Stan

• Stan documentation
  • the Reference Manual describes the syntax and workings of a Stan program
  • the Functions Reference is where you look up “what’s that function again?”
  • the User’s Guide has examples of complex models implemented in Stan, and discusses good programming practice
• RStan documentation
• Example models in Stan: each contains a Stan program, code for simulating data, real data, and model output and diagnostics
• Vignette on stanfit objects
• Brief guide to Stan’s warnings

tidyverse

• ggplot2 quick reference

Miscellaneous R tips

• How to print the source code for functions that don’t show it to you when you type their names. (tldr; showMethods(fun); getMethod(fun, c(x='class1', y='class2')))

Rstudio

• Strongly recommended global configuration:

General resources

• linuxcommand.org and bashguide
• Software Carpentry
• Reproducible Research by Karl Broman: talk and course
• Karl Broman’s excellent short tutorials on git/github, make, perl, and more.
• Bioinformatics Data Skills by Vince Buffalo
• Professional Skills for Data Science by Brian Yandell, and his course on the same topic Stat 627.
• Jenny Bryan’s stat 545 at UBC