Merge plot methods for nlme.mmkin and saem.mmkin

This avoids code duplication

1 files changed, 123 insertions, 0 deletions

diff --git a/man/plot_mixed.Rd b/man/plot_mixed.Rd
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+++ b/man/plot_mixed.Rd
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+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/plot_mixed.R
+\name{plot_mixed}
+\alias{plot_mixed}
+\alias{plot.saem.mmkin}
+\alias{plot.nlme.mmkin}
+\title{Plot predictions from a fitted nonlinear mixed model obtained via an mmkin row object}
+\usage{
+\method{plot}{saem.mmkin}(
+  x,
+  i = 1:ncol(x$mmkin),
+  obs_vars = names(x$mkinmod$map),
+  standardized = TRUE,
+  xlab = "Time",
+  xlim = range(x$data$time),
+  resplot = c("predicted", "time"),
+  ymax = "auto",
+  maxabs = "auto",
+  ncol.legend = ifelse(length(i) <= 3, length(i) + 1, ifelse(length(i) <= 8, 3, 4)),
+  nrow.legend = ceiling((length(i) + 1)/ncol.legend),
+  rel.height.legend = 0.03 + 0.08 * nrow.legend,
+  rel.height.bottom = 1.1,
+  pch_ds = 1:length(i),
+  col_ds = pch_ds + 1,
+  lty_ds = col_ds,
+  frame = TRUE,
+  ...
+)
+
+\method{plot}{nlme.mmkin}(
+  x,
+  i = 1:ncol(x$mmkin),
+  obs_vars = names(x$mkinmod$map),
+  standardized = TRUE,
+  xlab = "Time",
+  xlim = range(x$data$time),
+  resplot = c("predicted", "time"),
+  ymax = "auto",
+  maxabs = "auto",
+  ncol.legend = ifelse(length(i) <= 3, length(i) + 1, ifelse(length(i) <= 8, 3, 4)),
+  nrow.legend = ceiling((length(i) + 1)/ncol.legend),
+  rel.height.legend = 0.03 + 0.08 * nrow.legend,
+  rel.height.bottom = 1.1,
+  pch_ds = 1:length(i),
+  col_ds = pch_ds + 1,
+  lty_ds = col_ds,
+  frame = TRUE,
+  ...
+)
+}
+\arguments{
+\item{x}{An object of class \link{saem.mmkin} or \link{nlme.mmkin}}
+
+\item{i}{A numeric index to select datasets for which to plot the individual predictions,
+in case plots get too large}
+
+\item{obs_vars}{A character vector of names of the observed variables for
+which the data and the model should be plotted. Defauls to all observed
+variables in the model.}
+
+\item{standardized}{Should the residuals be standardized? Only takes effect if
+\code{resplot = "time"}.}
+
+\item{xlab}{Label for the x axis.}
+
+\item{xlim}{Plot range in x direction.}
+
+\item{resplot}{Should the residuals plotted against time or against
+predicted values?}
+
+\item{ymax}{Vector of maximum y axis values}
+
+\item{maxabs}{Maximum absolute value of the residuals. This is used for the
+scaling of the y axis and defaults to "auto".}
+
+\item{ncol.legend}{Number of columns to use in the legend}
+
+\item{nrow.legend}{Number of rows to use in the legend}
+
+\item{rel.height.legend}{The relative height of the legend shown on top}
+
+\item{rel.height.bottom}{The relative height of the bottom plot row}
+
+\item{pch_ds}{Symbols to be used for plotting the data.}
+
+\item{col_ds}{Colors used for plotting the observed data and the
+corresponding model prediction lines for the different datasets.}
+
+\item{lty_ds}{Line types to be used for the model predictions.}
+
+\item{frame}{Should a frame be drawn around the plots?}
+
+\item{...}{Further arguments passed to \code{\link{plot}}.}
+}
+\value{
+The functions are called for their side effect.
+}
+\description{
+Plot predictions from a fitted nonlinear mixed model obtained via an mmkin row object
+}
+\examples{
+ds <- lapply(experimental_data_for_UBA_2019[6:10],
+ function(x) x$data[c("name", "time", "value")])
+names(ds) <- paste0("ds ", 6:10)
+dfop_sfo <- mkinmod(parent = mkinsub("DFOP", "A1"),
+  A1 = mkinsub("SFO"), quiet = TRUE)
+\dontrun{
+f <- mmkin(list("DFOP-SFO" = dfop_sfo), ds, quiet = TRUE)
+plot(f[, 3:4], standardized = TRUE)
+
+library(nlme)
+# For this fit we need to increase pnlsMaxiter, and we increase the
+# tolerance in order to speed up the fit for this example evaluation
+f_nlme <- nlme(f, control = list(pnlsMaxIter = 120, tolerance = 1e-3))
+plot(f_nlme)
+
+f_saem <- saem(f)
+plot(f_saem)
+}
+}
+\author{
+Johannes Ranke
+}