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-rw-r--r--R/multistart.R26
-rw-r--r--R/parms.mkinfit.R30
2 files changed, 42 insertions, 14 deletions
diff --git a/R/multistart.R b/R/multistart.R
index db482cc4..819fcc1b 100644
--- a/R/multistart.R
+++ b/R/multistart.R
@@ -7,18 +7,38 @@
#' inspired by the article on practical identifiabiliy in the frame of nonlinear
#' mixed-effects models by Duchesne et al (2021).
#'
+#' Currently, parallel execution of the fits is only supported using
+#' [parallel::mclapply], i.e. not available on Windows.
+#'
+#' @param object The fit object to work with
+#' @param n How many different combinations of starting parameters should be
+#' used?
+#' @param cores How many fits should be run in parallel?
+#' @param \dots Passed to the update function.
+#' @return A list of [saem.mmkin] objects, with class attributes
+#' 'multistart.saem.mmkin' and 'multistart'.
+#'
#' @references Duchesne R, Guillemin A, Gandrillon O, Crauste F. Practical
#' identifiability in the frame of nonlinear mixed effects models: the example
#' of the in vitro erythropoiesis. BMC Bioinformatics. 2021 Oct 4;22(1):478.
#' doi: 10.1186/s12859-021-04373-4.
#' @export
-multistart <- function(object, n = 50, ...)
+multistart <- function(object, n = 50, cores = 1, ...)
{
UseMethod("multistart", object)
}
#' @rdname multistart
#' @export
-multistart.saem.mmkin <- function(object, n = 50, ...) {
-
+multistart.saem.mmkin <- function(object, n = 50, cores = 1, ...) {
+ start_parms <- apply(
+ parms(object$mmkin, errparms = FALSE), 1,
+ function(x) stats::runif(n, min(x), max(x))
+ )
+
+ res <- parallel::mclapply(1:n, function(x) {
+ update(object, degparms_start = start_parms[x], ...)
+ }, mc.cores = cores)
+ class(res) <- c("multistart.saem.mmkin", "multistart")
+ return(res)
}
diff --git a/R/parms.mkinfit.R b/R/parms.mkinfit.R
index a1f2d209..31ca05bc 100644
--- a/R/parms.mkinfit.R
+++ b/R/parms.mkinfit.R
@@ -8,9 +8,9 @@
#' [mkinfit()] objects and for [mmkin()] objects.
#' @param \dots Not used
#' @return For mkinfit objects, a numeric vector of fitted model parameters.
-#' For mmkin row objects, a matrix with the parameters with a
-#' row for each dataset. If the mmkin object has more than one row, a list of
-#' such matrices is returned.
+#' For mmkin row objects, a matrix with the parameters with a row for each
+#' dataset. If the mmkin object has more than one row, a list of such matrices
+#' is returned.
#' @examples
#' # mkinfit objects
#' fit <- mkinfit("SFO", FOCUS_2006_C, quiet = TRUE)
@@ -34,27 +34,35 @@ parms <- function(object, ...)
UseMethod("parms", object)
}
-#' @param transformed Should the parameters be returned
-#' as used internally during the optimisation?
+#' @param transformed Should the parameters be returned as used internally
+#' during the optimisation?
+#' @param errparms Should the error model parameters be returned
+#' in addition to the degradation parameters?
#' @rdname parms
#' @export
-parms.mkinfit <- function(object, transformed = FALSE, ...)
+parms.mkinfit <- function(object, transformed = FALSE, errparms = TRUE, ...)
{
- if (transformed) object$par
- else c(object$bparms.optim, object$errparms)
+ res <- if (transformed) object$par
+ else c(object$bparms.optim, object$errparms)
+ if (!errparms) {
+ res[setdiff(names(res), names(object$errparms))]
+ }
+ else return(res)
}
#' @rdname parms
#' @export
-parms.mmkin <- function(object, transformed = FALSE, ...)
+parms.mmkin <- function(object, transformed = FALSE, errparms = TRUE, ...)
{
if (nrow(object) == 1) {
- res <- sapply(object, parms, transformed = transformed, ...)
+ res <- sapply(object, parms, transformed = transformed,
+ errparms = errparms, ...)
colnames(res) <- colnames(object)
} else {
res <- list()
for (i in 1:nrow(object)) {
- res[[i]] <- parms(object[i, ], transformed = transformed, ...)
+ res[[i]] <- parms(object[i, ], transformed = transformed,
+ errparms = errparms, ...)
}
names(res) <- rownames(object)
}

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