Further formatting improvement of benchmark vignette

Also, use .rmd extension instead of .Rmd for vignettes.

1 files changed, 0 insertions, 73 deletions

diff --git a/vignettes/FOCUS_D.Rmd b/vignettes/FOCUS_D.Rmd
deleted file mode 100644
index 02c2c467..00000000
--- a/vignettes/FOCUS_D.Rmd
+++ /dev/null
@@ -1,73 +0,0 @@
----

-title: Example evaluation of FOCUS Example Dataset D

-author: Johannes Ranke

-date: "`r Sys.Date()`"

-output:

-rmarkdown::html_vignette:

-    mathjax: null

-vignette: >

-  %\VignetteIndexEntry{Example evaluation of FOCUS Example Dataset D}

-  %\VignetteEngine{knitr::rmarkdown}

-  %\VignetteEncoding{UTF-8}

----

-

-```{r, include = FALSE, message = FALSE}

-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`.

-

-

-```{r data}

-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.

-

-```{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)

-```