knitr-markdown.Rmd

<!--
%\VignetteEngine{knitr::knitr}
%\VignetteIndexEntry{An R Markdown Vignette with knitr}
-->

This is an example of Markdown vignettes in R. Before R 3.0.0, only Sweave/PDF vignettes were supported in R. Markdown is gaining popularity over the years due to its simplicity, and R 3.0.0 starts to support package vignettes written in [R Markdown](http://www.rstudio.com/ide/docs/authoring/using_markdown).

## Package vignettes

To enable Markdown vignettes in an R package, you need to

- add `*.Rmd` files under the `vignettes` directory
- add `VignetteBuilder: knitr` to the `DESCRIPTION` file
- specify the vignette engine `\VignetteEngine{knitr::knitr}` in the `Rmd` files (inside HTML comments)

## View vignettes

And R will load the **knitr** package to build these vignettes to HTML files, and you can see them when you open the HTML help:

```{r eval=FALSE}
help(package = 'YourPackage', help_type = 'html')
```

## Examples

Below are some code chunks as examples.

```{r hello, results='asis'}
cat('_hello_ **markdown**!', '\n')
```

Normally you do not need any chunk options.

```{r}
1+1
10:1
rnorm(5)^2
strsplit('hello, markdown vignettes', '')
```

Feel free to draw beautiful plots and write math $P(X>x)=\alpha/2$.

```{r}
n=300; set.seed(123)
par(mar=c(4,4,.1,.1))
plot(rnorm(n), rnorm(n), pch=21, cex=5*runif(n), col='white', bg='gray')
```

You can use your own CSS file instead of the built-in style in the **markdown** package -- just set the option `markdown.HTML.stylesheet`, e.g.

```{r css, eval=FALSE}
options(markdown.HTML.stylesheet = 'path/to/a/custom/style.css')
```

For this vignette, I use the `markdown.HTML.header` option to modify a few CSS rules in the default CSS style:

```{r header}
options(markdown.HTML.header = system.file('misc', 'vignette.css', package='knitr'))
```