Rename parhist to parplot and make it generic

That parhist name was not the brightest idea, as it does
not show histograms.

3 files changed, 14 insertions, 11 deletions

diff --git a/man/logLik.saem.mmkin.Rd b/man/logLik.saem.mmkin.Rd
index 603f4607..bd0bb72e 100644
--- a/man/logLik.saem.mmkin.Rd
+++ b/man/logLik.saem.mmkin.Rd
@@ -4,7 +4,7 @@
 \alias{logLik.saem.mmkin}
 \title{logLik method for saem.mmkin objects}
 \usage{
-\method{logLik}{saem.mmkin}(object, ..., method = c("lin", "is", "gq"))
+\method{logLik}{saem.mmkin}(object, ..., method = c("is", "lin", "gq"))
 }
 \arguments{
 \item{object}{The fitted \link{saem.mmkin} object}
diff --git a/man/multistart.Rd b/man/multistart.Rd
index ebcc7d80..1f6773fe 100644
--- a/man/multistart.Rd
+++ b/man/multistart.Rd
@@ -77,7 +77,7 @@ dmta_ds[["Elliot 1"]] <- dmta_ds[["Elliot 2"]] <- NULL
 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 = "bottomleft")
+parplot(f_saem_full_multi, lpos = "bottomleft")
 illparms(f_saem_full)
 
 f_saem_reduced <- update(f_saem_full, no_random_effect = "log_k2")
@@ -89,7 +89,7 @@ library(parallel)
 cl <- makePSOCKcluster(12)
 clusterExport(cl, "f_mmkin")
 f_saem_reduced_multi <- multistart(f_saem_reduced, n = 16, cluster = cl)
-parhist(f_saem_reduced_multi, lpos = "topright")
+parplot(f_saem_reduced_multi, lpos = "topright")
 }
 }
 \references{
@@ -99,5 +99,5 @@ of the in vitro erythropoiesis. BMC Bioinformatics. 2021 Oct 4;22(1):478.
 doi: 10.1186/s12859-021-04373-4.
 }
 \seealso{
-\link{parhist}, \link{llhist}
+\link{parplot}, \link{llhist}
 }
diff --git a/man/parhist.Rd b/man/parplot.Rd
index f86ff734..37c5841d 100644
--- a/man/parhist.Rd
+++ b/man/parplot.Rd
@@ -1,10 +1,13 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/parhist.R
-\name{parhist}
-\alias{parhist}
-\title{Plot parameter distributions from multistart objects}
+% Please edit documentation in R/parplot.R
+\name{parplot}
+\alias{parplot}
+\alias{parplot.multistart.saem.mmkin}
+\title{Plot parameter variability of multistart objects}
 \usage{
-parhist(
+parplot(object, ...)
+
+\method{parplot}{multistart.saem.mmkin}(
   object,
   llmin = -Inf,
   scale = c("best", "median"),
@@ -16,6 +19,8 @@ parhist(
 \arguments{
 \item{object}{The \link{multistart} object}
 
+\item{\dots}{Passed to \link{boxplot}}
+
 \item{llmin}{The minimum likelihood of objects to be shown}
 
 \item{scale}{By default, scale parameters using the best available fit.
@@ -24,8 +29,6 @@ If 'median', parameters are scaled using the median parameters from all fits.}
 \item{lpos}{Positioning of the legend.}
 
 \item{main}{Title of the plot}
-
-\item{\dots}{Passed to \link{boxplot}}
 }
 \description{
 Produces a boxplot with all parameters from the multiple runs, scaled