.gitignore

# ---- R and RStudio files -----------------------------------------------
.Rhistory
.Rapp.history
.RData
.Rproj.user
.Rproj.user/

# Output files from R CMD build
/*.tar.gz

# Output files from R CMD check
/*.Rcheck/

# produced vignettes
vignettes/*.html
vignettes/*.pdf

# The devtools zip is downloaded when the package is updating itself.  If it's not deleted, there's no reason to commit it to the repository.
devtools.zip

# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
.httr-oauth

# Temporary files created by R markdown
*.utf8.md
*.knit.md

# ---- Protected Information -----------------------------------------------
# see cubuspl42's answer in http://stackoverflow.com/questions/2415873/exceptions-in-gitignore
/unshared-material/*
/data-unshared/*
/data/unshared/*

# Dataset Exceptions
!utility/package-dependency-list.csv

# Keep the README files in the unshared directories.  They provide documentation, and also force the directories to be created on other machines.
# Depending on how you do it, you might need to add w/ the command line (eg, git add -f ./data-unshared/raw/README.md)
!README.md
!data-unshared/contents.md
!data-unshared/raw/README.md
!data-unshared/derived/README.md
!data/unshared/contents.md
!data/unshared/raw/README.md
!data/unshared/derived/README.md

# ---- Caches -----------------------------------------------
# Exclude caches in case they contain PHI
cache/
*/cache/
*/*/cache/

# knitr and R markdown default cache directories
/*_cache/
/cache/

# ---- Windows -----------------------------------------------
# Cached small image files
Thumbs.db

# Folder config file
Desktop.ini