aboutsummaryrefslogtreecommitdiff
path: root/R
diff options
context:
space:
mode:
authorJohannes Ranke <jranke@uni-bremen.de>2022-11-04 18:12:03 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2022-11-04 18:12:03 +0100
commit9d013773edc0dc30a98c6218655726d3ad944e3f (patch)
tree4776d72b2fe2e5bddd97249fcff040db668d6936 /R
parent85cb80385bb26f40d1c1a40bbda457dd29c4cc23 (diff)
Attempt at automatic setting of random effects
Based on parameters in the separate fits that fail the t-test.
Diffstat (limited to 'R')
-rw-r--r--R/mhmkin.R28
1 files changed, 24 insertions, 4 deletions
diff --git a/R/mhmkin.R b/R/mhmkin.R
index de41c733..1f29dc40 100644
--- a/R/mhmkin.R
+++ b/R/mhmkin.R
@@ -12,6 +12,13 @@
#' degradation models to the same data
#' @param backend The backend to be used for fitting. Currently, only saemix is
#' supported
+#' @param no_random_effect Default is NULL and will be passed to [saem]. If
+#' you specify "auto", random effects are only included if the number
+#' of datasets in which the parameter passed the t-test is at least 'auto_ranef_threshold'.
+#' Beware that while this may make for convenient model reduction or even
+#' numerical stability of the algorithm, it will likely lead to
+#' underparameterised models.
+#' @param auto_ranef_threshold See 'no_random_effect.
#' @param algorithm The algorithm to be used for fitting (currently not used)
#' @param \dots Further arguments that will be passed to the nonlinear mixed-effects
#' model fitting function.
@@ -31,7 +38,7 @@
#' @author Johannes Ranke
#' @seealso \code{\link{[.mhmkin}} for subsetting [mhmkin] objects
#' @export
-mhmkin <- function(objects, backend = "saemix", algorithm = "saem", ...) {
+mhmkin <- function(objects, ...) {
UseMethod("mhmkin")
}
@@ -43,7 +50,8 @@ mhmkin.mmkin <- function(objects, ...) {
#' @export
#' @rdname mhmkin
-mhmkin.list <- function(objects, backend = "saemix",
+mhmkin.list <- function(objects, backend = "saemix", algorithm = "saem",
+ no_random_effect = NULL, auto_ranef_threshold = 3,
...,
cores = if (Sys.info()["sysname"] == "Windows") 1 else parallel::detectCores(), cluster = NULL)
{
@@ -94,7 +102,19 @@ mhmkin.list <- function(objects, backend = "saemix",
deg_index <- w[1]
error_index <- w[2]
mmkin_row <- objects[[error_index]][deg_index, ]
- res <- try(do.call(backend_function, args = c(list(mmkin_row), dot_args)))
+ if (identical(no_random_effect, "auto")) {
+ ip <- illparms(mmkin_row)
+ ipt <- table(unlist(lapply(as.list(ip), strsplit, ", ")))
+ no_ranef <- names(ipt)[which((length(ds) - ipt) <= auto_ranef_threshold)]
+ transparms <- rownames(mmkin_row[[1]]$start_transformed)
+ bparms <- rownames(mmkin_row[[1]]$start)
+ names(transparms) <- bparms
+ no_ranef_trans <- transparms[no_ranef]
+ } else {
+ no_ranef_trans <- no_random_effect
+ }
+ res <- try(do.call(backend_function,
+ args = c(list(mmkin_row), dot_args, list(no_random_effect = no_ranef_trans))))
return(res)
}
@@ -207,7 +227,7 @@ anova.mhmkin <- function(object, ...,
if (identical(model.names, "auto")) {
model.names <- outer(rownames(object), colnames(object), paste)
}
- rlang::inject(anova(!!!(object), method = method, test = test,
+ rlang::inject(anova(!!!(object), method = method, test = test,
model.names = model.names))
}

Contact - Imprint