path: root/man/plot.mkinfit.Rd

\name{plot.mkinfit}
\alias{plot.mkinfit}
\alias{plot_sep}
\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}.
}
\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_obs = FALSE, rel.height.middle = 0.9,
  lpos = "topright", inset = c(0.05, 0.05),
  show_errmin = FALSE, errmin_digits = 3, \dots)
plot_sep(fit, sep_obs = TRUE,  show_residuals = TRUE, show_errmin = TRUE, \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? 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{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{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{\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)
plot(fit, show_residuals = TRUE)

# Show the observed variables separately
plot(fit, sep_obs = TRUE, lpos = c("topright", "bottomright"))

# Show the observed variables separately, with residuals
plot(fit, sep_obs = TRUE, show_residuals = TRUE, lpos = c("topright", "bottomright"),
     show_errmin = TRUE)

# The same can be obtained with less typing, using the convenience function plot_sep
plot_sep(fit, lpos = c("topright", "bottomright"))
}
\author{
  Johannes Ranke
}