Description Usage Arguments Value Author(s) Examples
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.
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
.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | ## 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(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, ...)
|
x |
Alias for fit introduced for compatibility with the generic S3 method. |
fit |
An object of class |
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 |
inset |
Passed to |
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 |
The function is called for its side effect.
Johannes Ranke
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | # 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" ))
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"))
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.