Test for distribution of biomass over age class
Source:R/diag_cohortBiomass.r
diag_cohortBiomass.RdDetermine 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=1infgsfile)- 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()