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

+ + +

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,
+  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.
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?

+ +

Value

+ +

The function is called for its side effect.

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.

+ +

Examples


+# One parent compound, one metabolite, both single first order, path from
+# parent to sink included
+# \dontrun{
+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)
#> Warning: Observations with value of zero were removed from the data
fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE, error_model = "tc")
#> Warning: Observations with value of zero were removed from the data
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)
# }
+
+

+ +