diag_stability: Test for functional group stability

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

Test for functional group stability

Description

diag_stability determines whether the model reaches a steady state over the last n years of a run. Stability is loosely defined as a species/groups biomass reaching a stable level (measured as having tolerable trend in a defined time range).

Usage

diag_stability(
  fgs,
  biomind,
  initialYr = 1964,
  speciesCodes,
  nYrs = 20,
  relChangeThreshold = 0.01
)

Arguments

fgs	A character string. Path to location of functional groups file.
biomind	A character string. Path to the BiomIndx.txt file.
initialYr	Numeric Scalar. Year in which the model run was initiated. (Default = 1964)
speciesCodes	Character vector. A vector of Atlantis species codes in which to test for stability. (Default = NULL, uses all species found in modelBiomass)
nYrs	Numeric scalar. Number of years from the end of the time series that stability must occur. (Default = 20 years)
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 stability criterion

code	Atlantis Code for species/functional group
species	The common name of the species/functional group
t1Fit	Value of fitted biomass for the first of year data used in the fit
mtPerYear	Double. The value of the slope parameter (year)
relChange	Rate of increase relative to t1Fit(mtPerYear/t1Fit)
aveBio	mean biomass for the last nYrs years
pass	Logical. Does the species/group pass the test for stability

Details

Formally the following model is fit to the last n years of the run:

biomass_t = \mu + \beta.t + \epsilon_t where \epsilon_t ~ IID N(0,\sigma^2)

where null hypothesis,

H0:\beta=0

Note: annual biomass is used in fitting. Species with mean annual biomass < 1 metric ton over the last n years of the run are not considered stable. They are reported to Fail the test and NaNs returned

Examples

## Not run: 
# Declare paths to files required

biomind <- paste("Full path to file","xxxBiomIndx.txt")
fgs <- paste("Full path to file","functioalGgroups.csv")

# Perform stability test on all species/groups using the last 20 years of the run
diag_stability(fgs, biomind, nYrs = 20)

# Only perform test on herring and white hake.
# Require stability over the last 10 years of the run and and use a
# relative change in the slope = 0.01 as the criterion for pass or fail
diag_stability(fgs,biomind, speciesCodes=c("HER","WHK"), nYrs = 10, relChangeThreshold = 0.01)

## End(Not run)

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