From e7c74250594f3d1acc9bc9f298ed35fea0426360 Mon Sep 17 00:00:00 2001
From: Dominic Tong <dominic@insight-rx.com>
Date: Tue, 2 Dec 2025 01:56:52 +0000
Subject: [PATCH 1/7] initial commit with dose_cmts

---
 DESCRIPTION          | 2 +-
 R/parse_input_data.R | 9 +++++++--
 R/run_eval.R         | 2 ++
 3 files changed, 10 insertions(+), 3 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 5e0ae21..ca32725 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -42,6 +42,6 @@ Remotes:
 Config/testthat/edition: 3
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3
 VignetteBuilder: knitr
 LazyData: true
diff --git a/R/parse_input_data.R b/R/parse_input_data.R
index 3264cf9..0a5c4d3 100644
--- a/R/parse_input_data.R
+++ b/R/parse_input_data.R
@@ -9,6 +9,7 @@ parse_input_data <- function(
     data,
     covariates,
     ids,
+    dose_cmts,
     group = NULL,
     verbose = TRUE
 ) {
@@ -31,6 +32,7 @@ parse_input_data <- function(
     new_data,
     parse_nm_data,
     covariates = covariates,
+    dose_cmts = dose_cmts,
     group = group
   )
 
@@ -39,10 +41,13 @@ parse_input_data <- function(
   out
 }
 
-parse_nm_data <- function(data, covariates, group = NULL) {
+parse_nm_data <- function(data, covariates, dose_cmts, group = NULL) {
   out <- list()
   out$covariates <- make_covariates_object(data, covariates)
-  out$regimen <- PKPDsim::nm_to_regimen(data)
+  out$regimen <- PKPDsim::nm_to_regimen(
+    data,
+    dose_cmts = dose_cmts
+  )
   obs <- data |>
     dplyr::filter(.data$EVID == 0)
   if(!is.null(group)) {
diff --git a/R/run_eval.R b/R/run_eval.R
index 23d738f..61e9348 100644
--- a/R/run_eval.R
+++ b/R/run_eval.R
@@ -49,6 +49,7 @@
 run_eval <- function(
   model,
   data,
+  dose_cmts,
   ids = NULL,
   parameters = NULL,
   fixed = NULL,
@@ -102,6 +103,7 @@ run_eval <- function(
     data = input_data,
     covariates = covariates,
     ids = ids,
+    dose_cmts = dose_cmts,
     group = group,
     verbose = verbose
   )

From 82a607c8158478ddb93dc59a968cf515011499f3 Mon Sep 17 00:00:00 2001
From: Dominic Tong <dominic@insight-rx.com>
Date: Wed, 3 Dec 2025 00:45:11 +0000
Subject: [PATCH 2/7] rm dose_cmts

---
 R/parse_input_data.R | 9 ++-------
 R/run_eval.R         | 2 --
 2 files changed, 2 insertions(+), 9 deletions(-)

diff --git a/R/parse_input_data.R b/R/parse_input_data.R
index 0a5c4d3..3264cf9 100644
--- a/R/parse_input_data.R
+++ b/R/parse_input_data.R
@@ -9,7 +9,6 @@ parse_input_data <- function(
     data,
     covariates,
     ids,
-    dose_cmts,
     group = NULL,
     verbose = TRUE
 ) {
@@ -32,7 +31,6 @@ parse_input_data <- function(
     new_data,
     parse_nm_data,
     covariates = covariates,
-    dose_cmts = dose_cmts,
     group = group
   )
 
@@ -41,13 +39,10 @@ parse_input_data <- function(
   out
 }
 
-parse_nm_data <- function(data, covariates, dose_cmts, group = NULL) {
+parse_nm_data <- function(data, covariates, group = NULL) {
   out <- list()
   out$covariates <- make_covariates_object(data, covariates)
-  out$regimen <- PKPDsim::nm_to_regimen(
-    data,
-    dose_cmts = dose_cmts
-  )
+  out$regimen <- PKPDsim::nm_to_regimen(data)
   obs <- data |>
     dplyr::filter(.data$EVID == 0)
   if(!is.null(group)) {
diff --git a/R/run_eval.R b/R/run_eval.R
index 61e9348..23d738f 100644
--- a/R/run_eval.R
+++ b/R/run_eval.R
@@ -49,7 +49,6 @@
 run_eval <- function(
   model,
   data,
-  dose_cmts,
   ids = NULL,
   parameters = NULL,
   fixed = NULL,
@@ -103,7 +102,6 @@ run_eval <- function(
     data = input_data,
     covariates = covariates,
     ids = ids,
-    dose_cmts = dose_cmts,
     group = group,
     verbose = verbose
   )

From cb2583ba39983678b5e8d46a267be42ab6fdbc09 Mon Sep 17 00:00:00 2001
From: Ron Keizer <ron@insight-rx.com>
Date: Wed, 3 Dec 2025 18:09:06 +0000
Subject: [PATCH 3/7] skip in case of fit error

---
 R/calculate_stats.R |  1 +
 R/run_eval_core.R   | 47 ++++++++++++++++++++++++++++++---------------
 2 files changed, 33 insertions(+), 15 deletions(-)

diff --git a/R/calculate_stats.R b/R/calculate_stats.R
index fd94c7f..776488b 100644
--- a/R/calculate_stats.R
+++ b/R/calculate_stats.R
@@ -25,6 +25,7 @@ calculate_stats <- function(
       cols = c("pred", "map_ipred", "iter_ipred"), names_to = "type"
     ) |>
     dplyr::group_by(.data$type, .data$apriori) |>
+    dplyr::filter(!is.na(value)) |>
     dplyr::summarise(
       rmse = rmse(.data$dv, .data$value),
       nrmse = nrmse(.data$dv, .data$value),
diff --git a/R/run_eval_core.R b/R/run_eval_core.R
index 08bbdf9..be62a22 100644
--- a/R/run_eval_core.R
+++ b/R/run_eval_core.R
@@ -67,22 +67,39 @@ run_eval_core <- function(
       iov_bins = mod_obj$bins,
       verbose = FALSE
     )
+    if(inherits(fit, "error")) {
+      ## create NA records for this fit
+      pred_data <- tibble::tibble(
+        id = obs_data$id,
+        t = obs_data$t,
+        dv = NA,
+        ipred = NA,
+        pred = NA,
+        ofv = NA,
+        ss_w = NA,
+        `_iteration` = iterations[i],
+        `_grouper` = obs_data$`_grouper`
+      )
+      par_dummy <- as.data.frame(mod_upd$parameters)
+      par_dummy[, 1:ncol(par_dummy)] <- NA
+      fit_pars <- dplyr::mutate(as.data.frame(par_dummy), id = obs_data$id[1])
+    } else {
+      ## Data frame with predictive data
+      pred_data <- tibble::tibble(
+        id = obs_data$id,
+        t = obs_data$t,
+        dv = fit$dv,
+        ipred = fit$ipred,
+        pred = fit$pred,
+        ofv = fit$fit$value,
+        ss_w = ss(fit$dv, fit$ipred, weights),
+        `_iteration` = iterations[i],
+        `_grouper` = obs_data$`_grouper`
+      )
+      ## Add parameter estimates
+      fit_pars <- dplyr::mutate(as.data.frame(fit$parameters), id = obs_data$id[1])
+    }
 
-    ## Data frame with predictive data
-    pred_data <- tibble::tibble(
-      id = obs_data$id,
-      t = obs_data$t,
-      dv = fit$dv,
-      ipred = fit$ipred,
-      pred = fit$pred,
-      ofv = fit$fit$value,
-      ss_w = ss(fit$dv, fit$ipred, weights),
-      `_iteration` = iterations[i],
-      `_grouper` = obs_data$`_grouper`
-    )
-
-    ## Add parameter estimates
-    fit_pars <- dplyr::mutate(as.data.frame(fit$parameters), id = obs_data$id[1])
     comb <- dplyr::bind_rows(
       comb, dplyr::left_join(pred_data, fit_pars, by = "id")
     )

From 20f5d2aff584a1a284450991c9849d03bbdd23d2 Mon Sep 17 00:00:00 2001
From: Ron Keizer <ron@insight-rx.com>
Date: Wed, 3 Dec 2025 18:22:32 +0000
Subject: [PATCH 4/7] add warning when errors

---
 R/calculate_stats.R | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/R/calculate_stats.R b/R/calculate_stats.R
index 776488b..45939c6 100644
--- a/R/calculate_stats.R
+++ b/R/calculate_stats.R
@@ -20,12 +20,17 @@ calculate_stats <- function(
   if(inherits(res, "mipdeval_results")) {
     res <- res$results
   }
+  ## Check for errors during fits / predictions
+  errors <- res |>
+    dplyr::filter(is.na(pred) | (is.na(map_ipred) & !apriori) | is.na(iter_ipred))
+  if(nrow(errors) > 0) {
+    cli::cli_warn("Errors where encountered in {nrow(errors)} out of {nrow(res)} evaluated predictions. The problems occurred in patient(s) {unique(errors$id)}.")
+  }
   out <- res |>
     tidyr::pivot_longer(
       cols = c("pred", "map_ipred", "iter_ipred"), names_to = "type"
     ) |>
     dplyr::group_by(.data$type, .data$apriori) |>
-    dplyr::filter(!is.na(value)) |>
     dplyr::summarise(
       rmse = rmse(.data$dv, .data$value),
       nrmse = nrmse(.data$dv, .data$value),

From 02be7896b9e0f2673cfc326f073c021d4b794529 Mon Sep 17 00:00:00 2001
From: dominic-irx <59584945+dominic-irx@users.noreply.github.com>
Date: Wed, 3 Dec 2025 10:45:20 -0800
Subject: [PATCH 5/7] fix typo

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

diff --git a/R/calculate_stats.R b/R/calculate_stats.R
index 45939c6..a01c462 100644
--- a/R/calculate_stats.R
+++ b/R/calculate_stats.R
@@ -24,7 +24,7 @@ calculate_stats <- function(
   errors <- res |>
     dplyr::filter(is.na(pred) | (is.na(map_ipred) & !apriori) | is.na(iter_ipred))
   if(nrow(errors) > 0) {
-    cli::cli_warn("Errors where encountered in {nrow(errors)} out of {nrow(res)} evaluated predictions. The problems occurred in patient(s) {unique(errors$id)}.")
+    cli::cli_warn("Errors were encountered in {nrow(errors)} out of {nrow(res)} evaluated predictions. The problems occurred in patient(s) {unique(errors$id)}.")
   }
   out <- res |>
     tidyr::pivot_longer(

From a0a4f9a39e2cc88ddb3a3e26dd9125edb3fe42a0 Mon Sep 17 00:00:00 2001
From: Ron Keizer <ron@insight-rx.com>
Date: Wed, 3 Dec 2025 20:35:04 +0000
Subject: [PATCH 6/7] add arg to pass MAP options to get_map_estimates()

---
 R/run_eval.R         |  6 ++++++
 R/run_eval_core.R    | 37 ++++++++++++++++++++++---------------
 man/run_eval.Rd      |  6 ++++++
 man/run_eval_core.Rd |  8 +++++++-
 4 files changed, 41 insertions(+), 16 deletions(-)

diff --git a/R/run_eval.R b/R/run_eval.R
index 23d738f..c190463 100644
--- a/R/run_eval.R
+++ b/R/run_eval.R
@@ -32,6 +32,10 @@
 #'   result from a call to [stats_summ_options()].
 #' @param .vpc_options Options for VPC simulations. This must be the result from
 #'   a call to [vpc_options()].
+#' @param .fit_options Options for controlling MAP Bayesian fit. E.g.
+#' `.map_options = list(control = list(reltol = 1e-04))` will perform a slightly
+#' coarser fit (but more stable) which can be useful in some case (default 
+#' `reltol = 1e-05`).
 #' @param threads number of threads to divide computations on. Default is 1,
 #'   i.e. no parallel execution
 #' @param ruv residual error variability magnitude, specified as list.
@@ -63,6 +67,7 @@ run_eval <- function(
   incremental = FALSE,
   .stats_summ_options = stats_summ_options(),
   .vpc_options = vpc_options(),
+  .fit_options = list(),
   threads = 1,
   progress = TRUE,
   verbose = TRUE
@@ -127,6 +132,7 @@ run_eval <- function(
     weight_prior = weight_prior,
     incremental = incremental,
     progress_function = p,
+    .fit_options = .fit_options,
     .threads = threads,
     .skip = .vpc_options$vpc_only
   )
diff --git a/R/run_eval_core.R b/R/run_eval_core.R
index be62a22..42eec80 100644
--- a/R/run_eval_core.R
+++ b/R/run_eval_core.R
@@ -14,7 +14,8 @@ run_eval_core <- function(
   weight_prior = 1,
   censor_covariates = TRUE,
   incremental = FALSE,
-  progress_function = function() {}
+  progress_function = function() {},
+  .fit_options = NULL
 ) {
 
   progress_function()
@@ -52,20 +53,26 @@ run_eval_core <- function(
       mod_upd$parameters <- fit$parameters # take params from previous fit
       mod_upd$omega <- fit$vcov
     }
-    fit <- PKPDmap::get_map_estimates(
-      model = mod_obj$model,
-      parameters = mod_upd$parameters,
-      omega = mod_upd$omega,
-      error = mod_obj$ruv,
-      fixed = mod_obj$fixed,
-      as_eta = mod_obj$kappa,
-      data = data$observations,
-      covariates = cov_data,
-      regimen = data$regimen,
-      weight_prior = weight_prior,
-      weights = weights,
-      iov_bins = mod_obj$bins,
-      verbose = FALSE
+    fit <- do.call(
+      PKPDmap::get_map_estimates,
+      c(
+        list(
+          model = mod_obj$model,
+          parameters = mod_upd$parameters,
+          omega = mod_upd$omega,
+          error = mod_obj$ruv,
+          fixed = mod_obj$fixed,
+          as_eta = mod_obj$kappa,
+          data = data$observations,
+          covariates = cov_data,
+          regimen = data$regimen,
+          weight_prior = weight_prior,
+          weights = weights,
+          iov_bins = mod_obj$bins,
+          verbose = FALSE
+        ),
+        .fit_options
+      )
     )
     if(inherits(fit, "error")) {
       ## create NA records for this fit
diff --git a/man/run_eval.Rd b/man/run_eval.Rd
index 1c49a8d..73a71a9 100644
--- a/man/run_eval.Rd
+++ b/man/run_eval.Rd
@@ -21,6 +21,7 @@ run_eval(
   incremental = FALSE,
   .stats_summ_options = stats_summ_options(),
   .vpc_options = vpc_options(),
+  .fit_options = list(),
   threads = 1,
   progress = TRUE,
   verbose = TRUE
@@ -88,6 +89,11 @@ result from a call to \code{\link[=stats_summ_options]{stats_summ_options()}}.}
 \item{.vpc_options}{Options for VPC simulations. This must be the result from
 a call to \code{\link[=vpc_options]{vpc_options()}}.}
 
+\item{.fit_options}{Options for controlling MAP Bayesian fit. E.g.
+\code{.map_options = list(control = list(reltol = 1e-04))} will perform a slightly
+coarser fit (but more stable) which can be useful in some case (default
+\code{reltol = 1e-05}).}
+
 \item{threads}{number of threads to divide computations on. Default is 1,
 i.e. no parallel execution}
 
diff --git a/man/run_eval_core.Rd b/man/run_eval_core.Rd
index 23de731..2314866 100644
--- a/man/run_eval_core.Rd
+++ b/man/run_eval_core.Rd
@@ -13,7 +13,8 @@ run_eval_core(
   censor_covariates = TRUE,
   incremental = FALSE,
   progress_function = function() {
- }
+ },
+  .fit_options = NULL
 )
 }
 \arguments{
@@ -46,6 +47,11 @@ approach has been called "model predictive control (MPC)"
 "regular" MAP in some scenarios. Default is \code{FALSE}.}
 
 \item{progress_function}{function to increment progress bar}
+
+\item{.fit_options}{Options for controlling MAP Bayesian fit. E.g.
+\code{.map_options = list(control = list(reltol = 1e-04))} will perform a slightly
+coarser fit (but more stable) which can be useful in some case (default
+\code{reltol = 1e-05}).}
 }
 \value{
 a \code{data.frame} with individual predictions

From 428fffdc266ebd63afe5ff3e964e32857ba49776 Mon Sep 17 00:00:00 2001
From: Michael McCarthy <51542091+mccarthy-m-g@users.noreply.github.com>
Date: Thu, 22 Jan 2026 16:56:32 -0800
Subject: [PATCH 7/7] use `fit_options()` for `.fit_options` arg input

---
 NAMESPACE            |  1 +
 R/run_eval.R         | 31 ++++++++++++++++++++++++++-----
 man/fit_options.Rd   | 20 ++++++++++++++++++++
 man/run_eval.Rd      |  8 +++-----
 man/run_eval_core.Rd |  6 ++----
 5 files changed, 52 insertions(+), 14 deletions(-)
 create mode 100644 man/fit_options.Rd

diff --git a/NAMESPACE b/NAMESPACE
index 916d326..683b32d 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -15,6 +15,7 @@ export(calculate_shrinkage)
 export(calculate_stats)
 export(compare_psn_execute_results)
 export(compare_psn_proseval_results)
+export(fit_options)
 export(group_by_dose)
 export(group_by_time)
 export(install_default_literature_model)
diff --git a/R/run_eval.R b/R/run_eval.R
index c190463..c04c3cf 100644
--- a/R/run_eval.R
+++ b/R/run_eval.R
@@ -32,10 +32,8 @@
 #'   result from a call to [stats_summ_options()].
 #' @param .vpc_options Options for VPC simulations. This must be the result from
 #'   a call to [vpc_options()].
-#' @param .fit_options Options for controlling MAP Bayesian fit. E.g.
-#' `.map_options = list(control = list(reltol = 1e-04))` will perform a slightly
-#' coarser fit (but more stable) which can be useful in some case (default 
-#' `reltol = 1e-05`).
+#' @param .fit_options Options for controlling MAP Bayesian fit. This must be
+#'   the result from a call to [fit_options()].
 #' @param threads number of threads to divide computations on. Default is 1,
 #'   i.e. no parallel execution
 #' @param ruv residual error variability magnitude, specified as list.
@@ -67,7 +65,7 @@ run_eval <- function(
   incremental = FALSE,
   .stats_summ_options = stats_summ_options(),
   .vpc_options = vpc_options(),
-  .fit_options = list(),
+  .fit_options = fit_options(),
   threads = 1,
   progress = TRUE,
   verbose = TRUE
@@ -195,3 +193,26 @@ run_eval <- function(
   ## 5. Return results
   out
 }
+
+#' Options for controlling MAP Bayesian fit
+#'
+#' @param ... These dots are reserved for future extensibility and must be empty.
+#' @param reltol Relative convergence tolerance. `reltol = 1e-04` will perform a
+#'   slightly coarser but more stable fit, which can be useful in some case.
+#'
+#' @returns A list.
+#' @export
+fit_options <- function(
+    ...,
+    reltol = 1e-05
+) {
+  rlang::check_dots_empty()
+  out <- list(
+    control = list(
+      reltol = vctrs::vec_assert(
+        reltol, ptype = numeric(), size = 1L, arg = "reltol"
+      )
+    )
+  )
+  structure(out, class = "mipdeval_fit_options")
+}
diff --git a/man/fit_options.Rd b/man/fit_options.Rd
new file mode 100644
index 0000000..47f320c
--- /dev/null
+++ b/man/fit_options.Rd
@@ -0,0 +1,20 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/run_eval.R
+\name{fit_options}
+\alias{fit_options}
+\title{Options for controlling MAP Bayesian fit}
+\usage{
+fit_options(..., reltol = 1e-05)
+}
+\arguments{
+\item{...}{These dots are reserved for future extensibility and must be empty.}
+
+\item{reltol}{Relative convergence tolerance. \code{reltol = 1e-04} will perform a
+slightly coarser but more stable fit, which can be useful in some case.}
+}
+\value{
+A list.
+}
+\description{
+Options for controlling MAP Bayesian fit
+}
diff --git a/man/run_eval.Rd b/man/run_eval.Rd
index 73a71a9..9c0c94c 100644
--- a/man/run_eval.Rd
+++ b/man/run_eval.Rd
@@ -21,7 +21,7 @@ run_eval(
   incremental = FALSE,
   .stats_summ_options = stats_summ_options(),
   .vpc_options = vpc_options(),
-  .fit_options = list(),
+  .fit_options = fit_options(),
   threads = 1,
   progress = TRUE,
   verbose = TRUE
@@ -89,10 +89,8 @@ result from a call to \code{\link[=stats_summ_options]{stats_summ_options()}}.}
 \item{.vpc_options}{Options for VPC simulations. This must be the result from
 a call to \code{\link[=vpc_options]{vpc_options()}}.}
 
-\item{.fit_options}{Options for controlling MAP Bayesian fit. E.g.
-\code{.map_options = list(control = list(reltol = 1e-04))} will perform a slightly
-coarser fit (but more stable) which can be useful in some case (default
-\code{reltol = 1e-05}).}
+\item{.fit_options}{Options for controlling MAP Bayesian fit. This must be
+the result from a call to \code{\link[=fit_options]{fit_options()}}.}
 
 \item{threads}{number of threads to divide computations on. Default is 1,
 i.e. no parallel execution}
diff --git a/man/run_eval_core.Rd b/man/run_eval_core.Rd
index 2314866..a9c6020 100644
--- a/man/run_eval_core.Rd
+++ b/man/run_eval_core.Rd
@@ -48,10 +48,8 @@ approach has been called "model predictive control (MPC)"
 
 \item{progress_function}{function to increment progress bar}
 
-\item{.fit_options}{Options for controlling MAP Bayesian fit. E.g.
-\code{.map_options = list(control = list(reltol = 1e-04))} will perform a slightly
-coarser fit (but more stable) which can be useful in some case (default
-\code{reltol = 1e-05}).}
+\item{.fit_options}{Options for controlling MAP Bayesian fit. This must be
+the result from a call to \code{\link[=fit_options]{fit_options()}}.}
 }
 \value{
 a \code{data.frame} with individual predictions