From 8eb5fad9a7780b62b8718206dac0de2110e20054 Mon Sep 17 00:00:00 2001
From: Andy Baxter <andy@andybaxter.me>
Date: Fri, 1 Mar 2024 10:29:58 +0000
Subject: [PATCH 1/4] suggested error catch and message

---
 R/pred.R | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/R/pred.R b/R/pred.R
index d3bcf3f..9966889 100644
--- a/R/pred.R
+++ b/R/pred.R
@@ -413,6 +413,9 @@ pred_fun_Y <- function(model, yrestrictions, outcome_type, outcome_name,
     # Fit GLM for outcome variable using user-specified model and entire dataset
     fitY <- stats::glm(model, family = outcome_fam, data = obs_data, y = TRUE)
   }
+  if(anyNA(coefficients(fitY))) {
+    stop("`NA` coefficients produced in prediction model. This may be due to (multi)collinearity in `ymodel` predictor variables, or including `time_name` variable in a 'continuous_eof' model.")
+  }
   fitY$rmse <- add_rmse(fitY)
   fitY$stderr <- add_stderr(fitY)
   fitY$vcov <- add_vcov(fitY)

From 1f94392858d68276cf2719fea1504ea395ef02e7 Mon Sep 17 00:00:00 2001
From: Andy Baxter <andy@andybaxter.me>
Date: Fri, 1 Mar 2024 11:13:35 +0000
Subject: [PATCH 2/4] fuller error message with listed problem vars

---
 R/pred.R | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/R/pred.R b/R/pred.R
index 9966889..b87274a 100644
--- a/R/pred.R
+++ b/R/pred.R
@@ -414,7 +414,13 @@ pred_fun_Y <- function(model, yrestrictions, outcome_type, outcome_name,
     fitY <- stats::glm(model, family = outcome_fam, data = obs_data, y = TRUE)
   }
   if(anyNA(coefficients(fitY))) {
-    stop("`NA` coefficients produced in prediction model. This may be due to (multi)collinearity in `ymodel` predictor variables, or including `time_name` variable in a 'continuous_eof' model.")
+    stop(
+      "`NA` coefficients produced in prediction model. ",
+      "This may be due to (multi)collinearity in `ymodel` predictor variables, ",
+      "or including `time_name` variable in a 'continuous_eof' model.\n",
+      "Variables returning `NA` coefficients:\n - ",
+      paste(names(coefficients(fitY)[is.na(coefficients(fitY))]), collapse = "\n - ")
+      )
   }
   fitY$rmse <- add_rmse(fitY)
   fitY$stderr <- add_stderr(fitY)

From c3e04ef3c3cd5b723cfc186c7d0f05c17d93d807 Mon Sep 17 00:00:00 2001
From: Andy Baxter <andy@andybaxter.me>
Date: Fri, 1 Mar 2024 11:47:31 +0000
Subject: [PATCH 3/4] added messages in covmodels predictions

---
 R/simulate.R | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)

diff --git a/R/simulate.R b/R/simulate.R
index 4042707..bfa5e3f 100644
--- a/R/simulate.R
+++ b/R/simulate.R
@@ -145,6 +145,28 @@ simulate <- function(o, fitcov, fitY, fitD,
                      min_time, show_progress, pb, int_visit_type, ...){
   set.seed(subseed)
 
+  invalid_coefs <- vapply(lapply(fitcov, coefficients), anyNA, logical(1)) |> any()
+
+  if (invalid_coefs) {
+
+    coefficients <- lapply(fitcov, coefficients)
+
+    errored_parts <- out_coefs[vapply(out_coefs, anyNA, logical(1))]  |>
+      lapply(\(coefs) {names(coefs[is.na(coefs)])})
+
+
+    paste(names(errored_parts), errored_parts, sep = "\n - ", collapse = "\n\n")
+
+    stop(
+        "`NA` coefficients produced in covariate prediction model. ",
+        "This may be due to (multi)collinearity in `covmodels` predictor variables, ",
+        "or including `time_name` variable in a 'continuous_eof' model.\n",
+        "Variables returning `NA` coefficients:\n",
+        paste(names(errored_parts), errored_parts, sep = "\n - ", collapse = "\n\n")
+    )
+
+  }
+
   # Mechanism of passing intervention variable and intervention is different for parallel
   # and non-parallel versions
   if (parallel){

From fa02ce1f51dfe4f4cd6e6eec1b0dc89b735c12c7 Mon Sep 17 00:00:00 2001
From: Andy Baxter <andy@andybaxter.me>
Date: Fri, 1 Mar 2024 11:52:24 +0000
Subject: [PATCH 4/4] correcting variable call

---
 R/simulate.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/simulate.R b/R/simulate.R
index bfa5e3f..07d8c31 100644
--- a/R/simulate.R
+++ b/R/simulate.R
@@ -151,7 +151,7 @@ simulate <- function(o, fitcov, fitY, fitD,
 
     coefficients <- lapply(fitcov, coefficients)
 
-    errored_parts <- out_coefs[vapply(out_coefs, anyNA, logical(1))]  |>
+    errored_parts <- coefficients[vapply(coefficients, anyNA, logical(1))]  |>
       lapply(\(coefs) {names(coefs[is.na(coefs)])})