Test for functional group stability — diag_stability • atlantisdiagnostics

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

if (FALSE) { # \dontrun{
# 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)
} # }