aboutsummaryrefslogtreecommitdiff
path: root/R/nlmixr.R
diff options
context:
space:
mode:
authorJohannes Ranke <jranke@uni-bremen.de>2021-06-11 11:14:45 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2021-06-11 11:14:45 +0200
commit0c9b2f0e3c8ce65cb790c9e048476784cbbea070 (patch)
tree578f716c9daaff9502a95178e2d6ba63da438fbe /R/nlmixr.R
parentc6eb6b2bb598002523c3d34d71b0e4a99671ccd6 (diff)
Finished 'summary.nlmixr.mmkin', checks, docs
Diffstat (limited to 'R/nlmixr.R')
-rw-r--r--R/nlmixr.R29
1 files changed, 22 insertions, 7 deletions
diff --git a/R/nlmixr.R b/R/nlmixr.R
index 223b23a1..98783ca7 100644
--- a/R/nlmixr.R
+++ b/R/nlmixr.R
@@ -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
}

Contact - Imprint