3 files changed, 41 insertions, 103 deletions
diff --git a/man/plot.saem.mmkin.Rd b/man/plot.saem.mmkin.Rd
deleted file mode 100644
index 1f674bd7..00000000
--- a/man/plot.saem.mmkin.Rd
+++ /dev/null
@@ -1,94 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/plot.saem.mmkin.R
-\name{plot.saem.mmkin}
-\alias{plot.saem.mmkin}
-\title{Plot an saem 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,
-  ...
-)
-}
-\arguments{
-\item{x}{An object of class \code{\link{saem.mmkin}}}
-
-\item{i}{A numeric index to select datasets for which to plot the saem fit,
-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 function is called for its side effect.
-}
-\description{
-Plot an saem 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)
-
-f_saem <- saem(f)
-plot(f_saem)
-}
-}
-\author{
-Johannes Ranke
-}
diff --git a/man/plot.nlme.mmkin.Rd b/man/plot_mixed.Rd
index f426f77b..d3cee7c9 100644
--- a/man/plot.nlme.mmkin.Rd
+++ b/man/plot_mixed.Rd
@@ -1,9 +1,32 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/plot.nlme.mmkin.R
-\name{plot.nlme.mmkin}
+% Please edit documentation in R/plot_mixed.R
+\name{plot_mixed}
+\alias{plot_mixed}
+\alias{plot.saem.mmkin}
 \alias{plot.nlme.mmkin}
-\title{Plot a fitted nonlinear mixed model obtained via an mmkin row object}
+\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),
@@ -21,13 +44,14 @@
   pch_ds = 1:length(i),
   col_ds = pch_ds + 1,
   lty_ds = col_ds,
-  frame = TRUE
+  frame = TRUE,
+  ...
 )
 }
 \arguments{
-\item{x}{An object of class \code{\link{nlme.mmkin}}}
+\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 nlme fit,
+\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
@@ -65,12 +89,14 @@ 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 function is called for its side effect.
+The functions are called for their side effect.
 }
 \description{
-Plot a fitted nonlinear mixed model obtained via an mmkin row object
+Plot predictions from a fitted nonlinear mixed model obtained via an mmkin row object
 }
 \examples{
 ds <- lapply(experimental_data_for_UBA_2019[6:10],
@@ -87,6 +113,9 @@ library(nlme)
 # 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{
diff --git a/man/reexports.Rd b/man/reexports.Rd
index bb77acc5..ccba7567 100644
--- a/man/reexports.Rd
+++ b/man/reexports.Rd
@@ -1,9 +1,10 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/lrtest.mkinfit.R
+% Please edit documentation in R/lrtest.mkinfit.R, R/nlme.mmkin.R
 \docType{import}
 \name{reexports}
 \alias{reexports}
 \alias{lrtest}
+\alias{nlme}
 \title{Objects exported from other packages}
 \keyword{internal}
 \description{
@@ -12,5 +13,7 @@ below to see their documentation.
 
 \describe{
   \item{lmtest}{\code{\link[lmtest]{lrtest}}}
+
+  \item{nlme}{\code{\link[nlme]{nlme}}}
 }}