diag_cohortBiomass: Test for distribution of biomass over age class

In sgaichas/atlantisdiagnostics: Process Atlantis model output and implements model performance diagnostics

Test for distribution of biomass over age class

Description

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

See Also

Other diagnostics: diag_fleet_catch(), diag_footprints(), diag_maxsize(), diag_persistence(), diag_reasonability(), diag_temp_thresholds()

sgaichas/atlantisdiagnostics documentation built on June 13, 2025, 6:11 a.m.