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----
-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)
-```