stanza_settings: Detailed control for stanza structure

Description

Define a list of control parameters.

Usage

stanza_settings(
  taxa,
  stanza_groups,
  K,
  d,
  Wmat,
  Amax,
  SpawnX,
  Leading,
  fit_K = c(),
  fit_d = c(),
  fit_phi = vector(),
  Amat = NULL,
  Wmatslope,
  STEPS_PER_YEAR = 1,
  comp_weight = c("multinom", "dir", "dirmult")
)

Value

An S3 object of class "stanza_settings" that specifies detailed model settings related to age-structured dynamics (e.g., stanzas), allowing user specification while also specifying default values

Arguments

taxa: Character vector of taxa included in model.
stanza_groups: character-vector with names corresponding to taxa and elements specifying the multi-stanza group (i.e., age-structured population) for a given taxa
K: numeric-vector with names matching unique(stanza_groups), providing the von Bertalanffy growth coefficient for length
d: numeric-vector with names matching unique(stanza_groups), providing the von Bertalanffy allometric consumption-at-weight (default is 2/3)
Wmat: numeric-vector with names matching unique(stanza_groups), providing the weight-at-maturity relative to asymptotic weight
Amax: numeric-vector with names matching names(stanza_groups), providing the maximum age (in units years) for a given taxon (and the oldest taxon for a given stanza_group is treated as a plus-group)
SpawnX: numeric-vector with names matching unique(stanza_groups), providing the larval vulnerability (density dependence) parameter
Leading: Boolean vector with names matching names(stanza_groups), with TRUE for the taxon for which scale (B or EE) is specified or estimated, where this is then calculated determinstically for other taxa for a given stanza_group
fit_K: Character-vector listing stanza_groups for which K is estimated
fit_d: Character-vector listing stanza_groups for which d is estimated (note that this currently does not work)
fit_phi: Character-vector listing stanza_groups for which the model should estimate annual recruitment deviations, representing nonconsumptive variation in larval survival (e.g., oceanographic advection)
Amat: numeric-vector with names matching unique(stanza_groups), providing the integer age-at-maturity (in units years)
Wmatslope: numeric-vector with names matching unique(stanza_groups), providing the slope at 0.5 maturity for a logistic maturity-at-weight ogive
STEPS_PER_YEAR: integer number of Euler steps per year for calculating integrating individual weight-at-age
comp_weight: method used for weighting age-composition data