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-rw-r--r--man/multistart.Rd20
-rw-r--r--man/parhist.Rd16
2 files changed, 32 insertions, 4 deletions
diff --git a/man/multistart.Rd b/man/multistart.Rd
index 78ff4614..d20c0465 100644
--- a/man/multistart.Rd
+++ b/man/multistart.Rd
@@ -4,6 +4,10 @@
\alias{multistart}
\alias{multistart.saem.mmkin}
\alias{print.multistart}
+\alias{best}
+\alias{best.default}
+\alias{which.best}
+\alias{which.best.default}
\title{Perform a hierarchical model fit with multiple starting values}
\usage{
multistart(
@@ -17,6 +21,14 @@ multistart(
\method{multistart}{saem.mmkin}(object, n = 50, cores = 1, cluster = NULL, ...)
\method{print}{multistart}(x, ...)
+
+best(object, ...)
+
+\method{best}{default}(object, ...)
+
+which.best(object, ...)
+
+\method{which.best}{default}(object, ...)
}
\arguments{
\item{object}{The fit object to work with}
@@ -36,6 +48,10 @@ for parallel execution.}
\value{
A list of \link{saem.mmkin} objects, with class attributes
'multistart.saem.mmkin' and 'multistart'.
+
+The object with the highest likelihood
+
+The index of the object with the highest likelihood
}
\description{
The purpose of this method is to check if a certain algorithm for fitting
@@ -69,8 +85,10 @@ f_mmkin <- mmkin("DFOP", dmta_ds, error_model = "tc", cores = 7, quiet = TRUE)
f_saem_full <- saem(f_mmkin)
f_saem_full_multi <- multistart(f_saem_full, n = 16, cores = 16)
parhist(f_saem_full_multi, lpos = "bottomright")
+illparms(f_saem_full)
-f_saem_reduced <- update(f_saem_full, covariance.model = diag(c(1, 1, 0, 1)))
+f_saem_reduced <- update(f_saem_full, no_random_effect = "log_k2")
+illparms(f_saem_reduced)
# On Windows, we need to create a cluster first. When working with
# such a cluster, we need to export the mmkin object to the cluster
# nodes, as it is referred to when updating the saem object on the nodes.
diff --git a/man/parhist.Rd b/man/parhist.Rd
index a8319283..67bbadad 100644
--- a/man/parhist.Rd
+++ b/man/parhist.Rd
@@ -4,11 +4,20 @@
\alias{parhist}
\title{Plot parameter distributions from multistart objects}
\usage{
-parhist(object, lpos = "bottomleft", main = "", ...)
+parhist(
+ object,
+ scale = c("best", "median"),
+ lpos = "bottomleft",
+ main = "",
+ ...
+)
}
\arguments{
\item{object}{The \link{multistart} object}
+\item{scale}{By default, scale parameters using the best available fit.
+If 'median', parameters are scaled using the median parameters from all fits.}
+
\item{lpos}{Positioning of the legend.}
\item{main}{Title of the plot}
@@ -16,8 +25,9 @@ parhist(object, lpos = "bottomleft", main = "", ...)
\item{\dots}{Passed to \link{boxplot}}
}
\description{
-Produces a boxplot with all parameters from the multiple runs, divided by
-using their medians as in the paper by Duchesne et al. (2021).
+Produces a boxplot with all parameters from the multiple runs, scaled
+either by the parameters of the run with the highest likelihood,
+or by their medians as proposed in the paper by Duchesne et al. (2021).
}
\references{
Duchesne R, Guillemin A, Gandrillon O, Crauste F. Practical

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