plot.mkinfit: Plot the observed data and the fitted model of an mkinfit...
In mkin: Kinetic Evaluation of Chemical Degradation Data

Description Usage Arguments Value Author(s) Examples

View source: R/plot.mkinfit.R

Solves the differential equations with the optimised and fixed parameters from a previous successful call to mkinfit and plots the observed data together with the solution of the fitted model.

If the current plot device is a tikz device, then latex is being used for the formatting of the chi2 error level, if show_errmin = TRUE.

## S3 method for class 'mkinfit'
plot(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, maxabs = "auto",
  sep_obs = FALSE, rel.height.middle = 0.9,
  lpos = "topright", inset = c(0.05, 0.05),
  show_errmin = FALSE, errmin_digits = 3, ...)
plot_sep(fit, sep_obs = TRUE,  show_residuals = TRUE, show_errmin = TRUE, ...)

`x`	Alias for fit introduced for compatibility with the generic S3 method.
`fit`	An object of class `mkinfit`.
`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.
`xlab`	Label for the x axis.
`ylab`	Label for the y axis.
`xlim`	Plot range in x direction.
`ylim`	Plot range in y direction.
`col_obs`	Colors used for plotting the observed data and the corresponding model prediction lines.
`pch_obs`	Symbols to be used for plotting the data.
`lty_obs`	Line types to be used for the model predictions.
`add`	Should the plot be added to an existing plot?
`legend`	Should a legend be added to the plot?
`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.
`maxabs`	Maximum absolute value of the residuals. This is used for the scaling of the y axis and defaults to "auto".
`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.
`rel.height.middle`	The relative height of the middle plot, if more than two rows of plots are shown.
`lpos`	Position(s) of the legend(s). Passed to `legend` as the first argument. If not length one, this should be of the same length as the obs_var argument.
`inset`	Passed to `legend` if applicable.
`show_errmin`	Should the FOCUS chi2 error value be shown in the upper margin of the plot?
`errmin_digits`	The number of significant digits for rounding the FOCUS chi2 error percentage.
`...`	Further arguments passed to `plot`.

The function is called for its side effect.

Johannes Ranke

# One parent compound, one metabolite, both single first order, path from
# 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, method.modFit = "Marq")
plot(fit)
plot(fit, show_residuals = TRUE)

# Show the observed variables separately
plot(fit, sep_obs = TRUE, lpos = c("topright", "bottomright"))

# Show the observed variables separately, with residuals
plot(fit, sep_obs = TRUE, show_residuals = TRUE, lpos = c("topright", "bottomright"),
     show_errmin = TRUE)

# The same can be obtained with less typing, using the convenience function plot_sep
plot_sep(fit, lpos = c("topright", "bottomright"))