06104701 0 0.09405646 - 18 3.843747 67.80288 0.2056648 1 0.07270782 0 0.07868634 - 19 4.005418 67.09663 0.2037665 1 0.07063172 0 0.10041499 - 20 3.988539 67.15033 0.2015780 1 0.06780923 0 0.09632218 - 21 4.315006 68.16353 0.1958835 1 0.07113135 0 0.10648345 - 22 3.975249 68.53082 0.2040278 1 0.08818818 0 0.08984173 - 23 3.921943 69.60221 0.1979640 1 0.07267085 0 0.12511286 - 24 3.983742 67.76555 0.2031760 1 0.06717891 0 0.10367067 - 25 3.895660 69.47939 0.1993874 1 0.06817941 0 0.08973712 - 26 3.958638 69.74054 0.1949952 1 0.07217236 0 0.09218806 - 27 3.985585 68.95600 0.1997755 1 0.06356015 0 0.10439573 - 28 3.920165 70.13811 0.1952001 1 0.07006469 0 0.06607858 - 29 4.135315 69.01056 0.1978472 1 0.07398465 0 0.07513122 - 30 3.827007 68.56629 0.2015357 1 0.05506670 0 0.09303089 - 31 3.893408 67.49121 0.1975671 1 0.04499286 0 0.08351562 - 32 4.025988 70.45182 0.1990793 1 0.07242308 0 0.09782781 - 33 4.019942 70.96364 0.2014000 1 0.08447572 0 0.08777964 - 34 3.884504 66.55993 0.1971079 1 0.07450460 0 0.08856721 - 35 3.996054 66.93821 0.1985125 1 0.06129866 0 0.08274537 - 36 4.081618 68.97580 0.2001548 1 0.07202699 0 0.09638920 - 37 3.993148 65.10763 0.1985139 1 0.06485045 0 0.07416839 - 38 3.908453 65.67802 0.1990315 1 0.06266032 0 0.09186744 - 39 3.935636 66.32350 0.2013148 1 0.07732190 0 0.08450629 - 40 3.803549 66.89265 0.1998202 1 0.06222067 0 0.09201371 - 41 3.794152 65.91168 0.2045937 1 0.08406271 0 0.09105954 - 42 3.966106 69.23118 0.1967659 1 0.06171561 0 0.09058125 - 43 3.889720 71.25744 0.1962289 1 0.07186124 0 0.10326919 - 44 4.154339 67.57126 0.1984505 1 0.06970990 0 0.09025829 - 45 3.930934 65.24055 0.1965228 1 0.07108583 0 0.08314434 - 46 3.846555 65.76844 0.1990567 1 0.07902672 0 0.07322697 - 47 3.758647 65.37698 0.1983753 1 0.08090015 0 0.07478860 - 48 4.209726 67.88323 0.1984188 1 0.07493575 0 0.08783786 - 49 4.077548 68.53444 0.1997585 1 0.06783113 0 0.07974986 - 50 3.901412 65.80751 0.2001533 1 0.06834075 0 0.08115616 - -# sample_omega - - Code - sample_omega("testData/runR001.xml", n = 50, seed = 740727) - Message - Reading testData/runR001.xml - Output - OMEGA1 OMEGA2 - 1 -0.485774017 -0.185195155 - 2 0.019057330 -0.201841117 - 3 -0.092220115 0.142531846 - 4 -0.053452246 -0.041899840 - 5 -0.005860621 0.097999946 - 6 -0.122117141 -0.491895640 - 7 0.047158306 -0.177104223 - 8 0.317216216 -0.176399096 - 9 -0.277511640 -0.039923984 - 10 -0.466124693 -0.047340588 - 11 -0.143078090 0.104464520 - 12 -0.317857393 0.037836851 - 13 -0.075626875 -0.567076755 - 14 -0.057431324 0.487740577 - 15 0.096573312 0.065719009 - 16 0.102980688 -0.088367559 - 17 0.381530989 -0.083297510 - 18 0.364015055 0.065651205 - 19 -0.085608934 0.176622932 - 20 -0.039014555 0.168189713 - 21 -0.910806987 0.008494193 - 22 0.017880132 -0.048991123 - 23 0.180236394 -0.217507094 - 24 -0.016373515 0.071400401 - 25 0.248784681 -0.198159213 - 26 0.081610619 -0.239302183 - 27 -0.003202234 -0.115894102 - 28 0.191494306 -0.301816487 - 29 -0.410335617 -0.124609535 - 30 0.421659420 -0.054440752 - 31 0.224514080 0.114643305 - 32 -0.090473167 -0.351267547 - 33 -0.066580283 -0.431786741 - 34 0.234546310 0.261169214 - 35 -0.063058274 0.201557182 - 36 -0.264244743 -0.119094904 - 37 -0.083333567 0.489565129 - 38 0.156144909 0.399898917 - 39 0.091808239 0.298321052 - 40 0.459855852 0.208893265 - 41 0.470330694 0.363237058 - 42 0.053542262 -0.159170186 - 43 0.292422796 -0.477895354 - 44 -0.483526786 0.101818212 - 45 0.088062709 0.468706416 - 46 0.325173266 0.385727743 - 47 0.558226034 0.447393843 - 48 -0.629438185 0.052686743 - 49 -0.260387425 -0.049650628 - 50 0.176918857 0.379532347 - -# sample_sigma - - Code - sample_sigma("testData/runR001.xml", n = 50, seed = 740727) - Message - Reading testData/runR001.xml - Output - SIGMA1 - 1 -0.61004507 - 2 -0.66487797 - 3 0.46950931 - 4 -0.13802084 - 5 0.32281829 - 6 -1.62033672 - 7 -0.58339300 - 8 -0.58107027 - 9 -0.13151224 - 10 -0.15594302 - 11 0.34411303 - 12 0.12463708 - 13 -1.86798828 - 14 1.60664967 - 15 0.21648276 - 16 -0.29108857 - 17 -0.27438750 - 18 0.21625940 - 19 0.58180760 - 20 0.55402802 - 21 0.02798043 - 22 -0.16137999 - 23 -0.71648273 - 24 0.23519764 - 25 -0.65274953 - 26 -0.78827719 - 27 -0.38176282 - 28 -0.99420344 - 29 -0.41047204 - 30 -0.17933143 - 31 0.37764262 - 32 -1.15709850 - 33 -1.42233404 - 34 0.86030864 - 35 0.66394267 - 36 -0.39230648 - 37 1.61265986 - 38 1.31729344 - 39 0.98268924 - 40 0.68810821 - 41 1.19652685 - 42 -0.52431711 - 43 -1.57421885 - 44 0.33539591 - 45 1.54394989 - 46 1.27061266 - 47 1.47374486 - 48 0.17355361 - 49 -0.16355245 - 50 1.25020461 - diff --git a/tests/testthat/_snaps/plot/est.svg b/tests/testthat/_snaps/plot/est.svg index fa588aa..d3ee1d9 100644 --- a/tests/testthat/_snaps/plot/est.svg +++ b/tests/testthat/_snaps/plot/est.svg @@ -116,15 +116,6 @@ - - - - - - - - - @@ -147,15 +138,6 @@ - - - - - - - - - diff --git a/tests/testthat/_snaps/plot/perc.svg b/tests/testthat/_snaps/plot/perc.svg index 0eba828..288d52b 100644 --- a/tests/testthat/_snaps/plot/perc.svg +++ b/tests/testthat/_snaps/plot/perc.svg @@ -115,15 +115,6 @@ - - - - - - - - - @@ -146,15 +137,6 @@ - - - - - - - - - diff --git a/tests/testthat/test-nm.R b/tests/testthat/test-nm.R index 5818747..e3c87b9 100644 --- a/tests/testthat/test-nm.R +++ b/tests/testthat/test-nm.R @@ -1,27 +1,32 @@ -library(testthat) - test_that("read_nm", { - expect_snapshot(read_nm("testData/runR001.xml")) - + expect_equal( + read_nm("testData/runR001.xml", quiet = TRUE), + readRDS("testData/read_nm.RDS") + ) }) test_that("rnm", { - expect_snapshot(rnm(index = "001", prefix="runR", pathNM = "testData", ext=".res", extmod = ".ctl")) - + expect_equal( + rnm(index = "001", prefix="runR", pathNM = "testData", ext=".res", extmod = ".ctl"), + readRDS("testData/rnm.RDS") + ) }) test_that("read_nmcov", { - expect_snapshot(read_nmcov("testData/runR001.cov")) - + expect_equal( + read_nmcov("testData/runR001.cov", quiet = TRUE), + readRDS("testData/nmcov.RDS") + ) }) test_that("read_nmext", { - expect_snapshot(read_nmext("testData/runR001.ext")) - + expect_equal( + read_nmext("testData/runR001.ext", quiet = TRUE), + readRDS("testData/nmext.RDS") + ) }) - -nm1 <- read_nm("testData/runR001.xml", quiet = T) +nm1 <- read_nm("testData/runR001.xml", quiet = TRUE) test_that("get_theta", { expect_equal( @@ -160,14 +165,22 @@ test_that("get_probinfo", { }) test_that("sample_uncertainty", { - expect_snapshot(sample_uncert("testData/runR001.xml", n=50, seed=740727)) + expect_equal( + suppressMessages(sample_uncert("testData/runR001.xml", n=50, seed=740727)), + readRDS("testData/sample_uncert.RDS") + ) }) test_that("sample_omega", { - expect_snapshot(sample_omega("testData/runR001.xml", n=50, seed=740727)) + expect_equal( + suppressMessages(sample_omega("testData/runR001.xml", n=50, seed=740727)), + readRDS("testData/sample_omega.RDS") + ) }) test_that("sample_sigma", { - expect_snapshot(sample_sigma("testData/runR001.xml", n=50, seed=740727)) + expect_equal( + suppressMessages(sample_sigma("testData/runR001.xml", n=50, seed=740727)), + readRDS("testData/sample_sigma.RDS") + ) }) - diff --git a/tests/testthat/test-plot.R b/tests/testthat/test-plot.R index f8fdf8d..fee5f22 100644 --- a/tests/testthat/test-plot.R +++ b/tests/testthat/test-plot.R @@ -1,16 +1,19 @@ -library(vdiffr) +skip_if_not_installed("vdiffr") -set.seed(740727) +withr::with_seed( + 740727, + { + df <- data.frame(wt = c(rnorm(1000, mean=70, sd=15), rnorm(1000,mean=85, sd=20)), + Group=rep(c("Group 1","Group 2"), each=1000)) -df <- data.frame(wt = c(rnorm(1000, mean=70, sd=15), rnorm(1000,mean=85, sd=20)), - Group=rep(c("Group 1","Group 2"), each=1000)) + test_that("plot_dist", { + vdiffr::expect_doppelganger("Single distplot", plot_dist(df[df$Group=="Group 1",], yvar="wt", ylb="Weight (kg)")) + vdiffr::expect_doppelganger("Conditioned distplot", plot_dist(df, yvar="wt", xvar="Group", ylb="Weight (kg)")) + }) -test_that("plot_dist", { - expect_doppelganger("Single distplot", plot_dist(df[df$Group=="Group 1",], yvar="wt", ylb="Weight (kg)")) - expect_doppelganger("Conditioned distplot", plot_dist(df, yvar="wt", xvar="Group", ylb="Weight (kg)")) -}) - -test_that("plot_nmprogress", { - expect_doppelganger("Est", plot_nmprogress(fileName = "testData/runR001", fileExt = ".res", metric = "est")) - expect_doppelganger("Perc", plot_nmprogress(fileName = "testData/runR001", fileExt = ".res")) -}) \ No newline at end of file + test_that("plot_nmprogress", { + vdiffr::expect_doppelganger("Est", plot_nmprogress(fileName = "testData/runR001", fileExt = ".res", metric = "est")) + vdiffr::expect_doppelganger("Perc", plot_nmprogress(fileName = "testData/runR001", fileExt = ".res")) + }) + } +) diff --git a/tests/testthat/testData/nmcov.RDS b/tests/testthat/testData/nmcov.RDS new file mode 100644 index 0000000000000000000000000000000000000000..93c6d2f4c57162400b03dedf549fd5e1532fac71 GIT binary patch literal 297 zcmV+^0oMK>iwFP!0000028-ZgU|?WoU||K4K+M3v8XDrJYr(+4#0TUU+P4UB?>_bM zn*G#}40DBlwRSTf7tVI}R%L(!yU$G5XWkM11>^6Rl6xv!J>dgPy#w!wF84S8X4|`7 zS+zxUvJp(3y%S%dgiiQ9INxjf-otw?D8bB!skeJjAH%8{vJh_H9xXq`w14t2{=TDk zx7RIgR$?F%z}ydW54!pGqSyCbDL<=@urJL(j644fx%R=s2kKvR_oJI{uiW&>;fDQh z1_l-;AeWJWg@F@DGpA(c0x4b~1_`r6Fp3fmppv}A+|*(qTNtYD9}o+G)k4&;g?PAz vI2xkxj8J&SP##yXr@ODCo*@vzMEreS-LZ)nVG%LX1KAD$y;YMRYytoPSn7?w literal 0 HcmV?d00001 diff --git a/tests/testthat/testData/nmext.RDS b/tests/testthat/testData/nmext.RDS new file mode 100644 index 0000000000000000000000000000000000000000..5c0a9221412a585fd3848bc57b762cd42ca87c1d GIT binary patch literal 838 zcmV-M1G)SkiwFP!000002E~?5Y)nxU$6vpc3YD-WcO`^*?ztcD-CJZjZQj&KX9k@% zwUVI^Bb}+t3^qit(1m>^Hew-`J{H14Y%BH>iCEg&k}BuEkM?!?h}t;GeR=Vu*~*VMP8)Balang;Jq7StL`r@kx)A^Q1g-+#9VFraY3LEa6SL zG(=7`=g!Xh^`k&0uAIFb35w#f-;5-nE|@AND|9$n(upG4&@3rbyi++-!)&N>%&X*p zgcb;v6g(0Wg|T989~^}JD9S}|tV6K1f(2sacvSN`Nf;$W+SHhLfTGYV0x@_bGDbi$ z3~agTp}+Nz3>S{HU8aH-$mlprz!Y$1pJLgR3d!j_Xj7 z#vlR)MS;f*ih&lZ3!^D$dd;hKCr!2n^$nF2S(gXe)!8fA;|R?Q@)X&|CwFTWRSn!#)b&zVknIPihu z(v1)1--F1FgM|Bbsly=dV#32vXvsF*5$E4J@|T_sfVk^A>qerp=l>!$0HT7ImjWt+ zW@Z>3R$weRg&ARUe2c*PlYkz|DHEwLP$59*Kc5k+w>$V;hCqFdYTa)|-^wk~LbbqsY?aXYe QZGKID0i(y|RK5rR00dH?T}+d1UnbLiAN?isDLyt9)^op!+iC^fDhkv%tNQ`@h!*oj-3kMu;5qqMa5}WBh70%&LQYV#eva0 z^AL1%u4t%W#oEPY1M{c&CC=Hzc*GbRvXQUgw>@unn%1#pR@ummT$owidJ$H1;qR}SMT@y(bVVL{#AcE^C$iVKMM|cr`PKa zr=0bE+@Ex3{b0mbyEFfQ5hU|}?lgHcC0yltGVw>VMI(M>zGfYU?bYswDSthh^#}ZT z5?oEXL*7S}{**u9sYD8x^p(ibCM+SlX_;-lVZQ=dShbo}@m#*)RINHP=%{Tr_!59M zti~RH0=$43^O~RtgyWsIePlPyI;_H~bz;?>7N9tM&AVR51VuWu%=$iGw@z)BcaJR? zr@haFVb*OIupBy8TcHaWi1X}2wqZ;S?5j!XstS%}E&U{@PdF@|U$vlHVXg$Aw|93Mgz0qU7?|dO^JsUP3;dzMaJW$KUCZO^ zPQ~=Ya6}wsq=sn$?3O9suW^T8OS~Rgk@N+##SS6S53v zBkxmyRN~O~%-eYwdT|pG1>C7xE&jx8+ssW<3JoK~aG_R`bX^MgZnFLqQRkirJ}q;WJSD4zAtTyoa96 zY1kg<W7aXj?Q&`fhKXaoCP`vH5T5&6fVFQ7W^?O1XcZr~c zw=}w?3cD5aK#lNLjBds7R>}jFmTze^Nd7z+e_VW&mDePlIH>aGw5ONrJ6jN7s*h`Hi4AoONl zY&2M;*fs*O%947>P_8xPlXTo5>ildgil1@8=6fbmEPp46Sa6f*pj zX%aj}?S?(F9T41lRjGHX7SMXai~#c;U{-4IAl-w_=}j>3r$2w-y-9a89S74s3t)mv z9%6~^Y|?+vmnz3jz3tR$dj}xkm(7lM>~^AS3Y$>|-UokbY+u{A*0s50>IgE55SYf#dTc&J9fx+*zG4R8&O5X8dvkD_nbh#Er zzbI4I{JK&HgIS6mFQ_0HQ15js0qHJ4J;&vczZKAhBJ{Nodp=f%6fc&Bk1;x+tIXho zwMS3sVYg^@5i&c%b^r+vzymZJDzaj^7yvYe1j!H<`n%a>lko2$NK#Cwkrt5H>@*HB z9>JS%3Y5wUcmIcv}{wf{bxN1On!Ne$}2|)i8WN3&Zy_)ae6`fC*`r zfd#JBykU5;oUaw;X|(Eekd>%eHcJc;u+>WC2^>zJ89~SjSl}L}7p1UNu*VU|LG4DT z5o^z(>Dm>(^%9~jNIxtuVkmg%oEAV+!w8ox>M$eQW5JkJw;Pb1-~&)D(B=|EM_@#< zIHE8QlfW1YSin=ej%K}if+@&iJdB{gj4;nps?_&b9&v)o0{16-DBzc1MOgV`5BAS%C%lS+h{YwB)|!R-fJ1^5Cemt% z8mg&F7Vd?p@e-mnfnlR_6cr%69nymoC6s-B35z2ClA#h8i=g9$)hTup&upnv0_)Nx z2j;`9hPDfcSyq5D4?($o)MPvc^=Uh&EL}J{O0l{46NUFFPP!Gd9&!E9cFYsgt|OYi zT5YEcHUkuA>DoMWo%Ug|G-_=#mU5_&(Fg3a89%R^M=1foM@n4(w8?df@u}wWCfCc; zC?^&RETJY?*;tEEZ&-}Q7WHzspR(Ot2v6&Fm|ue!7g^LF(u`y4ZyxeH%!pw52K!gg zgh!ccn6*Xu8HP;^HCin22%#l7LCsj3F2YAe@UU{a4wSJN!P)vT8xU`MYkDaNp3ulO z*{j5HWQj#Q=wlt`#gYq{6yy%!)IuKyOLrL@`5kpJF;j1b(51vm0^xzm9f2lkU3>0mm5; zr2&7#0H@dIXWhx9`+?pNel4$3@X|W?P#?z=|Kbdkrr-0^;{8G07x$HY!v0Yyy2#g$ z%V09>rdgntd{&I{vGC$!2_}7o#TcIzV|-SO!KS@@Z4J)T^lf2bCLcJv3La1~pK?$d zib}sm5l6E({wy=Yj3WNXz|PKt>(Ry8%%9HAf?AD z{$mJzn{lT7t6||d>4o}Z2z`rjzUc*THwNYqc*qj)wA?1sNm|hn*zaHYBhcRdC@qr$ zQl?|S*Y6J20)L0Vy;b{^d}7YAb59nHR)dT{R}-1M*%jcx_!&K^{)m2T%-pn zr^WD147~~P4g$}D%v3Xgj}WlC2_%!xD7efSKEn_;v)-FvFbOU%*R3li%b!Qrvp3W0 zVHUoC5)jSx&|k0WA=f6;?r=OvgKx9SbJ~0`*1b8;n2*fDU=jfx=>=KX^d!Gcz^0AZ zgIO@mo8tI#6U;Fcvk&9+{PJNh$HDZ%Un`c7ggnq3-JEsLH(%%oJh~p9`;&DXeuSV? zKZA6em0r@KM&KSSrk`)rW6~WB{n?u!L%4LEH%mWPlO9N!po!7`Zjy1S95Y*QyMt># z)ngZXT=w7l7vMjpXCxgS

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