mlumr/.gitignore at main · choxos/mlumr · GitHub

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# ============================================================================
# R and RStudio
# ============================================================================

# History
.Rhistory
.Rapp.history

# Session data
.RData
.Rdata
.RDataTmp
.Ruserdata

# Example code from R CMD build
*-Ex.R

# RStudio project metadata
.Rproj.user/

# R CMD build output
/*.tar.gz

# R CMD check output
/*.Rcheck/

# Local package build helpers: track the hand-written extra.css and the
# favicons built from the logo (pkgdown never builds them on CI).
pkgdown/*
!pkgdown/extra.css
!pkgdown/favicon/

# Vignette build output.
# introduction + data-preparation are plain knitr .Rmd (rebuilt at build time),
# so their stray .html are ignored. The 6 precompiled modeling vignettes ship
# their prebuilt .html + R.rsp .html.asis to CRAN (Stan never runs at build).
# Their knitted .Rmd and figure/ are tracked too, so pkgdown can build the
# articles site on a fresh checkout (multinma's pattern); both are kept out of
# the CRAN tarball via .Rbuildignore, so the package itself stays lean.
vignettes/introduction.html
vignettes/data-preparation.html

# knitr writes figures beside the working directory, so knitting a vignette
# from the repository root drops a figure/ there. Only vignettes/figure is
# tracked.
/figure/
vignettes/*.pdf

# knitr / R Markdown caches
*_cache/
/cache/
*.utf8.md
*.knit.md

# R environment
.Renviron

# OAuth tokens (httr)
.httr-oauth

# pkgdown rendered site
docs/

# rsconnect deployments
rsconnect/

# ============================================================================
# Compiled artifacts (Stan / C++)
# ============================================================================

*.o
*.so
*.dll
*.o.tmp
src/*.o
src/*.so
src/*.dll
src/*.o.tmp
src/Makevars
src/Makevars.win
src/stan_meta_header.hpp

# CmdStan-compiled binaries inside inst/stan (only .stan sources are tracked)
inst/stan/**
!inst/stan/*.stan
!inst/stan/include/
!inst/stan/include/*.stan

# ============================================================================
# Operating system
# ============================================================================

.DS_Store
man/figures/logo_backup.svg
Thumbs.db
ehthumbs.db
desktop.ini

# ============================================================================
# Editors and IDEs
# ============================================================================

# Vim
*.swp
*.swo
*~

# VS Code
.vscode/

# JetBrains
.idea/

# Local editor and assistant state. Hidden directories are never part of the
# package, so ignore them as a class rather than maintaining a vendor list that
# goes stale; .github is the one that must stay tracked.
.*/
!.github/
.github/prompts/

# Emacs
\#*\#
.\#*

# ============================================================================
# Local development (per-clone; see .git/info/exclude for personal additions)
# ============================================================================

# Conventional names for local-only working copies
private/
scratch/
wip/
_*/

# Backup archives
*.zip
*.tar
*.tgz
docs

# Reporting
reporting/
Rplots.pdf

# Simulation checkpoints. The study writes one file per fit so an
# interrupted run resumes; only the assembled CSV and its manifest are results.
data-raw/*.csv.cells/
# The two source spreadsheets behind the shoulder and caries datasets are
# downloaded into data-raw/ to rebuild them and are never tracked.
data-raw/*.xlsx
data-raw/*.rtf

# testthat writes this beside the tests after a failing run
tests/testthat/testthat-problems.rds