Initialize list of age structured group (stanza) parameters for dynamic simulation

Creates a list of stanza indices and parameters to be used by rsim.run.

Usage

rsim.stanzas(Rpath.params, state, params)

Arguments

Rpath.params: R object containing the parameters needed to create a Rpath model. This is generated either by the create.rpath.params() or read.rpath.params() functions.
state: List object of state variables generated by rsim.state.
params: Rsim parameter object generated by rsim.params.

Value

a list of 21 objects:

Nsplit, number of model groups with stanzas
Nstanzas, numeric vector length Nsplit+1, leading 0 for indexing followed by the number of age groups for each model group with stanzas
EcopathCode, numeric matrix of Rpath group numbers with Nsplit+1 species rows and Nstanzas+1 age group columns, first column and row empty for indexing
Age1, numeric matrix of age in months of first age group with Nsplit+1 species rows, first column and row empty for indexing, second column earliest age in months (0), third column max age in months
Age2, numeric matrix of age in months of last age group with Nsplit+1 species rows, first column and row empty for indexing, second column earliest age in months, third column max age in months
baseWageS, numeric matrix with rows of monthly weight relative to weight at infinity (Winf) calculated in rpath.stanzas with Nsplit+1 species columns
baseNageS, numeric matrix with rows of monthly numbers surviving, calculated in rpath.stanzas with Nsplit+1 species columns
baseQageS, numeric matrix with rows of monthly consumption, calculated as WageS^VBGFd in rpath.stanzas with Nsplit+1 species columns
Wmat, numeric vector length Nsplit+1, leading 0 for indexing followed by weight at 50% maturity relative to Winf for each model group with stanzas
RecPower, numeric vector length Nsplit+1, leading 0 for indexing followed by recruitment power parameter for each model group with stanzas
recruits, numeric vector length Nsplit+1, leading 0 for indexing followed by recruits per spawner entered as input to rpath.stanzas
VBGFd, numeric vector length Nsplit+1, leading 0 for indexing followed by von Bertalanffy d (default = 2/3) for each model group with stanzas
RzeroS, numeric vector length Nsplit+1, leading 0 for indexing followed by recruits per spawner entered as input to rpath.stanzas
vBM, numeric vector length Nsplit+1, leading 0 for indexing followed by von Bertalanffy growth coefficient for each model group with stanzas
SplitAlpha, numeric matrix of initial monthly (rows) growth coefficients for each model group with stanzas (Nsplit+1 species columns)
SpawnX, numeric vector length Nsplit+1, leading 0 for indexing followed by relative strength of spawner-recruit relationship for each model group with stanzas, currently set to 10000, no relationship
SpawnEnergy, numeric vector length Nsplit+1, leading 0 for indexing followed by relative energy going to recruitment rather than growth for each model group with stanzas, currently set to 1
baseEggsStanza, numeric vector length Nsplit+1, leading 0 for indexing followed by initial estimate of egg output for each model group with stanzas
baseSpawnBio, numeric vector length Nsplit+1, leading 0 for indexing followed by initial estimate of spawning biomass (=egg output) for each model group with stanzas
RscaleSplit, numeric vector length Nsplit+1, leading 0 for indexing followed by adult to juvenile metric scaling parameter for each model group with stanzas, currently set to 1
baseStanzaPred, numeric vector length NUM_GROUPS+1, base consumption (sum of QageS*NageS) for each model group with stanzas in full model group order; 0s entered for non-stanza groups

Examples

# Read in Rpath parameter file and generate model object
Rpath <- rpath(REco.params)
# Create default dynamic parameters from Rpath model
Rsim.params <- rsim.params(Rpath)
# Create state vectors with default values
Rsim.state <- rsim.state(Rsim.params)
# Create stanza object
Rsim.stanzas <- rsim.stanzas(REco.params, Rsim.state, Rsim.params)