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Diffstat (limited to 'man/plot.mkinfit.Rd')
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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 } |