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.gitignore
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##############
# R and RStudio files.
.Rhistory
.RData
.Rproj.user
.Rproj.user/
# 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
##############
# Protected Information; see cubuspl42's answer in http://stackoverflow.com/questions/2415873/exceptions-in-gitignore
/unshared_material/*
/unshared-material/*
/data_unshared/*
/data-unshared/*
/data/unshared/raw/*
/data/unshared/derived/*
# Unnecessary files for knitr reports
# Dataset Exceptions
!utility/package_dependency_list.csv
!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
##############
# Exclude caches in case they contain PHI
cache/
*/cache/
*/*/cache/
##############
# Exclude large report files
models/*/*
reports/*/*
sandbox/*/*
!/models/*/*.R
!/models/*/*.Rmd
!/models/*/*/*.R
!/models/*/*/*.Rmd
!/models/*/*/*/*.R
!/models/*/*/*/*.Rmd
!/reports/*/*.R
!/reports/*/*.Rmd
!/reports/*/*/*.R
!/reports/*/*/*.Rmd
!/reports/*/*/*/*.R
!/reports/*/*/*/*.Rmd
!/sandbox/*/*.R
!/sandbox/*/*.Rmd
!/sandbox/*/*/*.R
!/sandbox/*/*/*.Rmd
!/sandbox/*/*/*/*.R
!/sandbox/*/*/*/*.Rmd
!/models/README.md
!/models/*/README.md
!/models/*/*/README.md
!/models/*/*/*/README.md
!/reports/README.md
!/reports/*/README.md
!/reports/*/*/README.md
!/reports/*/*/*/README.md
!/sandbox/README.md
!/sandbox/*/README.md
!/sandbox/*/*/README.md
!/sandbox/*/*/*/README.md
##############
# Windows
# Cached small image files
Thumbs.db
# Folder config file
Desktop.ini
*.RDataTmp
*.back
*.html
data/shared/derived/models/models_local.rds
data/shared/derived/models/models_pooled.rds
data/shared/derived/models/local_custom.rds
# specific reports that must be published manually
#
manipulation/stitched-output/0-ellis-island.html
reports/harmonize-alcohol/harmonize-alcohol.html
reports/harmonize-age/harmonize-age.html
reports/harmonize-education/harmonize-education.html
reports/harmonize-marital/harmonize-marital.html
reports/harmonize-physique/harmonize-physique.html
reports/harmonize-smoking/harmonize-smoking.html
reports/harmonized-data/harmonized-data.html
# Exceptions
!models/exercise-report-3/exercise-report.html
!models/exercise-report-3/exercise-report.md
!models/exercise-report-3/exercise-report.docx
!models/exercise-report-3/exercise-report.pdf
!models/exercise-report-3/results-tables.html
!models/exercise-report-3/results-tables-nosidebar.html
!models/exercise-report-3/results-tables.docx
!models/exercise-report-3/results-tables.pdf
!models/exercise-report-3/predictors-in-focus.html
!models/exercise-report-3/predictors-in-focus.md
!models/exercise-report-3/predictors-in-focus.docx
!models/exercise-report-3/predictors-in-focus.pdf
!models/exercise-report-3/unadjusted-models.html