diff --git a/DESCRIPTION b/DESCRIPTION index 11b74e6..4776bda 100755 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -12,6 +12,6 @@ Depends: utils, stats Imports: PKPDsim, numDeriv, mvtnorm Suggests: testthat (>= 3.0.0) Remotes: InsightRX/PKPDsim -RoxygenNote: 7.3.2 +RoxygenNote: 7.3.3 Encoding: UTF-8 Config/testthat/edition: 3 diff --git a/R/calc_residuals.R b/R/calc_residuals.R index b3c4173..795fbca 100644 --- a/R/calc_residuals.R +++ b/R/calc_residuals.R @@ -32,8 +32,7 @@ calc_residuals <- function( censoring = NULL, censoring_idx = NULL, data_before_init = NULL, - ltbs = FALSE, - ... + ltbs = FALSE ) { ## Observation vectors @@ -61,8 +60,7 @@ calc_residuals <- function( iov_bins = iov_bins, output_include = output_include, t_init = t_init, - lagtime = lagtime, - ... + lagtime = lagtime ) }) suppressMessages({ @@ -81,8 +79,7 @@ calc_residuals <- function( iov_bins = iov_bins, A_init = A_init_population, t_init = t_init, - lagtime = lagtime, - ... + lagtime = lagtime ) }) diff --git a/R/get_map_estimates.R b/R/get_map_estimates.R index 20f260d..2b30872 100755 --- a/R/get_map_estimates.R +++ b/R/get_map_estimates.R @@ -61,8 +61,7 @@ #'option is `TRUE`. #' @param skip_hessian skip calculation of Hessian #' @param verbose show more output -#' @param ... parameters passed on to `sim_ode()` function -#' +#' #' @examples #' \dontrun{ #' ## define parameters @@ -134,8 +133,7 @@ get_map_estimates <- function( verbose = FALSE, A_init = NULL, skip_hessian = FALSE, - output_include = list(covariates = FALSE, parameters = FALSE), - ...) { + output_include = list(covariates = FALSE, parameters = FALSE)) { ## get prior weight for scaling of variance term weight_prior_var <- parse_weight_prior(weight_prior, type) @@ -232,8 +230,7 @@ get_map_estimates <- function( t_max = tail(t_obs, 1) + t_init + 1, iov_bins = iov_bins, return_design = TRUE, - t_init = t_init, - ... + t_init = t_init ) }) @@ -426,8 +423,7 @@ get_map_estimates <- function( censoring = censoring, censoring_idx = censoring_idx, data_before_init = data_before_init, - ltbs = ltbs, - ... + ltbs = ltbs ) } diff --git a/man/calc_residuals.Rd b/man/calc_residuals.Rd index f3c5619..241b17d 100644 --- a/man/calc_residuals.Rd +++ b/man/calc_residuals.Rd @@ -26,8 +26,7 @@ calc_residuals( censoring = NULL, censoring_idx = NULL, data_before_init = NULL, - ltbs = FALSE, - ... + ltbs = FALSE ) } \arguments{ @@ -83,8 +82,6 @@ in this column is < 0 then censoring is assumed 0 then >ULOQ.} \item{ltbs}{log-transform both sides? (`NULL` by default, meaning that it will be picked up from the PKPDsim model. Can be overridden with `TRUE`). Note: `error` should commonly only have additive part.} - -\item{...}{parameters passed on to `sim_ode()` function} } \description{ Function to calculate residuals from a fit, diff --git a/man/get_map_estimates.Rd b/man/get_map_estimates.Rd index 3a62806..49363bd 100755 --- a/man/get_map_estimates.Rd +++ b/man/get_map_estimates.Rd @@ -38,8 +38,7 @@ get_map_estimates( verbose = FALSE, A_init = NULL, skip_hessian = FALSE, - output_include = list(covariates = FALSE, parameters = FALSE), - ... + output_include = list(covariates = FALSE, parameters = FALSE) ) } \arguments{ @@ -137,8 +136,6 @@ will be slightly slower.} \item{output_include}{passed to PKPDsim::sim_ode(), returns covariates and parameter values over time in return object. Only invoked if `residuals` option is `TRUE`.} - -\item{...}{parameters passed on to `sim_ode()` function} } \description{ Get MAP estimates diff --git a/man/map_shrinkage_control.Rd b/man/map_shrinkage_control.Rd index 348abb3..4deb315 100755 --- a/man/map_shrinkage_control.Rd +++ b/man/map_shrinkage_control.Rd @@ -22,8 +22,6 @@ all parameters).} \item{fixed}{fix a specific parameters, supplied as vector of strings} \item{data}{data data.frame with columns `t` and `y` (and possibly evid)} - -\item{...}{parameters passed on to `sim_ode()` function} } \description{ Limits the amount of individual shrinkage to a certain specified number