diag_maxsize: Test for max fish size

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

Test for max fish size

Description

Calculate average size of fish through time and check to see if any fish exceed the user supplied observed maximum size. Both maximum weight and maximum length are used

Usage

diag_maxsize(
  nc,
  bgm,
  init,
  fgs,
  prm_run,
  prm_biol,
  speciesStats,
  speciesCodes = NULL
)

Arguments

nc	A character string. Path to location of main nc file.
bgm	A character string. Path to location of box coordinates bgm file.
init	A character string. Path to location of initial conditions nc file.
fgs	A character string. Path to location of functional groups file.
prm_run	A character string. Path to location of run parameter file file.
prm_biol	A character string. Path to location of biology parameter file.
speciesStats	Data frame. Must contain at least 3 columns labeled code - Atlantis species codes ,maxObsWeight - a value (g) indicating the maximum weight the species should weigh, maxObsLength - a value (cm) indicating the maximum length the species should grow to.
speciesCodes	Character vector. A vector of Atlantis species codes in which to test for large fish. (Default = NULL, uses all species)

Value

Returns a data frame indicating which species meet defined max weight/length criterion.

species	The common name of the species/functional group
code	Atlantis Code for species/functional group
polygon	Polygon in which the largest individual occupies
agecl	Age class of the largest individual
time	Time in which the largest individual was found (Decimal years)
maxLength	Maximum length of species in Atlantis (cm)
maxObsLength	Maximum observed length of species (cm) - from litereature
maxMeanWeight	Maximum mean weight of indivdual in Atlantis (g)
maxObsWeight	Maximum observed weight of species (g) - from litereature
passW	Boolean indicating whether species maximum weight (from Atlantis) falls below max observed weight
ratioW	ratio of atlantis max weight to observed max weight
passL	Boolean indicating whether species maximum length (from Atlantis) falls below max observed length
ratioL	ratio of atlantis max length to observed max length

See Also

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

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