diag_persistence: Test for functional group persistence

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

Test for functional group persistence

Description

Inspects each time point. If at any point in time a species falls below a predefined floor it is flagged. The floors are specifies as a proportion of initial biomass. The last n years of the run are used in the test

Usage

diag_persistence(
  fgs,
  biomind,
  speciesCodes = NULL,
  nYrs = NULL,
  floor = 0.1,
  display = NULL,
  tol = 1e-06
)

Arguments

fgs	A character string. Path to location of functional groups file.
biomind	A character string. Path to the BiomIndx.txt 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)
nYrs	Numeric scalar. Number of years from the end of the time series that persistence must occur. (Default = NULL, persistence must occur throughout entire time series)
floor	Numeric scalar. Proportion of initial biomass for which for which all species are measured against. (Default = 0.1, all species need to be above 10% of initial biomass). Range should be 0-1
display	Boolean. Flag to indicate whether to return only species that pass the test, fail the test, or all species (Default = NULL)
tol	Numeric scalar. Tolerance level to add to biomass floor (Default = 1E-6)

Value

Returns a data frame of species which do not meet defined persistence criteria.

species	The common name of the species/functional group
code	Atlantis Code for species/functional group
initialBiomass	Starting value of Biomass for species/functional group
minimumBiomass	The smallest value of biomass observed in the run
tminimumBiomass	The time step in which minimumBiomass occurred
proportionInitBio	The proportion of initial biomass at tminimumBiomass
t1	The first time step persistence was not met
tn	The last time step persistence was not met
nts	The total number of time steps that persistence was not met
pass	Boolean. Indicates if the Atlantis group passed persistence test

See Also

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

Examples

## Not run: 

# Declare paths to files required
biomind <- paste("Full path to file","xxxBiomIndx.txt")
fgs <- paste("Full path to file","functioalGgroups.csv")

# find all species that do not have biomass > 0 for any time during the run.
diag_persistence(fgs,biomind,speciesCodes=NULL, nYrs = NULL, floor = 0)

# only evaluate herring. Require stability over the last 10 years of the run and all values should
# exceed 10% of initial biomass
diag_persistence(fgs,biomind, speciesCodes="HER", nYrs = 10, floor = 0.1)


## End(Not run)

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