.gitignore

# History files
.Rhistory
.Rapp.history

# Session Data files
.RData
.RDataTmp

# User-specific files
.Ruserdata

# Example code in package build process
*-Ex.R

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

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

# RStudio files
.Rproj.user/

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

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

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

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

# R Environment Variables
.Renviron

# pkgdown site
docs/

# translation temp files
po/*~

# RStudio Connect folder
rsconnect/

# ignore certain folders within structure
data-raw/
literature/

# ignore R project
*.RProj

# ignore figures (take up a lot of space)
*.png
*.jpg
*.jpeg
*.zip
#except exploratory figures
!data_explore_figs/*.png
#and those within subfolders of exploratory figures
!data_explore_figs/*/*.png

# ignore stock synthesis files
admodel.cov
admodel.dep
admodel.hes
checkup.sso
*.tmp
console.output.txt
CumReport.sso
derived_posteriors.sso
echoinput.sso
fmin.log
gradient.*
ParmTrace.sso
plots/
plots_StartTime*/
posterior_obj_func.sso
posterior_vectors.sso
posteriors.sso
rebuild.sso
runnumber.ss
SIS_table.sso
ss3.b0*
ss3.bar
ss3.ecm
ss3.eva
ss3.exe
ss3.exe
ss3.log
ss3.mc2
ss3.mcm
ss3.p0*
ss3.r0*
ss3.rep
ss3.std

# rmarkdown / latex files
*.aux
*.log
*.out
*.tex
*.upa
*.upb
*.md
*.pdf
_main.Rmd

# Windows files
*Thumbs.db