key_run: Key_Run (Length-based Multispecies Analysis by numerical...

In NOAA-EDAB/LeMANS: length-based multispecies analysis by numerical simulation (LeMANS)

Description

Runs the LeMANS model with the bundled data. Bundled data conist of the 22 species used in the Rochet et al (2011) paper to represent Georges Bank. See rochet_GB_species. The code was adapted directly from MATLAB code used in the Hall et al (2006) and Rochet et al (2011) papers.

Usage

key_run(Ffull, nYrs, modelSetup, parameterValues, initialValues, foodweb,
  species)

Arguments

Ffull	Fishing mortaliy rate for a fully recruited fish
nYrs	Number of years to simulate.
modelSetup	list of parameters required for model (See rochet_GB_modelSetup)
parameterValues	matrix of species specific parameters (See rochet_GB_parameterValues)
initialValues	matrix of initial abundance estimates (See rochet_GB_initialValues)
foodweb	predator prey food web (See rochet_GB_foodweb)
species	matrix of species names and guild membership (See rochet_GB_species)

Value

A list containing:

N	3D array of abundance (numbers of animals). nsizeClass x nSpecies x nTimeSteps
M1	Matrix of M1 mortality ("natural"). nsizeClass x nSpecies
M2	3D array M2 mortality (predation). nsizeClass x nSpecies x nTimeSteps
F	3D array M2 mortality (predation). nsizeClass x nSpecies x nTimeSteps
catch	3D array of catch (numbers of animals). nsizeClass x nSpecies x nTimeSteps
SSB	Matrix of spawning stock biomass (SSB). nSpecies x nYears
recruits	Matrix of recruits (numbers of animals). nSpecies x nYears
suitability	3D array of prey suitability by predator. nsizeClass x nSpecies x (num Pred.size class combinations). See calc_sizepref_suitability
sizePreference	3D array of prey preference by predator. nsizeClass x nSpecies x (num Pred.size class combinations). See calc_sizepref_suitability
ration	Matrix. Amount consumed to account for growth. See calc_phi
growthEfficiency	Matrix of growth efficiencies. See calc_phi
growthProportions	Matrix of proportions. Proportion of individuals that leave each size class in each time step. See calc_phi
maturityProportions	Matrix of maturity proportions. See calc_maturity
modelTimeStep	scalar representing the fraction of a year each time step represents. See calc_phi

Using the Rochet et al data set

The number of size classes and the width of the size class was decided upon a priori. This decision was based on the maximum L_inf among all species. max(Linf) = 148 cm The rochet_GB_initialValues should be set up to represent the number of size classes and width.

The unit of output for Rochet et al data:

catch, N: number of individuals

M1, M2, eF: rates

recruits and SSB: were scaled to common recruit and spawning stock size units (individuals × 10^6 and tonnes × 10^3, respectively)

See Also

plot_key_run, rochet_GB_foodweb, rochet_GB_initialValues, rochet_GB_parameterValues, rochet_GB_species

Examples

## Not run: 
#'# runs the model with bundled data from Rochet et al (2011).
output <- key_run(Ffull=.4,nYrs=50,rochet_GB_modelSetup,rochet_GB_parameterValues,rochet_GB_initialValues,rochet_GB_foodweb,rochet_GB_species)

## End(Not run)

NOAA-EDAB/LeMANS documentation built on Feb. 7, 2021, 11:01 p.m.