Commonly used:
data.R
model.R
output.R
report.R
report.Rmd
utilities.R
Variations:
data_construct.R
data_export.R
data_maturity.R
data_survey.R
report_plots.R
report_tables.R
utilities_data.R
utilities_model.R
utilities_output.R
Required:
data/
catage.csv
maturity.csv
natmort.csv
wstock.csv
wcatch.csv
Survey indices should be saved as survey_{survey name}.csv, for example:
data/
survey_frgfs.csv
survey_ibtsq1.csv
survey_ibtsq3.csv
Additional:
data/
datage.csv
wdiscards.csv
latage.csv
wlandings.csv
propf.csv
propm.csv
Files containing the full age range if the assessment uses a plus group, can be
recorded using the suffix _full:
data/
catage_full.csv
wcatch_full.csv
datage_full.csv
wdiscards_full.csv
latage_full.csv
wlandings_full.csv
wstock_full.csv
Required:
output/
fatage.csv
natage.csv
qatage_ibtsq1.csv
qatage_ibtsq2.csv
summary.csv
If catches, and / or landings, discards and survey indices are estimated, these
can be recorded, using the suffix _est:
output/
catage_est.csv
datage_est.csv
latage_est.csv
survey_ibtsq1_est.csv
survey_ibtsq3_est.csv
Commonly used:
last_advice.csv
summary.csv
surveys_all.csv
Variations:
catch.csv
cpue.csv
survey.csv