varia.website/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 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_RENAME_PLOT (chunklabel): the figures generated for plots are named with a default prefix (usually unnamed-chunk) followed by a sequential number. That sequence starts on 1 for every processed file, which causes naming conflicts among files. In order to avoid these conflicts RMD_READER_RENAME_PLOT can be set chunklabel and that prefix is replaced with the name of the markdown source, without extension. Alternatively, RMD_READER_RENAME_PLOT can be set directory in which case the fig.path (defaults to figure/) is augmented with the path to markdown source including the name of the source file without extension. Another way to avoid conflicts is naming the chuncks and in that case this variable can be set to any other string.
• 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.
• RMD_READER_KNITR_OPTS_KNIT (None): sets knitr's opts_knit.

Plotting

I strongly suggest using the variable RMD_READER_RENAME_PLOT='chunklabel'. That helps with avoiding naming conflits among different posts. rmd_reader sets knitr's unnamed.chunk.label option to the Rmd file name (without extension) in runtime.

Alternatively, Rebecca Weiss (@rjweiss) suggested using opts_chunk to set knitr's fig.path (link). Now that can be done directly in pelicanconf thougth RMD_READER_KNITR_OPTS_CHUNK, that variable receives a dict with options to be passed to knitr's opts_chunk. With this scheme you can set RMD_READER_RENAME_PLOT='directory' and add the generated figures directory to STATIC_PATHS.

RMD_READER_RENAME_PLOT = 'directory'
RMD_READER_KNITR_OPTS_CHUNK = {'fig.path': 'figure/'}
STATIC_PATHS = ['figure']