Update way to specify encoding, improve FOCUS_L TOC

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)

 ```