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| author | Johannes Ranke <jranke@uni-bremen.de> | 2015-06-05 13:41:44 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2015-06-05 13:41:44 +0200 |
| commit | 58f46265cec1c3f51a6d2507e0f3e3b59243cc82 (patch) | |
| tree | 75df8415f82b927fc76933f366a81dba79d4531f /vignettes/FOCUS_D.Rmd | |
| parent | 2bab93a12caf947387ce34c5a96bba942b2ee317 (diff) | |
Add a simple vignette with an evaluation of FOCUS D
Diffstat (limited to 'vignettes/FOCUS_D.Rmd')
| -rw-r--r-- | vignettes/FOCUS_D.Rmd | 66 |
1 files changed, 66 insertions, 0 deletions
diff --git a/vignettes/FOCUS_D.Rmd b/vignettes/FOCUS_D.Rmd new file mode 100644 index 00000000..902d3d24 --- /dev/null +++ b/vignettes/FOCUS_D.Rmd @@ -0,0 +1,66 @@ +<!--
+%\VignetteEngine{knitr::knitr}
+%\VignetteIndexEntry{Simple Evaluation of FOCUS Example Dataset D}
+-->
+
+```{r, include = FALSE}
+library(knitr)
+library(methods)
+opts_chunk$set(tidy = FALSE, cache = FALSE)
+```
+# Example evaluation of FOCUS Example Dataset D
+
+This is just a very simple vignette showing how to fit a degradation model for a parent
+compound with one transformation product using `mkin`. After loading the
+library we look a the data. We have observed concentrations in the column named
+`value` at the times specified in column `time` for the two observed variables
+named `parent` and `m1`.
+
+
+```{r}
+library("mkin")
+print(FOCUS_2006_D)
+```
+
+Next we specify the degradation model: The parent compound degrades with simple first-order
+kinetics (SFO) to one metabolite named m1, which also degrades with SFO kinetics.
+
+The call to mkinmod returns a degradation model. The differential equations represented in
+R code can be found in the character vector `$diffs` of the `mkinmod` object. If
+the `ccSolve` package is installed and functional, the differential equation model
+will be compiled from auto-generated C code.
+
+
+```{r}
+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 <- 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` method for `mkinfit` objects.
+
+```{r, fig.height = 7}
+plot(fit, show_residuals = TRUE)
+```
+
+Confidence intervals for the parameter estimates are obtained using the `mkinparplot` function.
+
+
+```{r}
+mkinparplot(fit)
+```
+
+A comprehensive report of the results is obtained using the `summary` method for `mkinfit`
+objects.
+
+
+```{r}
+summary(fit)
+```
|