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
named `parent`

and `m1`

.

library("mkin") 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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