run: Run all the analysis together
In nwfsc-assess/nwfscDiscardBootstrap: Northwest Fisheries Science Center

View source: R/run.R

run	R Documentation

Run all the analysis together

Description

Run all the analysis together

Usage

run(
  species_name,
  data_grouping,
  len_bins = seq(10, 60, 2),
  age_bins = 1:30,
  catch_data,
  biological_data,
  em_catch_data = NULL,
  save_loc = NULL,
  n_boot = 10000
)

Arguments

`species_name`	Species that you want composition data for. Should match the species names in the WCGOP data.
`data_grouping`	A list of the groupings to apply to the data. The list should formatted as: list(gear_groups, gear_names, fleet_groups, fleet_names, fleet_colname).
`len_bins`	Length composition bins (example: seq(20, 90, 2)).
`age_bins`	Age composition bins (example: 1:50).
`catch_data`	A data frame of WCGOP catch data that includes all species. This data frame will be used to check confidentiality.
`biological_data`	A data frame of WCGOP biological data that includes all species.
`em_catch_data`	A data frame of WCGOP EM catch data that includes all species.
`save_loc`	Directory location to save files.
`n_boot`	Number of bootstraps to run.