From 08f6844c53d66527ee3d29f24d3e28b62082f17f Mon Sep 17 00:00:00 2001 From: Michael McCarthy <51542091+mccarthy-m-g@users.noreply.github.com> Date: Wed, 18 Mar 2026 11:00:57 -0700 Subject: [PATCH 1/4] add `.Rproj` file --- mipdtrial.Rproj | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 mipdtrial.Rproj diff --git a/mipdtrial.Rproj b/mipdtrial.Rproj new file mode 100644 index 0000000..eaa6b81 --- /dev/null +++ b/mipdtrial.Rproj @@ -0,0 +1,18 @@ +Version: 1.0 + +RestoreWorkspace: Default +SaveWorkspace: Default +AlwaysSaveHistory: Default + +EnableCodeIndexing: Yes +UseSpacesForTab: Yes +NumSpacesForTab: 2 +Encoding: UTF-8 + +RnwWeave: Sweave +LaTeX: pdfLaTeX + +BuildType: Package +PackageUseDevtools: Yes +PackageInstallArgs: --no-multiarch --with-keep.source +PackageRoxygenize: rd,collate,namespace From 048aa0224091806877fb20bf74cae197474f6127 Mon Sep 17 00:00:00 2001 From: Michael McCarthy <51542091+mccarthy-m-g@users.noreply.github.com> Date: Wed, 18 Mar 2026 11:01:28 -0700 Subject: [PATCH 2/4] update roxygen version --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 9340a38..4f9da69 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -12,7 +12,7 @@ Description: Functions for simulating dose adjustments given PKPD models, License: MIT + file LICENSE Encoding: UTF-8 Roxygen: list(markdown = TRUE) -RoxygenNote: 7.3.2 +RoxygenNote: 7.3.3 Suggests: dplyr, ggplot2, From 2f54dab51b744b722e87d412c02d8bad7418e887 Mon Sep 17 00:00:00 2001 From: Michael McCarthy <51542091+mccarthy-m-g@users.noreply.github.com> Date: Wed, 18 Mar 2026 11:07:01 -0700 Subject: [PATCH 3/4] remove `...` from `PKPDmap::get_map_estimates()` calls --- R/map_adjust_dose.R | 6 ++---- R/map_fit.R | 7 ++----- 2 files changed, 4 insertions(+), 9 deletions(-) diff --git a/R/map_adjust_dose.R b/R/map_adjust_dose.R index 8377b1e..d1190d6 100644 --- a/R/map_adjust_dose.R +++ b/R/map_adjust_dose.R @@ -9,8 +9,7 @@ #' @inheritParams dose_grid_search #' @param settings list of arguments to be used in dose update, e.g. #' `dose_resolution`. -#' @param ... arguments passed on to PKPDmap::get_map_estimates and/or -#' PKPDsim::sim +#' @param ... arguments passed on to [PKPDsim::sim] via `dose_grid_search` #' @returns Returns a named list: `regimen`: the updated regimen; #' `additional_info`: the MAP parameter estimates #' @export @@ -37,8 +36,7 @@ map_adjust_dose <- function( ruv = ruv, tdms = tdms, covariates = covariates, - regimen = regimen, - ... + regimen = regimen ) if(! all(c("parameters", "pred", "ipred", "dv", "weights") %in% names(fit))) { cli::cli_warn("Fit error, please investigate. Continuing but using population estimates.") diff --git a/R/map_fit.R b/R/map_fit.R index 0183e40..1ff38d4 100644 --- a/R/map_fit.R +++ b/R/map_fit.R @@ -15,7 +15,6 @@ #' @param tdms observations to be included in MAP estimates #' @param covariates named list of PKPDsim covariates #' @param regimen PKPDsim regimen object -#' @param ... arguments passed on to PKPDmap::get_map_estimates #' @returns named list of individual PK parameter estimates #' @export @@ -26,8 +25,7 @@ simulate_fit <- function( ruv, tdms, covariates, - regimen, - ... + regimen ){ iov_obj <- get_iov_specification(est_model, parameters, omega) @@ -45,8 +43,7 @@ simulate_fit <- function( fixed = iov_obj$fixed, verbose = FALSE, skip_hessian = TRUE, # faster - int_step_size = 0.01, - ... + int_step_size = 0.01 )}, error = function(e) list(parameters = NULL) ) From c1d2f35bf80dc7a73503a57771cec2738b8757ca Mon Sep 17 00:00:00 2001 From: Michael McCarthy <51542091+mccarthy-m-g@users.noreply.github.com> Date: Wed, 18 Mar 2026 11:07:20 -0700 Subject: [PATCH 4/4] update documentation --- man/map_adjust_dose.Rd | 3 +-- man/map_adjust_interval.Rd | 3 +-- man/simulate_fit.Rd | 4 +--- 3 files changed, 3 insertions(+), 7 deletions(-) diff --git a/man/map_adjust_dose.Rd b/man/map_adjust_dose.Rd index fa462db..9310615 100644 --- a/man/map_adjust_dose.Rd +++ b/man/map_adjust_dose.Rd @@ -46,8 +46,7 @@ Example: \code{seq(from = 50, to = 500, by = (500 - 50) / 10)}} \item{settings}{list of arguments to be used in dose update, e.g. \code{dose_resolution}.} -\item{...}{arguments passed on to PKPDmap::get_map_estimates and/or -PKPDsim::sim} +\item{...}{arguments passed on to \link[PKPDsim:sim]{PKPDsim::sim} via \code{dose_grid_search}} } \value{ Returns a named list: \code{regimen}: the updated regimen; diff --git a/man/map_adjust_interval.Rd b/man/map_adjust_interval.Rd index 2794db6..6b08533 100644 --- a/man/map_adjust_interval.Rd +++ b/man/map_adjust_interval.Rd @@ -47,8 +47,7 @@ Example: \code{seq(from = 50, to = 500, by = (500 - 50) / 10)}} \item{settings}{list of arguments to be used in dose update, e.g. \code{dose_resolution}.} -\item{...}{arguments passed on to PKPDmap::get_map_estimates and/or -PKPDsim::sim} +\item{...}{arguments passed on to \link[PKPDsim:sim]{PKPDsim::sim} via \code{dose_grid_search}} } \value{ Returns a named list: \code{regimen}: the updated regimen; diff --git a/man/simulate_fit.Rd b/man/simulate_fit.Rd index b3f95c4..facd09e 100644 --- a/man/simulate_fit.Rd +++ b/man/simulate_fit.Rd @@ -4,7 +4,7 @@ \alias{simulate_fit} \title{Get MAP Bayesian parameters} \usage{ -simulate_fit(est_model, parameters, omega, ruv, tdms, covariates, regimen, ...) +simulate_fit(est_model, parameters, omega, ruv, tdms, covariates, regimen) } \arguments{ \item{est_model}{model used for estimation} @@ -21,8 +21,6 @@ elements for \code{prop} (proportional) and \code{add} (additive).} \item{covariates}{named list of PKPDsim covariates} \item{regimen}{PKPDsim regimen object} - -\item{...}{arguments passed on to PKPDmap::get_map_estimates} } \value{ named list of individual PK parameter estimates