diff options
Diffstat (limited to 'man')
| -rw-r--r-- | man/Extract.mmkin.Rd | 3 | ||||
| -rw-r--r-- | man/plot.nlme.mmkin.Rd | 83 | ||||
| -rw-r--r-- | man/print.mmkin.Rd | 16 |
3 files changed, 72 insertions, 30 deletions
diff --git a/man/Extract.mmkin.Rd b/man/Extract.mmkin.Rd index 7677bdba..fd54755c 100644 --- a/man/Extract.mmkin.Rd +++ b/man/Extract.mmkin.Rd @@ -22,7 +22,7 @@ either a list of mkinfit objects or a single mkinfit object.} An object of class \code{\link{mmkin}}. } \description{ -Subsetting method for mmkin objects. +Subsetting method for mmkin objects } \examples{ @@ -37,7 +37,6 @@ Subsetting method for mmkin objects. # This extracts an mkinfit object with lots of components fits[["FOMC", "B"]] ) - } \author{ Johannes Ranke diff --git a/man/plot.nlme.mmkin.Rd b/man/plot.nlme.mmkin.Rd index 91130402..d1fde212 100644 --- a/man/plot.nlme.mmkin.Rd +++ b/man/plot.nlme.mmkin.Rd @@ -7,16 +7,24 @@ \method{plot}{nlme.mmkin}( x, i = 1:ncol(x$mmkin_orig), - main = "auto", + main = rownames(x$mmkin_orig), + obs_vars = names(x$mkinmod$map), + standardized = TRUE, + xlab = "Time", + ylab = "Observed", + xlim = range(x$data$time), legends = 1, - resplot = c("time", "errmod"), - standardized = FALSE, - show_errmin = TRUE, - errmin_var = "All data", - errmin_digits = 3, + lpos = "topright", + inset = c(0.05, 0.05), + resplot = c("predicted", "time"), + ymax = "auto", + maxabs = "auto", cex = 0.7, rel.height.middle = 0.9, - ymax = "auto", + pch_ds = 1:length(i), + col_ds = pch_ds + 1, + lty_ds = col_ds, + frame = TRUE, ... ) } @@ -28,31 +36,48 @@ 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{resplot}{Should the residuals plotted against time, using -\code{\link{mkinresplot}}, or as squared residuals against predicted -values, with the error model, using \code{\link{mkinerrplot}}.} +\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{standardized}{Should the residuals be standardized? This option -is passed to \code{\link{mkinresplot}}, it only takes effect if -\code{resplot = "time"}.} +\item{inset}{Passed to \code{\link{legend}} if applicable.} -\item{show_errmin}{Should the chi2 error level be shown on top of the plots -to the left?} +\item{resplot}{Should the residuals plotted against time or against +predicted values?} -\item{errmin_var}{The variable for which the FOCUS chi2 error value should -be shown.} +\item{ymax}{Vector of maximum y axis values} -\item{errmin_digits}{The number of significant digits for rounding the FOCUS -chi2 error percentage.} +\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{ymax}{Maximum y axis value for \code{\link{plot.mkinfit}}.} +\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}}.} @@ -65,15 +90,17 @@ Plot a fitted nonlinear mixed model obtained via an mmkin row object } \examples{ ds <- lapply(experimental_data_for_UBA_2019[6:10], - function(x) subset(x$data[c("name", "time", "value")], name == "parent")) -f <- mmkin("SFO", ds, quiet = TRUE, cores = 1) -#plot(f) # too many panels for pkgdown -plot(f[, 3:4]) + function(x) x$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) -f_nlme <- nlme(f) - -#plot(f_nlme) # too many panels for pkgdown -plot(f_nlme, 3:4) +# 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 diff --git a/man/print.mmkin.Rd b/man/print.mmkin.Rd new file mode 100644 index 00000000..29abe143 --- /dev/null +++ b/man/print.mmkin.Rd @@ -0,0 +1,16 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/mmkin.R +\name{print.mmkin} +\alias{print.mmkin} +\title{Print method for mmkin objects} +\usage{ +\method{print}{mmkin}(x, ...) +} +\arguments{ +\item{x}{An \link{mmkin} object.} + +\item{\dots}{Not used.} +} +\description{ +Print method for mmkin objects +} |