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-rw-r--r--man/plot.mkinfit.Rd213
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
}

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