'Workflow: tools and templates'

The workflow and templates to generate nice documents using knitr, markdown, LaTeX, pandoc (all under version control).

Pre-requisites

LaTeX
R
the knitr package
pandoc
A text editor! (I use Vim.)
Git (version control)
Stephan Hennig's LaTeX version control package

Dependencies

tom-style.sty is where I put code to load relevant LaTeX packages etc.
tom.xelatex is the template which pandoc uses to convert a Markdown document to TeX code. The pandoc documentation explains how these work here.
template/custom-local.sty loads any additional LaTeX packages for a specific document.
BONUS: elsevier.xelatex is a template for writing manuscripts to be submitted to Elsevier journals.
html.template is a pandoc template downloaded from Kieran Healy's pandoc-templates repository, and can be used when building HTML files from Markdown source.
kutiad-serif.css is a CSS file downloaded from Kieran Healy's pandoc-templates repository, and can be used in conjunction with the HTML pandoc template, for a nicely styled HTML output, when building from Markdown source.

Setup

Download the contents of this repository into a known location, for example ~/workflow.

In order to keep all the dependencies and templates together in one directory (which can then be kept under version control), I use symlinks so pandoc and LaTeX can search the locations they expect for the dependencies.

 ln -s ~/workflow/tom-style.sty ~/texmf/tex/latex/myStyles/tom-style.sty
 ln -s ~/workflow/tom.xelatex ~/.pandoc/templates/tom.xelatex
 ln -s ~/workflow/html.template ~/.pandoc/templates/html.template
 ln -s ~/workflow/marked/kultiad-serif.css~/.pandoc/marked/kultiad-serif.css

I can then come back the workflow/ directory and make edits to the dependencies, which will be automatically updated in their linked-to locations.

Writing a document and building a PDF

The contents of the template/ subdirectory will build the paper.pdf document. To generate a PDF from using R and markdown.

Initialise a new writing project with an Rmd file in a new directory, e.g. ~/working-directory/paper.Rmd.
Copy build-pdf.sh into the working directory.
Copy the version control files (vc and vc-git.awk) to the working directory.
Write a document using R-markdown syntax (e.g. paper.Rmd)
Run build-pdf.sh. This will use R to 'knit' the Rmd file into a md file, and then use pandoc to covert the md file into a PDF using LaTeX. It will also open the PDF and a word count (as a HTML file).

More information

Please email Tom Ravalde.