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authorJohannes Ranke <jranke@uni-bremen.de>2021-03-09 17:35:47 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2021-03-09 17:35:47 +0100
commitc73b2f30ec836c949885784ab576e814eb8070a9 (patch)
tree7cfff70c5dae646fb464f4071e4ec444bbf40de1 /R/saem.R
parent9a414d01985f9177745ce0ad234ef7fc1b9822bb (diff)
Some improvements for borderline cases
- fit_with_errors for saem() - test_log_parms for mean_degparms() and saem()
Diffstat (limited to 'R/saem.R')
-rw-r--r--R/saem.R31
1 files changed, 26 insertions, 5 deletions
diff --git a/R/saem.R b/R/saem.R
index fd2a77b4..460edede 100644
--- a/R/saem.R
+++ b/R/saem.R
@@ -24,8 +24,16 @@ utils::globalVariables(c("predicted", "std"))
#' SFO or DFOP is used for the parent and there is either no metabolite or one.
#' @param degparms_start Parameter values given as a named numeric vector will
#' be used to override the starting values obtained from the 'mmkin' object.
+#' @param test_log_parms If TRUE, an attempt is made to use more robust starting
+#' values for population parameters fitted as log parameters in mkin (like
+#' rate constants) by only considering rate constants that pass the t-test
+#' 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 fail_with_errors Should a failure to compute standard errors
+#' from the inverse of the Fisher Information Matrix be a failure?
#' @param quiet Should we suppress the messages saemix prints at the beginning
#' and the end of the optimisation process?
#' @param control Passed to [saemix::saemix]
@@ -51,7 +59,7 @@ utils::globalVariables(c("predicted", "std"))
#' # The returned saem.mmkin object contains an SaemixObject, therefore we can use
#' # functions from saemix
#' library(saemix)
-#' compare.saemix(list(f_saem_sfo$so, f_saem_fomc$so, f_saem_dfop$so))
+#' compare.saemix(f_saem_sfo$so, f_saem_fomc$so, f_saem_dfop$so)
#' plot(f_saem_fomc$so, plot.type = "convergence")
#' plot(f_saem_fomc$so, plot.type = "individual.fit")
#' plot(f_saem_fomc$so, plot.type = "npde")
@@ -59,7 +67,7 @@ utils::globalVariables(c("predicted", "std"))
#'
#' f_mmkin_parent_tc <- update(f_mmkin_parent, error_model = "tc")
#' f_saem_fomc_tc <- saem(f_mmkin_parent_tc["FOMC", ])
-#' compare.saemix(list(f_saem_fomc$so, f_saem_fomc_tc$so))
+#' compare.saemix(f_saem_fomc$so, f_saem_fomc_tc$so)
#'
#' sfo_sfo <- mkinmod(parent = mkinsub("SFO", "A1"),
#' A1 = mkinsub("SFO"))
@@ -104,19 +112,32 @@ saem <- function(object, ...) UseMethod("saem")
saem.mmkin <- function(object,
transformations = c("mkin", "saemix"),
degparms_start = numeric(),
+ test_log_parms = FALSE,
+ conf.level = 0.6,
solution_type = "auto",
control = list(displayProgress = FALSE, print = FALSE,
save = FALSE, save.graphs = FALSE),
+ fail_with_errors = TRUE,
verbose = FALSE, quiet = FALSE, ...)
{
transformations <- match.arg(transformations)
m_saemix <- saemix_model(object, verbose = verbose,
- degparms_start = degparms_start, solution_type = solution_type,
+ degparms_start = degparms_start,
+ test_log_parms = test_log_parms, conf.level = conf.level,
+ solution_type = solution_type,
transformations = transformations, ...)
d_saemix <- saemix_data(object, verbose = verbose)
fit_time <- system.time({
utils::capture.output(f_saemix <- saemix::saemix(m_saemix, d_saemix, control), split = !quiet)
+ FIM_failed <- NULL
+ if (any(is.na(f_saemix@results@se.fixed))) FIM_failed <- c(FIM_failed, "fixed effects")
+ if (any(is.na(c(f_saemix@results@se.omega, f_saemix@results@se.respar)))) {
+ FIM_failed <- c(FIM_failed, "random effects and residual error parameters")
+ }
+ if (!is.null(FIM_failed) & fail_with_errors) {
+ stop("Could not invert FIM for ", paste(FIM_failed, collapse = " and "))
+ }
})
transparms_optim <- f_saemix@results@fixed.effects
@@ -203,13 +224,13 @@ print.saem.mmkin <- function(x, digits = max(3, getOption("digits") - 3), ...) {
#' @return An [saemix::SaemixModel] object.
#' @export
saemix_model <- function(object, solution_type = "auto", transformations = c("mkin", "saemix"),
- degparms_start = numeric(), verbose = FALSE, ...)
+ degparms_start = numeric(), test_log_parms = FALSE, verbose = FALSE, ...)
{
if (nrow(object) > 1) stop("Only row objects allowed")
mkin_model <- object[[1]]$mkinmod
- degparms_optim <- mean_degparms(object)
+ degparms_optim <- mean_degparms(object, test_log_parms = test_log_parms)
if (transformations == "saemix") {
degparms_optim <- backtransform_odeparms(degparms_optim,
object[[1]]$mkinmod,

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