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\name{plot.mkinfit}
\alias{plot.mkinfit}
\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.
}
\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, maxabs = "auto",
sep_vars = FALSE, rel.height.middle = 0.9,
lpos = "topright", inset = c(0.05, 0.05), \dots)
}
\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 in the lower third of the plot?
}
\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?
}
\item{rel.height.middle}{
The relative height of the middle plot, if more than two rows of plots are shown.
}
\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{\dots}{
Further arguments passed to \code{\link{plot}}.
}
}
\value{
The function is called for its side effect.
}
\examples{
# One parent compound, one metabolite, both single first order, path from
# parent to sink included, use Levenberg-Marquardt for speed
SFO_SFO <- mkinmod(parent = mkinsub("SFO", "m1", full = "Parent"),
m1 = mkinsub("SFO", full = "Metabolite M1" ))
fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE, method.modFit = "Marq")
plot(fit)
# Show the observed variables separately
plot(fit, sep_obs = TRUE)
# Show the observed variables separately, with residuals
plot(fit, sep_obs = TRUE, show_residuals = TRUE, lpos = c("topright", "bottomright"))
}
\author{
Johannes Ranke
}
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