plot.mkinfit: Plot the observed data and the fitted model of an mkinfit...

In mkin: Kinetic Evaluation of Chemical Degradation Data

Plot the observed data and the fitted model of an mkinfit object

Description

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.

Usage

## S3 method for class 'mkinfit'
plot(
  x,
  fit = x,
  obs_vars = names(fit$mkinmod$map),
  xlab = "Time",
  ylab = "Residue",
  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,
  show_errplot = FALSE,
  maxabs = "auto",
  sep_obs = FALSE,
  rel.height.middle = 0.9,
  row_layout = FALSE,
  lpos = "topright",
  inset = c(0.05, 0.05),
  show_errmin = FALSE,
  errmin_digits = 3,
  frame = TRUE,
  ...
)

plot_sep(
  fit,
  show_errmin = TRUE,
  show_residuals = ifelse(identical(fit$err_mod, "const"), TRUE, "standardized"),
  ...
)

plot_res(
  fit,
  sep_obs = FALSE,
  show_errmin = sep_obs,
  standardized = ifelse(identical(fit$err_mod, "const"), FALSE, TRUE),
  ...
)

plot_err(fit, sep_obs = FALSE, show_errmin = sep_obs, ...)

Arguments

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. If given as a list, plot ranges for the different plot rows can be given for row layout.
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. If this is set to 'standardized', a plot of the residuals divided by the standard deviation given by the fitted error model will be shown.
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.
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.
row_layout	Should we use a row layout where the residual plot or the error model plot is shown to the right?
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.
frame	Should a frame be drawn around the plots?
...	Further arguments passed to plot.
standardized	When calling 'plot_res', should the residuals be standardized in the residual plot?

Details

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.

Value

The function is called for its side effect.

Author(s)

Johannes Ranke

Examples

# One parent compound, one metabolite, both single first order, path from
# parent to sink included
## Not run: 
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_res(fit)
plot_res(fit, standardized = FALSE)
plot_err(fit)

# 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"))

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

## End(Not run)

mkin documentation built on April 12, 2025, 2:24 a.m.