Test for functional group reasonability

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

Examples

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