write_SS_dat: Read SS dat
In r4atlantis/atlantisom: Generates Data Sets From Atlantis Scenarios

write_SS_dat

R Documentation

Read SS dat

Description

A wrapper function to read in an SS .dat file, modify it to add a catch vector, survey CPUE, CAAL and length comp data from a survey, and age and length comp data from a fishery using the atlantisom functions to take data from atlantis.

Usage

write_SS_dat(
  model_dir,
  datfile_name,
  survey_ts,
  fishery_ts,
  survey_config,
  fishery_config,
  fleets = c(2, 1),
  survey_lencomp,
  fishery_lencomp
)

Arguments

`model_dir`	the directory (relative to inst extdata) your SS files are in
`datfile_name`	the name of your stock synthesis .dat file
`survey_ts`	a data frame with columns `atoutput` and `time` where atoutput is survey CPUE in biomass (tons)
`fishery_ts`	a data frame with columns `atoutput` and `time` where atoutput is fished catch in biomass (tons)
`survey_config`	the name of your survey config fils
`fishery_config`	the name of your fishery config file
`fleets`	a vector corresponding to the index of your fishing fleet followed by the index of your survey fleet
`survey_lencomp`	output from the atlantisom `calc_age2length()` function for the survey
`fishery_lencomp`	output from the atlantisom `calc_age2length()` function for the fishery