Test for distribution of biomass over age class — diag_cohortBiomass • atlantisdiagnostics

Determine which age classes contain the most biomass and compare to neighboring age classes. A species fails the test if all biomass is contained in either the smallest or largest age class

Usage

diag_cohortBiomass(
  fgs,
  mortality,
  agebiomind,
  speciesCodes = NULL,
  neusPriority,
  fishedSpecies = 2
)

Arguments

fgs: A character string. Path to location of functional groups file.
mortality: A character string. Path to location of Mort.txt file.
agebiomind: A character string. Path to location of AgeBiomIndx file.
speciesCodes: Character vector. A vector of Atlantis species codes in which to test for persistence. (Default = NULL, uses all species with IsTurnedOn=1 in fgs file)
neusPriority: A character string. Path to location of Species Priorities file.
fishedSpecies: Numeric scalar. Filter by how much species are fished. Values = 1 (most), 2, 3, 4 (least) (Default = 2. Only species fished at level <= 2 will be returned)

Value

code: Atlantis species code
status: Boolean indicating whether species passes test
maxCohort: Age class with the highes biomass
stability
priority: Scale defining priority of species in the model, High (H), Low(L)
fishing: Scale defining level of fishing, 1 is highest