resources.md

Links to other resources

The following are links to resources of interest to participants in SISBID Module 3: Reproducible Research.

R Markdown

• R Markdown documentation
• Knitr in a Knutshell tutorial
• Yihui Xie, Dynamic Documents with R and knitr, 2e (2015)
• Document templates

R Packages

• Hadley Wickham, R Packages (2015)
• Releasing to CRAN
• Leek group guide to R packages
• Karl's R Package Primer
• When to trust an R package

GNU Make

• Karl's Minimal Make tutorial
• remake package (GNU Make reimagined for R)

Git

• Happy Git and GitHub for the useR
• Hadley on Git/GitHub
• Nice R Code guide to Git branches
• Git subtrees
• Also look at git tag and git remote (the latter in the Leek Group guide to R packages)

Sharing

• Leek Group guide to data sharing
• Sharing, publishing, archiving (slides) from the Data Carpentry Reproducible Research workshop materials

Coding conventions

• Hadley's recommendations
• Google's recommendations

Code Review

• Software Carpentry blog post
• Titus Brown's blog post

Software testing

• testthat package
• Testing R code (book)

Dependency management

• packrat package
• checkpoint package
• Rocker: docker for R
• R Docker tutorial

Writing

• A book on writing: Style: Lessons in Clarity and Grace
• The science of scientific writing (pdf)
• Turning tables into graphs

Using C++ code in R packages

• Rcpp
• Rcpp book

Better graphics

• ggplot2 book
• How to display data badly (pdf)