Hadley Wickham’s talk in the Simply Statistics Unconference on the Future of Statistics
Daring Fireball's markdown page. Kind of where it all begins, but other references that are more recent and specific to our context are more relevant.
Carson Sievert's talk Reproducible web documents with R, knitr & Markdown
MathJax is an open source JavaScript display engine for mathematics that works in all browsers ... It just works.
MathJax + RStudio specifics:
- RStudio documentation page about Equations in R Markdown
- Note that one should probably add a
latexqualifier to equations that use the$or$$as delimiter in Markdown document. The simple demo from today worked fine without it but presumably that's not always true. Read the RStudio blog announcement about this change. - Note that the multiline display equation in our simple demo used 4 backslashes to indicate line breaks. Presumably due to escaping issues, 2 backslashes were not enough to survive the conversion process and be seen by MathJax.
Pandoc: If you need to convert files from one markup format into another, pandoc is your swiss-army knife.
knitr, an R package for elegant, flexible and fast dynamic report generation.
RStudio + R Markdown specifics:
- http://www.rstudio.com/ide/docs/authoring/using_markdown
- http://www.rstudio.com/ide/docs/r_markdown
- http://www.rstudio.com/ide/docs/authoring/markdown_notebooks
Jeromy Anglim's blog post Getting Started with R Markdown, knitr, and Rstudio 0.96 and a Gist containing the source
Yihui Xie blog post about when to use Markdown and when to use LaTeX
How to change the CSS used when R markdown is converted to HTML
- Step-by-step instructions from Jenny Bryan's STAT 545A course
- http://www.rstudio.com/ide/docs/authoring/markdown_custom_rendering
Ram, K 2013. Git can facilitate greater reproducibility and increased transparency in science. Source Code for Biology and Medicine 2013 8:7. Go to the associated github repo to get the PDF (link at bottom of README) and to see a great example of how someone managed the process of writing a manuscript with git(hub).
Karl Broman's tutorial, aimed at stats / data science types: An introduction to Git/Github.
SourceTree Git client, with a GUI. Available for Windows or Mac.
RStudio + Git(Hub)
- http://www.rstudio.com/ide/docs/version_control/overview
- Blog post from The Molecular Ecologist on using GitHub with R and RStudio
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