% Generated by roxygen2: do not edit by hand % Please edit documentation in R/plot.nlme.mmkin.R \name{plot.nlme.mmkin} \alias{plot.nlme.mmkin} \title{Plot a fitted nonlinear mixed model obtained via an mmkin row object} \usage{ \method{plot}{nlme.mmkin}( x, i = 1:ncol(x$mmkin_orig), main = rownames(x$mmkin_orig), obs_vars = names(x$mkinmod$map), standardized = TRUE, xlab = "Time", ylab = "Observed", xlim = range(x$data$time), legends = 1, lpos = "topright", inset = c(0.05, 0.05), resplot = c("predicted", "time"), ymax = "auto", maxabs = "auto", cex = 0.7, rel.height.middle = 0.9, pch_ds = 1:length(i), col_ds = pch_ds + 1, lty_ds = col_ds, frame = TRUE, ... ) } \arguments{ \item{x}{An object of class \code{\link{nlme.mmkin}}} \item{i}{A numeric index to select datasets for which to plot the nlme fit, in case plots get too large} \item{main}{The main title placed on the outer margin of the plot.} \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{standardized}{Should the residuals be standardized? Only takes effect if \code{resplot = "time"}.} \item{xlab}{Label for the x axis.} \item{ylab}{Label for the y axis.} \item{xlim}{Plot range in x direction.} \item{legends}{An index for the fits for which legends should be 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{resplot}{Should the residuals plotted against time or against predicted values?} \item{ymax}{Vector of maximum y axis values} \item{maxabs}{Maximum absolute value of the residuals. This is used for the scaling of the y axis and defaults to "auto".} \item{cex}{Passed to the plot functions and \code{\link{mtext}}.} \item{rel.height.middle}{The relative height of the middle plot, if more than two rows of plots are shown.} \item{pch_ds}{Symbols to be used for plotting the data.} \item{col_ds}{Colors used for plotting the observed data and the corresponding model prediction lines for the different datasets.} \item{lty_ds}{Line types to be used for the model predictions.} \item{frame}{Should a frame be drawn around the plots?} \item{\dots}{Further arguments passed to \code{\link{plot.mkinfit}} and \code{\link{mkinresplot}}.} } \value{ The function is called for its side effect. } \description{ Plot a fitted nonlinear mixed model obtained via an mmkin row object } \examples{ ds <- lapply(experimental_data_for_UBA_2019[6:10], function(x) x$data[c("name", "time", "value")]) names(ds) <- paste0("ds ", 6:10) dfop_sfo <- mkinmod(parent = mkinsub("DFOP", "A1"), A1 = mkinsub("SFO"), quiet = TRUE) f <- mmkin(list("DFOP-SFO" = dfop_sfo), ds, quiet = TRUE, cores = 1) plot(f[, 3:4], standardized = TRUE) library(nlme) # For this fit we need to increase pnlsMaxiter, and we increase the # tolerance in order to speed up the fit for this example evaluation f_nlme <- nlme(f, control = list(pnlsMaxIter = 120, tolerance = 1e-4)) plot(f_nlme) } \author{ Johannes Ranke }