Bootstrap uncertainty and summarize WCGOP discard data

Bootstrap uncertainty and summarize WCGOP discard data

do_discard_bootstrap(
  data,
  species_name,
  boot_number,
  gear_groups,
  gear_names,
  fleet_colname,
  fleet_groups,
  fleet_names,
  dir = NULL,
  seed_number = 1,
  rm_em_data = FALSE
)

Arguments

data

A data frame of WCGOP catch data

species_name

species name that should match the name in the ob data file, can be single species or multiple names (e.g. c("Gopher Rockfish", "Black and Yellow Rockfish"))

boot_number

The number of bootstraps to conduct

gear_groups

List of gear types to group together (example: list(c("Bottom Trawl", "Midwater Trawl"), c("Hook & Line", "Pot", "Shrimp Trawl"))).

gear_names

Vector of gear group names (example: c("trawl", "fixed gear")).

fleet_colname

Column to use to determine areas for fleets (example: "r_state.x")

fleet_groups

List of fleet groups to use (example: list(c("WA", "OR", "CA"))).

fleet_names

Vector of fleet names (example: c("coastwide")).

dir

Directory location to save files.

seed_number

The seed number.

rm_em_data

Logical indicating whether EM records should be removed from the observer catch records (OBCatch) data file.

Author

Chantel Wetzel, Allan Hicks, and Jason Jannot