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
diag_persistence(
fgs,
biomind,
speciesCodes = NULL,
nYrs = NULL,
floor = 0.1,
display = NULL,
tol = 1e-06
)A character string. Path to location of functional groups file.
A character string. Path to the BiomIndx.txt file.
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)
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)
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
Boolean. Flag to indicate whether to return only species that pass the test, fail the test, or all species (Default = NULL)
Numeric scalar. Tolerance level to add to biomass floor (Default = 1E-6)
Returns a data frame of species which do not meet defined persistence criteria.
The common name of the species/functional group
Atlantis Code for species/functional group
Starting value of Biomass for species/functional group
The smallest value of biomass observed in the run
The time step in which minimumBiomass occurred
The proportion of initial biomass at tminimumBiomass
The first time step persistence was not met
The last time step persistence was not met
The total number of time steps that persistence was not met
Boolean. Indicates if the Atlantis group passed persistence test
Other diags:
diag_fleet_catch(),
diag_reasonability(),
diag_stability()
if (FALSE) { # \dontrun{
# 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)
} # }