diag_reasonability: Test for functional group reasonability

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

Test for functional group reasonability

Description

Inspects each time point. If at any point in time a species falls below or rises above predefined bounds it is flagged. The term "reasonable" is based on survey data when available.

Usage

diag_reasonability(
  fgs,
  biomind,
  initialYr = 1964,
  startYr = 1998,
  speciesCodes = NULL,
  realBiomass,
  useVariance = F,
  nYrs = NULL,
  surveyBounds = c(1, 1),
  initBioBounds = c(0.5, 10)
)

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)
startYr	Numeric Scalar. Year in which the model finishes spin up period. (Default = 1998)
speciesCodes	Character vector. A vector of Atlantis species codes in which to test for reasonableness (Default = NULL, uses all species found in modelBiomass. Species codes should be a subset of the Atlantis species codes
realBiomass	A data frame. biomass time series (from assessments, stock SMART or otherwise) for species. realBiomass should be in long format with column labels (YEAR,variable,value,Code,Species,isFishedSpecies) variable should contain value = "biomass" (Biomass units should be in metric tonnes) and/or "var" if useVariance = T
useVariance	Boolean. If to use variance estimates of biomass (included in realBiomass) (Default = F, reverts to using surveyBounds as upper and lover bounds)
nYrs	Numeric scalar. Number of years from the end of the time series for which reasonableness is checked. (Default = NULL, contemporary period from startYr is used)
surveyBounds	Numeric vector. Size of 1x2 containing the values in which to multiple lower and upper bounds of observed data. For example (Default = c(1,1)) indicating use of min and max of observed biomass
initBioBounds	Numeric vector. Size of 1x2 containing lower and upper bound proportions used to scale initial biomass. This is used for groups/species that dont have surveys

Value

Returns a data frame of species

species	The common name of the species/functional group as described in Atlantis input file
code	Atlantis Code for species/functional group
initialBiomass	Starting value of Biomass for species/functional group. From model output
minBiomass	The smallest value of biomass observed in the run
maxBiomass	The largest value of biomass observed in the run
propInitiBio	The maxBiomass as a proportion of the inintial biomass
propBelowLower	Magnitude of lower bound excedence as a proportion of lower threshold
propAboveUpper	Magnitude of upper bound excedence as a proportion of upper threshold
maxExceedance	max of propBelowLower and propAboveUpper
t1	The first year reasonableness was not met
tn	The last year reasonableness was not met
nts	The total number of years that reasonableness was not met
modelSkill	Measure of the goodness of fit
nObs	number of observations used in the goodness of fit
pass	Boolean. Indicates if the Atlantis group passed reasonability
test	Character. Indicate how pass was determined. If the Atlantis species is fished and the species is a stand alone species in the model then survey data is used to assess reasonability. Otherwise deviations from initial biomass is used

See Also

Other diagnostics: diag_cohortBiomass(), diag_fleet_catch(), diag_footprints(), diag_maxsize(), diag_persistence(), 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","functionalGroups.csv")

# read in survey biomass and convert to metric tons
realBiomass <- readRDS(paste0(dataDir,"sweptAreaBiomassNEUS.rds")) %>%
      dplyr::filter(variable %in% c("tot.biomass")) %>%
      dplyr::mutate(value=ifelse(grepl("kg$",units),value/1000,value)) %>%
      dplyr::select(-units)

# Perform reasonability test on all species/groups using the last 20 years of the run.
# Allow species with data to be bounded by 100 x max observed biomass and 1 x min observed biomass.
# For species without data allow model biomass to lie between 0.5 and 2 times initial biomass

diag_reasonability(fgs, biomind, initialYr = 1964, realBiomass=realBiomass,
surveyBounds = c(1,100), initBioBounds = c(0.5,2))

# Only perform test on herring and white hake.
diag_reasonability(fgs, biomind, initialYr = 1964, speciesCodes =c("MAK","WHK"),
 realBiomass=realBiomass, surveyBounds = c(1,100), initBioBounds = c(0.5,2))

## End(Not run)

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