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.gitignore
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.gitignore
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.Rproj.user
.Rhistory
.RData
.Ruserdata
# remove raw data as could be confidential
data/raw/*
!data/raw/README.md
# M Head doesn't want us to share the maturity data
SST_maturitydata_forassessment03152023.csv
# remove exploratory plots, can be generated is interested
outputs/plots/exploratory/*
# remove intermediate .RMarkdown LaTeX compilation files
*.tex
!doc/*.tex
*.log
# Mac hidden files
.DS_store
.ds_store
# Intermediate RMarkdown Files
*/unnamed-chunk*
# SS Model Files
model/*/plots*/* # Dont track SS plots
admodel.* # These are ADMB outputs
ss*.b0* # ADMB binary file output
ss.b01
ss.b02
ss.b03
ss.b04
ss.b05
ss*.p0*
ss.p0*
ss*.r0*
ss.r0*
*.cov
*.dep
*.hes
data_boot_001.ss
/*/run/ss.b0* # ADMB binary file output
/*/run/ss.p0* # ADMB binary file output
/*/run/ss.r0* # ADMB binary file output
*.bar
*.eva
*.cor
*.std
*.ss_new
!data_echo.ss_new
posterior_vector*.sso
posterior*.sso
rebuild.sso
runnumber.ss
# Ignore most outputs from likelihood profiles
model/Sensitivity_Anal/5.8_Francis_Reweighting_2/1_23.model.francis_2_profile*/*
model/Sensitivity_Anal/5.8_Francis_Reweighting_2/1_23.model.francis_2_jitter*/*
model/Sensitivity_Anal/5.8_Francis_Reweighting_2/1_23.model.francis_2_retro*/*
model/Sensitivity_Anal/Base_Model/profiles/*
model/Sensitivity_Anal/Base_Model/jitters/*
model/Sensitivity_Anal/Base_Model/retros/*
# Ignore plots
# JPEG
*.jpg, *.jpeg, *.jpe, *.jif, *.jfif
# Portable Network Graphics
*.png
!doc/*.png
!doc/FinalFigs/Base/*.png
!doc/FinalFigs/Intro/*.png
!doc/FinalFigs/Data/*.png
!doc/FinalFigs/Sensitivities/Growth/*.png
!doc/FinalFigs/Sensitivities/Landings/*.png
!doc/FinalFigs/Sensitivities/Maturity/*.png
!doc/FinalFigs/Sensitivities/Selectivity/*.png
!doc/FinalFigs/Sensitivities/Retention/*.png
!doc/FinalFigs/Sensitivities/Surveys/*.png
!doc/FinalFigs/bridging/*.png
!doc/FinalFigs/Jitters/*.png
!doc/FinalFigs/Profiles/*.png
!doc/FinalFigs/Retros/*.png
!model/Sensitivity_Anal/5.8_Francis_Reweighting_2/1_23.model.francis_2_profile*/*.png
!model/Sensitivity_Anal/5.8_Francis_Reweighting_2/1_23.model.francis_2_profile*/*.csv
!model/Sensitivity_Anal/5.8_Francis_Reweighting_2/1_23.model.francis_2_jitter*/*.png
!model/Sensitivity_Anal/5.8_Francis_Reweighting_2/1_23.model.francis_2_jitter*/*.csv
!model/Sensitivity_Anal/5.8_Francis_Reweighting_2/1_23.model.francis_2_retro*/*.png
!model/Sensitivity_Anal/5.8_Francis_Reweighting_2/1_23.model.francis_2_retro*/*.csv
!model/Sensitivity_Anal/Base_Model/profiles/*.png
!model/Sensitivity_Anal/Base_Model/profiles/*.csv
!model/Sensitivity_Anal/Base_Model/jitters/*/*.png
!model/Sensitivity_Anal/Base_Model/jitters/*/*.csv
!model/Sensitivity_Anal/Base_Model/retros/*/*.png
!model/Sensitivity_Anal/Base_Model/retros/*/*.csv
# Tagged Image File Format
*.tiff, *.tif
# BMP
*.bmp, *.dib
# Ignore the .html from the model directories
model/*/run/plots
model/*/*/*/run/plots
doc/_main.pdf