---
title: Example evaluation of FOCUS Example Dataset D
author: Johannes Ranke
date: "`r Sys.Date()`"
output:
  html_document:
    mathjax: null
    theme: united
    fig_retina: null
vignette: >
  %\VignetteIndexEntry{Example evaluation of FOCUS Example Dataset D}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r, include = FALSE}
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`.


```{r data}
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.

```{r model}
SFO_SFO <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"))
print(SFO_SFO$diffs)
```

We do the fitting without progress report (`quiet = TRUE`).


```{r fit}
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.

```{r plot, fig.height = 6, fig.width = 8}
plot_sep(fit, lpos = c("topright", "bottomright"))
```

Confidence intervals for the parameter estimates are obtained using the `mkinparplot` function.


```{r plot_2, fig.height = 4, fig.width = 8}
mkinparplot(fit)
```

A comprehensive report of the results is obtained using the `summary` method for `mkinfit`
objects.


```{r}
summary(fit)
```
