Create Diet Table

Generic function for creating diet tables from model data.

Usage

create_diet_table(x, ...)

Arguments

x

Object containing diet/bio data

...

Additional arguments

Value

A data.frame representing the diet table with predator-prey relationships

Details

In Atlantis model, the availability of prey is determined by the product of the prey biomass and the prey choice coefficient pPREY. The latter is a proportion (between 0 and 1) of prey biomass actually available to the predator. The function finds this information in the model and creates the diet table that is the collection of the pPREY values.

Atlantis distinguishes prey choice values for juveniles and adults. The distinction exists if species have ontogenetic stages and if the flag age_structured_prey_XXX is set to one. Note that for those species the first mature age group is given by XXX_age_mat. Therefore there are up to 4 pPREY values per prey-predator combination:

• pPREY1XXX1: juvenile-juvenile

• pPREY1XXX2: juvenile-adult

• pPREY2XXX1: adult-juvenile

• pPREY2XXX2: adult-adult where XXX denotes the code for the prey species. Note that the realised diet in Atlantis will depend on other factor, for instance the coeficient mum, assuming it is used by the functional response (see predcase_XXXX).

References

• Asta Audzijonyte, Rebecca Gorton, Isaac Kaplan, Jacob M. Kasper, Elizabeth A. Fulton, 2025. Atlantis User’s Guide Part I: General Overview, Physics & Ecology https://research.csiro.au/atlantis/wp-content/uploads/sites/52/2025/05/AtlantisUserGuide_PartI.pdf

Examples

my_model <- new_atlantis() |>
  atlantis_load_files(
    c(
      system.file("examples", "inputs", "tiny.bgm", package = "atlantio"),
      system.file("examples", "inputs", "tiny_biol.prm", package = "atlantio"),
      system.file("examples", "inputs", "tiny_groups.csv", package = "atlantio")
    )
  )