diff options
Diffstat (limited to 'man')
| -rw-r--r-- | man/mmkin.Rd | 8 | ||||
| -rw-r--r-- | man/plot.mkinfit.Rd | 49 | ||||
| -rw-r--r-- | man/plot.mmkin.Rd | 2 |
3 files changed, 39 insertions, 20 deletions
diff --git a/man/mmkin.Rd b/man/mmkin.Rd index f701890a..44caf8d2 100644 --- a/man/mmkin.Rd +++ b/man/mmkin.Rd @@ -56,13 +56,19 @@ m_synth_FOMC_lin <- mkinmod(parent = list(type = "FOMC", to = "M1"), models <- list(SFO_lin = m_synth_SFO_lin, FOMC_lin = m_synth_FOMC_lin) datasets <- lapply(synthetic_data_for_UBA_2014[1:3], function(x) x$data) -time_default <- system.time(fits <- mmkin(models, datasets)) +time_default <- system.time(fits.0 <- mmkin(models, datasets)) time_1 <- system.time(fits.1 <- mmkin(models, datasets, cores = 1)) time_default time_1 endpoints(fits[["SFO_lin", 2]]) + +# Plot.mkinfit handles rows or columns of mmkin result objects +plot(fits.0[1, ]) +# Double brackets to select a single mkinfit object, which will be +# plotted by plot.mkinfit +plot(fits.0[[1, 1]], sep_obs = TRUE, show_residuals = TRUE) } } \keyword{ optimize } diff --git a/man/plot.mkinfit.Rd b/man/plot.mkinfit.Rd index 494dc38d..b80928f7 100644 --- a/man/plot.mkinfit.Rd +++ b/man/plot.mkinfit.Rd @@ -14,10 +14,11 @@ xlab = "Time", ylab = "Observed", xlim = range(fit$data$time), ylim = "default", - col_obs = 1:length(fit$mkinmod$map), pch_obs = col_obs, - lty_obs = rep(1, length(fit$mkinmod$map)), + 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_vars = FALSE, rel.height.middle = 0.9, lpos = "topright", inset = c(0.05, 0.05), \dots) } \arguments{ @@ -25,7 +26,7 @@ Alias for fit introduced for compatibility with the generic S3 method. } \item{fit}{ - an object of class \code{\link{mkinfit}}. + An object of class \code{\link{mkinfit}}. } \item{obs_vars}{ A character vector of names of the observed variables for which the @@ -33,47 +34,54 @@ in the model. } \item{xlab}{ - label for the x axis. + Label for the x axis. } \item{ylab}{ - label for the y axis. + Label for the y axis. } \item{xlim}{ - plot range in x direction. + Plot range in x direction. } \item{ylim}{ - plot range in y direction. + Plot range in y direction. } \item{col_obs}{ - colors used for plotting the observed data and the corresponding model prediction lines. + Colors used for plotting the observed data and the corresponding model prediction lines. } \item{pch_obs}{ - symbols to be used for plotting the data. + Symbols to be used for plotting the data. } \item{lty_obs}{ - line types to be used for the model predictions. + Line types to be used for the model predictions. } \item{add}{ - should the plot be added to an existing plot? + Should the plot be added to an existing plot? } \item{legend}{ - should a legend be added to the plot? + Should a legend be added to the plot? } \item{show_residuals}{ - should residuals be shown in the lower third of the plot? + Should residuals be shown in the lower third of the plot? } \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? + } + \item{rel.height.middle}{ + The relative height of the middle plot, if more than two rows of plots are shown. + } \item{lpos}{ - position of the legend. Passed to \code{\link{legend}} as the first argument. + 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{\dots}{ - further arguments passed to \code{\link{plot}}. + Further arguments passed to \code{\link{plot}}. } } \value{ @@ -81,13 +89,18 @@ } \examples{ # One parent compound, one metabolite, both single first order, path from -# parent to sink included +# 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) +fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE, method.modFit = "Marq") plot(fit) + +# Show the observed variables separately +plot(fit, sep_obs = TRUE) + +# Show the observed variables separately, with residuals +plot(fit, sep_obs = TRUE, show_residuals = TRUE, lpos = c("topright", "bottomright")) } \author{ Johannes Ranke } -\keyword{ hplot } diff --git a/man/plot.mmkin.Rd b/man/plot.mmkin.Rd index 8362f16c..ffd83d2f 100644 --- a/man/plot.mmkin.Rd +++ b/man/plot.mmkin.Rd @@ -32,7 +32,7 @@ Passed to the plot functions and \code{\link{mtext}}. } \item{rel.height.middle}{ - The relative height of the middle plot. + The relative height of the middle plot, if more than two rows of plots are shown. } \item{\dots}{ Further arguments passed to \code{\link{plot.mkinfit}} and \code{\link{mkinresplot}}. |