library(knitr) opts_chunk$set(tidy = FALSE, cache = TRUE)
This is just a very simple vignette showing how to fit a degradation model for a parent
compound with one transformation product using
mkin. After loading the
library we look a the data. We have observed concentrations in the column named
value at the times specified in column
time for the two observed variables
library("mkin", quietly = TRUE) print(FOCUS_2006_D)
Next we specify the degradation model: The parent compound degrades with simple first-order kinetics (SFO) to one metabolite named m1, which also degrades with SFO kinetics.
The call to mkinmod returns a degradation model. The differential equations represented in
R code can be found in the character vector
$diffs of the
mkinmod object. If
a C compiler (gcc) is installed and functional, the differential equation model will
be compiled from auto-generated C code.
SFO_SFO <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO")) print(SFO_SFO$diffs)
We do the fitting without progress report (
quiet = TRUE).
fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)
A plot of the fit including a residual plot for both observed variables is obtained
plot_sep method for
mkinfit objects, which shows separate graphs for
all compounds and their residuals.
plot_sep(fit, lpos = c("topright", "bottomright"))
Confidence intervals for the parameter estimates are obtained using the
A comprehensive report of the results is obtained using the
summary method for
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