om_index: Generate index data from atlantisom

In r4atlantis/atlantisom: Generates Data Sets From Atlantis Scenarios

Generate index data from atlantisom

Description

#'@description A wrapper function to create survey and fishery index data for assessment input. 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_index(
  usersurvey = usersurvey_file,
  userfishery = userfishery_file,
  omlist_ss,
  n_reps = n_reps,
  save = TRUE
)

Arguments

usersurvey	survey config file in format of /config/usersurvey.R
userfishery	fishery config file in format of /config/fisherycensus.R
omlist_ss	output of om_species
n_reps	number of replicate indices to be generated
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:

• survObsBiomB, list of replicate dataframes of observed survey biomass (tons)

• fishObsCatchB, list of replicate dataframes of observed fishery catch (tons)

,

Author(s)

Sarah Gaichas

See Also

Other wrapper functions: om_comps(), om_consindex(), om_diet(), 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.