From 082be7baa35d7e8131a70ca8cc061d90e08fa584 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Wed, 15 Apr 2020 01:27:02 +0200
Subject: A plot method for nlme.mmkin fits

---
 man/nlme.Rd            |  2 +-
 man/nlme.mmkin.Rd      | 11 ++++++---
 man/plot.nlme.mmkin.Rd | 67 ++++++++++++++++++++++++++++++++++++++++++++++++++
 3 files changed, 76 insertions(+), 4 deletions(-)
 create mode 100644 man/plot.nlme.mmkin.Rd

(limited to 'man')

diff --git a/man/nlme.Rd b/man/nlme.Rd
index 971ba3f5..f31c7a4f 100644
--- a/man/nlme.Rd
+++ b/man/nlme.Rd
@@ -4,7 +4,7 @@
 \alias{nlme_function}
 \alias{mean_degparms}
 \alias{nlme_data}
-\title{Estimation of parameter distributions from mmkin row objects}
+\title{Helper functions to create nlme models from mmkin row objects}
 \usage{
 nlme_function(object)
 
diff --git a/man/nlme.mmkin.Rd b/man/nlme.mmkin.Rd
index 5f937488..1fecb5dd 100644
--- a/man/nlme.mmkin.Rd
+++ b/man/nlme.mmkin.Rd
@@ -54,11 +54,13 @@ parameters taken from the mmkin object are used}
 \item{verbose}{passed to nlme}
 }
 \value{
-Upon success, a fitted nlme.mmkin object, which is
-  an nlme object with additional elements
+Upon success, a fitted nlme.mmkin object, which is an nlme object
+  with additional elements
 }
 \description{
-Create an nlme model for an mmkin row object
+This functions sets up a nonlinear mixed effects model for an mmkin row
+object. An mmkin row object is essentially a list of mkinfit objects that
+have been obtained by fitting the same model to a list of datasets.
 }
 \examples{
 ds <- lapply(experimental_data_for_UBA_2019[6:10],
@@ -70,3 +72,6 @@ nlme(f, random = parent_0 ~ 1)
 f_nlme <- nlme(f, start = c(parent_0 = 100, log_k_parent_sink = 0.1))
 update(f_nlme, random = parent_0 ~ 1)
 }
+\seealso{
+\code{\link{nlme_function}}
+}
diff --git a/man/plot.nlme.mmkin.Rd b/man/plot.nlme.mmkin.Rd
new file mode 100644
index 00000000..c0e749aa
--- /dev/null
+++ b/man/plot.nlme.mmkin.Rd
@@ -0,0 +1,67 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/plot.nlme.mmkin.R
+\name{plot.nlme.mmkin}
+\alias{plot.nlme.mmkin}
+\title{Plot a fitted nonlinear mixed model obtained via an mmkin row object}
+\usage{
+\method{plot}{nlme.mmkin}(
+  x,
+  i = 1:ncol(x$mmkin_orig),
+  main = "auto",
+  legends = 1,
+  resplot = c("time", "errmod"),
+  standardized = FALSE,
+  cex = 0.7,
+  rel.height.middle = 0.9,
+  ymax = "auto",
+  ...
+)
+}
+\arguments{
+\item{x}{An object of class \code{\link{nlme.mmkin}}}
+
+\item{i}{A numeric index to select datasets for which to plot the nlme fit,
+in case plots get too large}
+
+\item{main}{The main title placed on the outer margin of the plot.}
+
+\item{legends}{An index for the fits for which legends should be shown.}
+
+\item{resplot}{Should the residuals plotted against time, using
+\code{\link{mkinresplot}}, or as squared residuals against predicted
+values, with the error model, using \code{\link{mkinerrplot}}.}
+
+\item{standardized}{Should the residuals be standardized? This option
+is passed to \code{\link{mkinresplot}}, it only takes effect if
+`resplot = "time"`.}
+
+\item{cex}{Passed to the plot functions and \code{\link{mtext}}.}
+
+\item{rel.height.middle}{The relative height of the middle plot, if more
+than two rows of plots are shown.}
+
+\item{ymax}{Maximum y axis value for \code{\link{plot.mkinfit}}.}
+
+\item{\dots}{Further arguments passed to \code{\link{plot.mkinfit}} and
+\code{\link{mkinresplot}}.}
+}
+\value{
+The function is called for its side effect.
+}
+\description{
+Plot a fitted nonlinear mixed model obtained via an mmkin row object
+}
+\examples{
+ds <- lapply(experimental_data_for_UBA_2019[6:10],
+ function(x) subset(x$data[c("name", "time", "value")], name == "parent"))
+f <- mmkin("SFO", ds, quiet = TRUE, cores = 1)
+#plot(f) # too many panels for pkgdown
+library(nlme)
+f_nlme <- nlme(f)
+
+#plot(f_nlme) # too many panels for pkgdown
+plot(f_nlme, 1:2)
+}
+\author{
+Johannes Ranke
+}
-- 
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