mkin (version 0.9-31)

plot.mkinfit: 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 = "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)),
  add = FALSE, legend = !add,
  show_residuals = FALSE, maxabs = "auto",
  lpos = "topright", inset = c(0.05, 0.05), ...)

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 in the lower third of the plot?

maxabs

Maximum absolute value of the residuals. This is used for the scaling of the y axis and defaults to "auto".

lpos

position of the legend. Passed to legend as the first argument.

inset

Passed to legend if applicable.

...

further arguments passed to plot.

Value

• The function is called for its side effect.

Examples

# One parent compound, one metabolite, both single first order.
SFO_SFO <- mkinmod(
  parent = list(type = "SFO", to = "m1", sink = TRUE),
  m1 = list(type = "SFO"))
# Fit the model to the FOCUS example dataset D using defaults
fit <- mkinfit(SFO_SFO, FOCUS_2006_D)
plot(fit)