From f820bf5b91be0f589de16c3e3250f5f79672df75 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Fri, 28 Oct 2022 13:39:15 +0200
Subject: Rename parhist to parplot and make it generic

That parhist name was not the brightest idea, as it does
not show histograms.
---
 man/logLik.saem.mmkin.Rd |  2 +-
 man/multistart.Rd        |  6 +++---
 man/parhist.Rd           | 43 -------------------------------------------
 man/parplot.Rd           | 46 ++++++++++++++++++++++++++++++++++++++++++++++
 4 files changed, 50 insertions(+), 47 deletions(-)
 delete mode 100644 man/parhist.Rd
 create mode 100644 man/parplot.Rd

(limited to 'man')

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/parhist.Rd
deleted file mode 100644
index f86ff734..00000000
--- a/man/parhist.Rd
+++ /dev/null
@@ -1,43 +0,0 @@
-% 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}
-\usage{
-parhist(
-  object,
-  llmin = -Inf,
-  scale = c("best", "median"),
-  lpos = "bottomleft",
-  main = "",
-  ...
-)
-}
-\arguments{
-\item{object}{The \link{multistart} object}
-
-\item{llmin}{The minimum likelihood of objects to be shown}
-
-\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}
-
-\item{\dots}{Passed to \link{boxplot}}
-}
-\description{
-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
-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.
-}
-\seealso{
-\link{multistart}
-}
diff --git a/man/parplot.Rd b/man/parplot.Rd
new file mode 100644
index 00000000..37c5841d
--- /dev/null
+++ b/man/parplot.Rd
@@ -0,0 +1,46 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/parplot.R
+\name{parplot}
+\alias{parplot}
+\alias{parplot.multistart.saem.mmkin}
+\title{Plot parameter variability of multistart objects}
+\usage{
+parplot(object, ...)
+
+\method{parplot}{multistart.saem.mmkin}(
+  object,
+  llmin = -Inf,
+  scale = c("best", "median"),
+  lpos = "bottomleft",
+  main = "",
+  ...
+)
+}
+\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.
+If 'median', parameters are scaled using the median parameters from all fits.}
+
+\item{lpos}{Positioning of the legend.}
+
+\item{main}{Title of the plot}
+}
+\description{
+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
+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.
+}
+\seealso{
+\link{multistart}
+}
-- 
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