Key_Run (Length-based Multispecies Analysis by numerical Simulation)

Source: R/key_run.R

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.

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)

Examples

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