pelican-plugins/rmd_reader/Readme.md

RMD Reader

This plugin helps you creating posts with knitr's RMarkdown files. knitr is a template engine which executes and displays embedded R code. So, being short you can write an executable paper with codes, formulas and graphics.

Dependency

This plugin needs rpy2 to work. Install it with:

pip install rpy2

Of course, R must be installed and also the knitr package. Execute the command below in R to get knitr installed.

R> install.packages('knitr')

Usage

The plugin detects RMD files ending with .Rmd or .rmd so you only have to write a RMarkdown files inside content directory.

This plugin calls R to process these files and generates markdown files that are processed by Python Markdown (with meta, codehilite(css_class=highlight), and extra extensions) before returning the content and metadata to pelican engine.

Plotting

The code below must be pasted inside the .Rmd file in order to correctly set the src attribute of img tag.

```{r, echo=FALSE}
hook_plot <- knit_hooks$get('plot')
knit_hooks$set(plot=function(x, options) {
    if (!is.null(options$pelican.publish) && options$pelican.publish) {
        x <- paste0("{filename}", x)
    }
    hook_plot(x, options)
})
opts_chunk$set(pelican.publish=TRUE)
```

I usually paste it just after the Markdown header.