diff options
Diffstat (limited to 'man')
| -rw-r--r-- | man/mkinerrplot.Rd | 75 | ||||
| -rw-r--r-- | man/plot.mkinfit.Rd | 21 | ||||
| -rw-r--r-- | man/plot.mmkin.Rd | 17 |
3 files changed, 106 insertions, 7 deletions
diff --git a/man/mkinerrplot.Rd b/man/mkinerrplot.Rd new file mode 100644 index 00000000..4cbb5eb7 --- /dev/null +++ b/man/mkinerrplot.Rd @@ -0,0 +1,75 @@ +\name{mkinerrplot} +\alias{mkinerrplot} +\title{ + Function to plot squared residuals and the error model for an mkin object +} +\description{ + This function plots the squared residuals for the specified subset of the + observed variables from an mkinfit object. In addition, one or more + dashed line(s) show the fitted error model. + A combined plot of the fitted model and this error model plot can be + obtained with \code{\link{plot.mkinfit}} + using the argument \code{show_errplot = TRUE}. +} +\usage{ + mkinerrplot(object, + obs_vars = names(object$mkinmod$map), + xlim = c(0, 1.1 * max(object$data$predicted)), + xlab = "Predicted", ylab = "Squared residual", + maxy = "auto", legend= TRUE, lpos = "topright", + col_obs = "auto", pch_obs = "auto", + ...) +} +\arguments{ + \item{object}{ + A fit represented in an \code{\link{mkinfit}} object. + } + \item{obs_vars}{ + A character vector of names of the observed variables for which residuals + should be plotted. Defaults to all observed variables in the model + } + \item{xlim}{ + plot range in x direction. + } + \item{xlab}{ + Label for the x axis. + } + \item{ylab}{ + Label for the y axis. + } + \item{maxy}{ + Maximum value of the residuals. This is used for the scaling of + the y axis and defaults to "auto". + } + \item{legend}{ + Should a legend be plotted? + } + \item{lpos}{ + Where should the legend be placed? Default is "topright". Will be passed on to + \code{\link{legend}}. + } + \item{col_obs}{ + Colors for the observed variables. + } + \item{pch_obs}{ + Symbols to be used for the observed variables. + } + \item{\dots}{ + further arguments passed to \code{\link{plot}}. + } +} +\value{ + Nothing is returned by this function, as it is called for its side effect, namely to produce a plot. +} +\author{ + Johannes Ranke +} +\seealso{ + \code{\link{mkinplot}}, for a way to plot the data and the fitted lines of the + mkinfit object. } +\examples{ +model <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO")) +fit <- mkinfit(model, FOCUS_2006_D, error_model = "tc", quiet = TRUE) +mkinerrplot(fit) +} +\keyword{ hplot } diff --git a/man/plot.mkinfit.Rd b/man/plot.mkinfit.Rd index 733cdf76..9514c5e5 100644 --- a/man/plot.mkinfit.Rd +++ b/man/plot.mkinfit.Rd @@ -10,7 +10,7 @@ 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, + then latex is being used for the formatting of the chi2 error level, if \code{show_errmin = TRUE}. } \usage{ @@ -22,7 +22,9 @@ 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", + show_residuals = FALSE, + show_errplot = 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) @@ -69,10 +71,16 @@ plot_sep(fit, sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE, \dots) } \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 + 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". @@ -109,9 +117,10 @@ plot_sep(fit, sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE, \dots) # parent to sink included SFO_SFO <- mkinmod(parent = mkinsub("SFO", "m1", full = "Parent"), m1 = mkinsub("SFO", full = "Metabolite M1" )) -fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE) +fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE, error_model = "tc") plot(fit) plot(fit, show_residuals = TRUE) +plot(fit, show_errplot = TRUE) # Show the observed variables separately plot(fit, sep_obs = TRUE, lpos = c("topright", "bottomright")) @@ -122,6 +131,10 @@ plot(fit, sep_obs = TRUE, show_residuals = TRUE, lpos = c("topright", "bottomrig # The same can be obtained with less typing, using the convenience function plot_sep plot_sep(fit, lpos = c("topright", "bottomright")) + +# Show the observed variables separately, with the error model +plot(fit, sep_obs = TRUE, show_errplot = TRUE, lpos = c("topright", "bottomright"), + show_errmin = TRUE) } \author{ Johannes Ranke diff --git a/man/plot.mmkin.Rd b/man/plot.mmkin.Rd index b3312292..44e5e4c7 100644 --- a/man/plot.mmkin.Rd +++ b/man/plot.mmkin.Rd @@ -12,8 +12,9 @@ then latex is being used for the formatting of the chi2 error level. } \usage{ -\method{plot}{mmkin}(x, main = "auto", legends = 1, errmin_var = "All data", errmin_digits = 3, - cex = 0.7, rel.height.middle = 0.9, ...) +\method{plot}{mmkin}(x, main = "auto", legends = 1, + resplot = c("time", "errmod"), errmin_var = "All data", errmin_digits = 3, + cex = 0.7, rel.height.middle = 0.9, ...) } \arguments{ \item{x}{ @@ -25,6 +26,11 @@ \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{errmin_var}{ The variable for which the FOCUS chi2 error value should be shown. } @@ -48,10 +54,11 @@ Johannes Ranke } \examples{ + \dontrun{ # Only use one core not to offend CRAN checks fits <- mmkin(c("FOMC", "HS"), list("FOCUS B" = FOCUS_2006_B, "FOCUS C" = FOCUS_2006_C), # named list for titles - cores = 1, quiet = TRUE) + cores = 1, quiet = TRUE, error_model = "tc") plot(fits[, "FOCUS C"]) plot(fits["FOMC", ]) @@ -59,4 +66,8 @@ # height should be smaller than the plot width (this is not possible for the html pages # generated by pkgdown, as far as I know). plot(fits["FOMC", "FOCUS C"]) # same as plot(fits[1, 2]) + + # Show the error models + plot(fits["FOMC", ], resplot = "errmod") + } } |