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authorJohannes Ranke <jranke@uni-bremen.de>2016-10-22 17:55:12 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2016-10-22 17:55:12 +0200
commit1c81442284a25a9cf4979d9236ec0c1a1cf8a8dd (patch)
treed19cceb5768ff33654dc04f67c5b55e4205b8aca /vignettes/FOCUS_D.Rmd
parent54cf070313c844f5ccf741fc7f1237fe2d260ded (diff)
Update way to specify encoding, improve FOCUS_L TOC
Diffstat (limited to 'vignettes/FOCUS_D.Rmd')
-rw-r--r--vignettes/FOCUS_D.Rmd12
1 files changed, 6 insertions, 6 deletions
diff --git a/vignettes/FOCUS_D.Rmd b/vignettes/FOCUS_D.Rmd
index 4edc7bf2..57b2d9d6 100644
--- a/vignettes/FOCUS_D.Rmd
+++ b/vignettes/FOCUS_D.Rmd
@@ -10,7 +10,7 @@ output:
vignette: >
%\VignetteIndexEntry{Example evaluation of FOCUS Example Dataset D}
%\VignetteEngine{knitr::rmarkdown}
- \usepackage[utf8]{inputenc}
+ %\VignetteEncoding{UTF-8}
---
```{r, include = FALSE}
@@ -25,7 +25,7 @@ library we look a the data. We have observed concentrations in the column named
named `parent` and `m1`.
-```{r}
+```{r data}
library("mkin")
print(FOCUS_2006_D)
```
@@ -38,7 +38,7 @@ R code can be found in the character vector `$diffs` of the `mkinmod` object. If
a C compiler (gcc) is installed and functional, the differential equation model will
be compiled from auto-generated C code.
-```{r}
+```{r model}
SFO_SFO <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"))
print(SFO_SFO$diffs)
```
@@ -46,21 +46,21 @@ print(SFO_SFO$diffs)
We do the fitting without progress report (`quiet = TRUE`).
-```{r}
+```{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` method for `mkinfit` objects.
-```{r, fig.height = 5}
+```{r plot, fig.height = 5}
plot(fit, show_residuals = TRUE)
```
Confidence intervals for the parameter estimates are obtained using the `mkinparplot` function.
-```{r, fig.height = 4}
+```{r plot_2, fig.height = 4}
mkinparplot(fit)
```

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