library(knitr) opts_chunk$set(tidy = FALSE, cache = FALSE) library(mkin)
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 at the data. We have observed concentrations in the column named
value
at the times specified in column time
for the two observed variables
named parent
and m1
.
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
using the 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 mkinparplot
function.
mkinparplot(fit)
A comprehensive report of the results is obtained using the summary
method for mkinfit
objects.
summary(fit)
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