om_species: Species-specific atlantisom outputs

In r4atlantis/atlantisom: Generates Data Sets From Atlantis Scenarios

Species-specific atlantisom outputs

Description

A wrapper function to reduce a set of atlantisom objects from atlantis output to a single species or subset of species for creating assessment input datasets. Optionally includes diet data (set diet=TRUE in function call, default is FALSE)

Usage

om_species(species = spp, omlist, save = TRUE, removefullom = TRUE)

Arguments

species	The species to sample in the survey and fishery (a vector)
omlist	output of om_init

Value

Returns an omlist_ss list object containing dataframes and lists:

• species_ss, species name(s)

• code_ss, species code from funct.groups

• truetotbio_ss, dataframe output of load_bioind, species_ss only

• truecatchbio_ss, dataframe output of load_catch, species_ss only

• YOY_ss, dataframe young of year output, code_ss only

• truenums_ss, numbers at age output of run_truth, species_ss only

• truebio_ss, biomass at age output of run_truth, species_ss only

• truebiopool_ss, biomass pool groups output of run_truth, species_ss only

• trueresn_ss, reserve nitrogen output of run_truth, species_ss only

• truestructn_ss, structural nitrogen output of run_truth, species_ss only

• truecatchnum_ss, fishery catch at age output of run_truth, species_ss only

• truecons_ss, total consumption output of run_truth, species_ss only

• truecatchtons_ss, fishery catch by fleet output of run_truth, code_ss only

• truedisctons_ss, fishery discard by fleet output of run_truth, code_ss only

• truenumsage_ss, true numbers at annual age output of run_truth, species_ss only

• truecatchage_ss, fishery catch at annual age output of run_truth, species_ss only

• truediscage_ss, fishery discard at annual age output of run_truth, species_ss only

• funct.groups_ss, dataframe of species characteristics, species_ss only

• biol, list of biological parameters passed from input omlist

• boxpars, dataframe of spatial parameters

• runpar, list of run parameters passed from input omlist

,

Author(s)

Sarah Gaichas

See Also

Other wrapper functions: om_comps(), om_consindex(), om_diet(), om_index(), om_init()

Examples

## Not run: 
# assuming CC3om is output of om_init(here("config/CC3config.r"))
CC3om_sardine <- om_species(c("Pacific_sardine"), CC3om)

CC3om_2spp <- om_species(c("Pacific_sardine", "Mesopel_M_Fish"), CC3om)

## End(Not run)

r4atlantis/atlantisom documentation built on Nov. 12, 2023, 2:59 a.m.