Use roxygen for functions and methods

1 files changed, 97 insertions, 116 deletions

diff --git a/man/plot.mkinfit.Rd b/man/plot.mkinfit.Rd
index fac5663a..3834eaf5 100644
--- a/man/plot.mkinfit.Rd
+++ b/man/plot.mkinfit.Rd
@@ -1,130 +1,110 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/plot.mkinfit.R
 \name{plot.mkinfit}
 \alias{plot.mkinfit}
 \alias{plot_sep}
 \alias{plot_res}
 \alias{plot_err}
-\title{
-  Plot the observed data and the fitted model of an mkinfit object
-}
-\description{
-  Solves the differential equations with the optimised and fixed parameters
-  from a previous successful call to \code{\link{mkinfit}} and plots
-  the observed data together with the solution of the fitted model.
-
-  If the current plot device is a \code{\link[tikzDevice]{tikz}} device,
-  then latex is being used for the formatting of the chi2 error level,
-  if \code{show_errmin = TRUE}.
-}
+\title{Plot the observed data and the fitted model of an mkinfit object}
 \usage{
-\method{plot}{mkinfit}(x, fit = x,
-  obs_vars = names(fit$mkinmod$map),
-  xlab = "Time", ylab = "Observed",
-  xlim = range(fit$data$time),
-  ylim = "default",
-  col_obs = 1:length(obs_vars), pch_obs = col_obs,
-  lty_obs = rep(1, length(obs_vars)),
-  add = FALSE, legend = !add,
-  show_residuals = FALSE,
-  show_errplot = FALSE,
-  maxabs = "auto",
-  sep_obs = FALSE, rel.height.middle = 0.9,
-  row_layout = FALSE,
-  lpos = "topright", inset = c(0.05, 0.05),
-  show_errmin = FALSE, errmin_digits = 3, frame = TRUE, \dots)
-plot_sep(fit, show_errmin = TRUE, \dots)
-plot_res(fit, sep_obs = FALSE, show_errmin = sep_obs, \dots)
-plot_err(fit, sep_obs = FALSE, show_errmin = sep_obs, \dots)
+\method{plot}{mkinfit}(x, fit = x, obs_vars = names(fit$mkinmod$map),
+  xlab = "Time", ylab = "Observed", xlim = range(fit$data$time),
+  ylim = "default", col_obs = 1:length(obs_vars), pch_obs = col_obs,
+  lty_obs = rep(1, length(obs_vars)), add = FALSE, legend = !add,
+  show_residuals = FALSE, show_errplot = FALSE, maxabs = "auto",
+  sep_obs = FALSE, rel.height.middle = 0.9, row_layout = FALSE,
+  lpos = "topright", inset = c(0.05, 0.05), show_errmin = FALSE,
+  errmin_digits = 3, frame = TRUE, ...)
+
+plot_sep(fit, show_errmin = TRUE, ...)
+
+plot_res(fit, sep_obs = FALSE, show_errmin = sep_obs, ...)
+
+plot_err(fit, sep_obs = FALSE, show_errmin = sep_obs, ...)
 }
 \arguments{
-  \item{x}{
-    Alias for fit introduced for compatibility with the generic S3 method.
-  }
-  \item{fit}{
-    An object of class \code{\link{mkinfit}}.
-  }
-  \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{xlab}{
-    Label for the x axis.
-  }
-  \item{ylab}{
-    Label for the y axis.
-  }
-  \item{xlim}{
-    Plot range in x direction.
-  }
-  \item{ylim}{
-    Plot range in y direction.
-  }
-  \item{col_obs}{
-    Colors used for plotting the observed data and the corresponding model prediction lines.
-  }
-  \item{pch_obs}{
-    Symbols to be used for plotting the data.
-  }
-  \item{lty_obs}{
-    Line types to be used for the model predictions.
-  }
-  \item{add}{
-    Should the plot be added to an existing plot?
-  }
-  \item{legend}{
-    Should a legend be added to the plot?
-  }
-  \item{show_residuals}{
-    Should residuals be shown? If only one plot of the fits is shown, the
-    residual plot is in the lower third of the plot. Otherwise, i.e. if
-    "sep_obs" is given, the residual plots will be located to the right of
-    the plots of the fitted curves.
-  }
-  \item{show_errplot}{
-    Should squared residuals and the error model be shown? If only one plot of
-    the fits is shown, this plot is in the lower third of the plot.
-    Otherwise, i.e. if "sep_obs" is given, the residual plots will be located
-    to the right of the plots of the fitted curves.
-  }
-  \item{maxabs}{
-    Maximum absolute value of the residuals. This is used for the scaling of
-    the y axis and defaults to "auto".
-  }
-  \item{sep_obs}{
-    Should the observed variables be shown in separate subplots? If yes, residual plots
-    requested by "show_residuals" will be shown next to, not below the plot of the fits.
-  }
-  \item{rel.height.middle}{
-    The relative height of the middle plot, if more than two rows of plots are shown.
-  }
-  \item{row_layout}{
-    Should we use a row layout where the residual plot or the error model plot is shown
-    to the right?
-  }
-  \item{lpos}{
-    Position(s) of the legend(s). Passed to \code{\link{legend}} as the first argument.
-    If not length one, this should be of the same length as the obs_var argument.
-  }
-  \item{inset}{
-    Passed to \code{\link{legend}} if applicable.
-  }
-  \item{show_errmin}{
-    Should the FOCUS chi2 error value be shown in the upper margin of the plot?
-  }
-  \item{errmin_digits}{
-    The number of significant digits for rounding the FOCUS chi2 error percentage.
-  }
-  \item{frame}{
-    Should a frame be drawn around the plots?
-  }
-  \item{\dots}{
-    Further arguments passed to \code{\link{plot}}.
-  }
+\item{x}{Alias for fit introduced for compatibility with the generic S3
+method.}
+
+\item{fit}{An object of class \code{\link{mkinfit}}.}
+
+\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{xlab}{Label for the x axis.}
+
+\item{ylab}{Label for the y axis.}
+
+\item{xlim}{Plot range in x direction.}
+
+\item{ylim}{Plot range in y direction.}
+
+\item{col_obs}{Colors used for plotting the observed data and the
+corresponding model prediction lines.}
+
+\item{pch_obs}{Symbols to be used for plotting the data.}
+
+\item{lty_obs}{Line types to be used for the model predictions.}
+
+\item{add}{Should the plot be added to an existing plot?}
+
+\item{legend}{Should a legend be added to the plot?}
+
+\item{show_residuals}{Should residuals be shown? If only one plot of the
+fits is shown, the residual plot is in the lower third of the plot.
+Otherwise, i.e. if "sep_obs" is given, the residual plots will be located
+to the right of the plots of the fitted curves.}
+
+\item{show_errplot}{Should squared residuals and the error model be shown?
+If only one plot of the fits is shown, this plot is in the lower third of
+the plot.  Otherwise, i.e. if "sep_obs" is given, the residual plots will
+be located to the right of the plots of the fitted curves.}
+
+\item{maxabs}{Maximum absolute value of the residuals. This is used for the
+scaling of the y axis and defaults to "auto".}
+
+\item{sep_obs}{Should the observed variables be shown in separate subplots?
+If yes, residual plots requested by "show_residuals" will be shown next
+to, not below the plot of the fits.}
+
+\item{rel.height.middle}{The relative height of the middle plot, if more
+than two rows of plots are shown.}
+
+\item{row_layout}{Should we use a row layout where the residual plot or the
+error model plot is shown to the right?}
+
+\item{lpos}{Position(s) of the legend(s). Passed to \code{\link{legend}} as
+the first argument.  If not length one, this should be of the same length
+as the obs_var argument.}
+
+\item{inset}{Passed to \code{\link{legend}} if applicable.}
+
+\item{show_errmin}{Should the FOCUS chi2 error value be shown in the upper
+margin of the plot?}
+
+\item{errmin_digits}{The number of significant digits for rounding the FOCUS
+chi2 error percentage.}
+
+\item{frame}{Should a frame be drawn around the plots?}
+
+\item{\dots}{Further arguments passed to \code{\link{plot}}.}
 }
 \value{
-  The function is called for its side effect.
+The function is called for its side effect.
+}
+\description{
+Solves the differential equations with the optimised and fixed parameters
+from a previous successful call to \code{\link{mkinfit}} and plots the
+observed data together with the solution of the fitted model.
+}
+\details{
+If the current plot device is a \code{\link[tikzDevice]{tikz}} device, then
+latex is being used for the formatting of the chi2 error level, if
+\code{show_errmin = TRUE}.
 }
 \examples{
+
 # One parent compound, one metabolite, both single first order, path from
 # parent to sink included
 \dontrun{
@@ -146,7 +126,8 @@ plot_sep(fit, lpos = c("topright", "bottomright"))
 plot(fit, sep_obs = TRUE, show_errplot = TRUE, lpos = c("topright", "bottomright"),
      show_errmin = TRUE)
 }
+
 }
 \author{
-  Johannes Ranke
+Johannes Ranke
 }