plot.mkinfit. mkin

+ +

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.

+ + +

# S3 method for 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, …)

+ +

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. +
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. +

+ +

Value

+ +

The function is called for its side effect.

+ +

Examples

# 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" ))
Successfully compiled differential equation model from auto-generated C code.
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"))

Author

+ + Johannes Ranke + +