pelican-plugins/rmd_reader

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.

Loading

It is a good idea to load rmd_reader at last. It uses settings loaded at runtime and it is important to be sure that all settings have been loaded.

PLUGINS = ['sitemap',
           'summary',
           ...
           'render_math',
           'rmd_reader']  # put it here!

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 Pelican's MarkdownReader in order to generate html files from ordinary .md files.

Configuration

rmd_reader has these 3 variables that can be set in pelicanconf.

• RMD_READER_CLEANUP (True): The RMarkdown file is converted into a Markdown file with the extension .aux (to avoid conflicts while pelican is processing). This file is processed by pelican's MarkdownReader and is removed after that (the cleanup step). So if you want to check this file set RMD_READER_CLEANUP=True.
• RMD_READER_KNITR_QUIET (True): sets knitr's quiet argument.
• RMD_READER_KNITR_ENCODING (UTF-8): sets knitr's encoding argument.
• RMD_READER_KNITR_OPTS_CHUNK (None): sets knitr's opts_chunk.

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. There is a R template available that has the base elements needed by rmd_reader.