om_diet: Generate diet composition data from atlantisom

In r4atlantis/atlantisom: Generates Data Sets From Atlantis Scenarios

Generate diet composition data from atlantisom

Description

#'@description A wrapper function to create survey diet composition data for model 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_diet(
  config = configfile,
  dietfile = file_diet,
  usersurvey = usersurvey_file,
  omlist_ss,
  n_reps = n_reps,
  save = TRUE
)

Arguments

config	file specifying directory with atlantis model outputs and identifying key files
dietfile	A character value, specifying the file name of the DetailedDietCheck.txt output file from Atlantis (or see load_detailed_diet). This file is read with data.table::fread(), so it can be compressed with a .gz suffix, or uncompressed as a .txt file. If is.null(dir), then file_diet can be the full file path or a file in your current working directory, or the file_diet will be appended to dir using file.path.
usersurvey	survey config file in format of /config/usersurvey.R
omlist_ss	output of om_species
n_reps	number of replicate age, length, and weight-at-age compositions 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 a list object containing dataframes of survey diet proportion:

• survObsDiets, list of replicate dataframes of observed survey diets (proportion)

,

Author(s)

Sarah Gaichas

See Also

Other wrapper functions: om_comps(), om_consindex(), 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_comp <- om_comps(usersurvey = here("config/usersurvey.R"),
    userfishery = here("config/fisherycensus.R"),
    omlist_ss = CC3om_sardine,
    n_reps = 1,
    save = TRUE)


## End(Not run)

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