plot.mkinfit. mkin 0.9.44.9000

Usage

"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, ...)

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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. -

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Description

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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.

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Value

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- The function is called for its side effect. -

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