diag_fleet_catch: Test fleet catch

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

Test fleet catch

Description

diag_fleet_catch determines whether the simulated fleets catcht the right magnitude and spatial distribution of catch over the last n years of a run.

Usage

diag_fleet_catch(
  fgs,
  fishery.prm,
  catch.file,
  bgm,
  catch.ref,
  speciesCodes = NULL,
  nYrs = 20,
  min.dist = 100,
  relChangeThreshold = 0.01
)

Arguments

fgs	A character string. Path to location of functional groups file.
fishery.prm	A character string. Path to the fishery definitions file.
catch.file	A character string. Path to catch nc file
bgm	A character string. Path to the bgm file.
catch.ref	A data.frame containing reference catch by fleet data (species|fleet|polygon|ref.value)
speciesCodes	Character vector. A vector of Atlantis species codes in which to test for stability.
nYrs	Numeric scalar. Number of years from the end of the time series that stability must occur.
min.dist	Numeric Scalar. Maximum distance between model and reference center of gravity
relChangeThreshold	Numeric Scalar. Maximum magnitude of relative change of slope (Default = 0.01)

Value

Returns a data frame of all species and how they measure up against the catch by fleet criteria

species	The common name of the species/functional group
fleet	The fleet name from the fisheries file
catch.model	Double. The mean catch in mT over the last nYrs of the model
catch.ref	Double. The reference catch (mT)
cog.x.model	Double. The mean x-coordinate center of gravity from the model
cog.x.ref	Double. The mean x-coordinate center of gravity from the reference
cog.y.model	Double. The mean y-coordinate center of gravity from the model
cog.y.ref	Double. The mean y-coordinate center of gravity from the reference
dist	Double. The mean distance between the center of gravity between the model and reference
catch.magnitude	Logical. Is the relative difference between model and refernece catch within +/- relChangeThreshold?
catch.dist	Logical. Is the distance between center of gravity betwene model and reference less than min.dist?

See Also

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

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