diff options
Diffstat (limited to 'R/nlmixr.R')
| -rw-r--r-- | R/nlmixr.R | 29 |
1 files changed, 22 insertions, 7 deletions
@@ -1,4 +1,7 @@ -utils::globalVariables(c("predicted", "std")) +utils::globalVariables(c("predicted", "std", "ID", "TIME", "CMT", "DV", "IPRED", "IRES", "IWRES")) + +#' @export +nlmixr::nlmixr #' Fit nonlinear mixed models using nlmixr #' @@ -10,8 +13,10 @@ utils::globalVariables(c("predicted", "std")) #' obtained by fitting the same model to a list of datasets using [mkinfit]. #' #' @importFrom nlmixr nlmixr tableControl +#' @importFrom dplyr %>% #' @param object An [mmkin] row object containing several fits of the same #' [mkinmod] model to different datasets +#' @param data Not used, the data are extracted from the mmkin row object #' @param est Estimation method passed to [nlmixr::nlmixr] #' @param degparms_start Parameter values given as a named numeric vector will #' be used to override the starting values obtained from the 'mmkin' object. @@ -21,22 +26,28 @@ utils::globalVariables(c("predicted", "std")) #' when calculating mean degradation parameters using [mean_degparms]. #' @param conf.level Possibility to adjust the required confidence level #' for parameter that are tested if requested by 'test_log_parms'. -#' @param solution_type Possibility to specify the solution type in case the -#' automatic choice is not desired -#' @param control Passed to [nlmixr::nlmixr]. +#' @param data Not used, as the data are extracted from the mmkin row object +#' @param table Passed to [nlmixr::nlmixr] +#' @param error_model Possibility to override the error model which is being +#' set based on the error model used in the mmkin row object. +#' @param control Passed to [nlmixr::nlmixr] #' @param \dots Passed to [nlmixr_model] +#' @param save Passed to [nlmixr::nlmixr] +#' @param envir Passed to [nlmixr::nlmixr] #' @return An S3 object of class 'nlmixr.mmkin', containing the fitted #' [nlmixr::nlmixr] object as a list component named 'nm'. The #' object also inherits from 'mixed.mmkin'. #' @seealso [summary.nlmixr.mmkin] [plot.mixed.mmkin] #' @examples +#' \dontrun{ #' ds <- lapply(experimental_data_for_UBA_2019[6:10], #' function(x) subset(x$data[c("name", "time", "value")])) #' names(ds) <- paste("Dataset", 6:10) +#' #' f_mmkin_parent <- mmkin(c("SFO", "FOMC", "DFOP", "HS"), ds, quiet = TRUE, cores = 1) #' f_mmkin_parent_tc <- mmkin(c("SFO", "FOMC", "DFOP"), ds, error_model = "tc", #' cores = 1, quiet = TRUE) -#' +#' #' f_nlmixr_sfo_saem <- nlmixr(f_mmkin_parent["SFO", ], est = "saem") #' f_nlmixr_sfo_focei <- nlmixr(f_mmkin_parent["SFO", ], est = "focei") #' @@ -66,7 +77,6 @@ utils::globalVariables(c("predicted", "std")) #' # solution, the two-component error model does not improve it #' plot(f_nlmixr_fomc_saem) #' -#' \dontrun{ #' sfo_sfo <- mkinmod(parent = mkinsub("SFO", "A1"), #' A1 = mkinsub("SFO")) #' fomc_sfo <- mkinmod(parent = mkinsub("FOMC", "A1"), @@ -167,7 +177,8 @@ nlmixr.mmkin <- function(object, data = NULL, return_data <- nlmixr_df %>% dplyr::transmute(ds = ID, name = CMT, time = TIME, value = DV, predicted = IPRED, residual = IRES, - std = IRES/IWRES, standardized = IWRES) + std = IRES/IWRES, standardized = IWRES) %>% + dplyr::arrange(ds, name, time) bparms_optim <- backtransform_odeparms(f_nlmixr$theta, object[[1]]$mkinmod, @@ -227,6 +238,9 @@ print.nlmixr.mmkin <- function(x, digits = max(3, getOption("digits") - 3), ...) } #' @rdname nlmixr.mmkin +#' @param add_attributes Should the starting values used for degradation model +#' parameters and their distribution and for the error model parameters +#' be returned as attributes? #' @return An function defining a model suitable for fitting with [nlmixr::nlmixr]. #' @export nlmixr_model <- function(object, @@ -435,6 +449,7 @@ nlmixr_model <- function(object, if (add_attributes) { attr(f, "mean_dp_start") <- degparms_optim + attr(f, "eta_start") <- degparms_mmkin$eta attr(f, "mean_ep_start") <- errparms_ini } |