From 1c81442284a25a9cf4979d9236ec0c1a1cf8a8dd Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Sat, 22 Oct 2016 17:55:12 +0200
Subject: Update way to specify encoding, improve FOCUS_L TOC

---
 vignettes/FOCUS_D.Rmd | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

(limited to 'vignettes/FOCUS_D.Rmd')

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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