Introduction

A demo of using markdown with version control for writing academic papers

Rmd. source here:

• https://raw.githubusercontent.com/UNFAOstatistics/faosyb_paper/master/faosyb_paper.Rmd

md. source is here:

• https://raw.githubusercontent.com/UNFAOstatistics/faosyb_paper/master/faosyb_paper.md

To see different formats rendered click the links from below:

Paper

• pdf: https://github.com/UNFAOstatistics/faosyb_paper/raw/master/faosyb_paper.pdf
• html: http://htmlpreview.github.io/?https://raw.githubusercontent.com/UNFAOstatistics/faosyb_paper/master/faosyb_paper.html
• Word: https://github.com/UNFAOstatistics/faosyb_paper/raw/master/faosyb_paper.docx
• Libreoffice: https://github.com/UNFAOstatistics/faosyb_paper/raw/master/faosyb_paper.odt

Slides

• html: http://htmlpreview.github.io/?https://raw.githubusercontent.com/UNFAOstatistics/faosyb_paper/master/slides.html

Processing the source files

To set up your software environment look at: https://github.com/digieast/digicoffee/blob/master/methods_tools.md

Commands

This has been tested in using pandoc 1.13.2 version in Windows 7 and Ubuntu linux 12.04

Use following scripts to convert slides into desired format

1. knit the faosyb_paper.Rmd into faosyb_paper.md In R with command

   knitr::knit("faosyb_paper.Rmd")

2. Then convert the faosyb_paper.md in terminal using

• pdf: pandoc -r markdown+simple_tables+table_captions+yaml_metadata_block -s -S --latex-engine=pdflatex --template=faosyb.pdf.template --filter pandoc-citeproc --toc --number-section --toc-depth=2 faosyb_paper.md -o faosyb_paper.pdf
• html: pandoc -r markdown+simple_tables+table_captions+yaml_metadata_block -w html -s -S --template=faosyb.html.template -H faosyb.css --filter pandoc-citeproc --number-section --toc faosyb_paper.md -o faosyb_paper.html
• docx: pandoc --toc --number-section faosyb_paper.md -o faosyb_paper.docx
• odt: pandoc --toc --number-section faosyb_paper.md -o faosyb_paper.odt

For converting the slides.md

• reveal.js html: pandoc -t revealjs -s slides.md -o slides.html -V revealjs-url=http://lab.hakim.se/reveal-js -V theme=simple -V transition=fade
• pdf: pandoc -t beamer slides.md -o slides.pdf