diff options
Diffstat (limited to 'man')
| -rw-r--r-- | man/multistart.Rd | 20 | ||||
| -rw-r--r-- | man/parhist.Rd | 16 |
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 |