om_consindex: Generate predator total consumption index data from...

In r4atlantis/atlantisom: Generates Data Sets From Atlantis Scenarios

Generate predator total consumption index data from atlantisom

Description

#'@description A wrapper function to create predator consumption index data for assessment input This is total consumption of all prey combined in tons by predator species. Generates true total consumption and saves as interim step (optionally adds to om_list). Takes the output of om_species. Wrapper can generate replicates. Saves output as .rds Results for more than one survey are generated with multiple survey config files and saved as separate .rds files.

Usage

om_consindex(
  usersurvey = usersurvey_file,
  omlist_ss,
  n_reps = n_reps,
  save = TRUE
)

Arguments

usersurvey	survey config file in format of /config/usersurvey.R
omlist_ss	output of om_species
n_reps	number of replicate indices to be generated
userfishery	fishery config file in format of /config/fisherycensus.R
A	logical value specifying if the function should save the output to the disk or not. The default is TRUE.

Value

Returns list objects containing dataframes of survey biomass index and total catch:

• survObsConsB, list of replicate dataframes of observed survey consumption (tons)

,

Author(s)

Sarah Gaichas

See Also

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

Examples

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

CC3om_sard_ind <- om_index(usersurvey = here("config/usersurvey.R"),
    userfishery = here("config/fisherycensus.R"),
    omlist_ss = CC3om_sardine,
    n_reps = 5,
    save = TRUE)

## End(Not run)

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