R: Gadget3 maturity action

action_mature {gadget3}

R Documentation

Gadget3 maturity action

Description

Add maturity actions to a g3 model

Usage

g3a_mature_continuous(
        alpha = g3_parameterized('mat.alpha', by_stock = by_stock),
        l50 = g3_parameterized('mat.l50', by_stock = by_stock),
        beta = 0,
        a50 = 0,
        by_stock = TRUE)

g3a_mature_constant(alpha = NULL, l50 = NA, beta = NULL, a50 = NA, gamma = NULL, 
    k50 = NA)

g3a_mature(stock, maturity_f, output_stocks, output_ratios = rep(1/length(output_stocks), 
    times = length(output_stocks)), run_f = ~TRUE,
    run_at = g3_action_order$grow,
    transition_at = g3_action_order$mature)

Arguments

`alpha`	A formula to substitute for `\alpha`.
`l50`	A formula to substitute for `l_{50}`. Must be defined if `alpha` is defined.
`beta`	A formula to substitute for `\beta`.
`a50`	A formula to substitute for `a_{50}`. Must be defined if `beta` is defined.
`gamma`	A formula to substitute for `\gamma`.
`k50`	A formula to substitute for `k_{50}`. Must be defined if `gamma` is defined.
`by_stock`	Change the default parameterisation (e.g. to be by 'species'), see `g3_parameterized`.
`stock`	`g3_stock` to mature.
`maturity_f`	A maturity formula, as defined by `g3a_mature_constant`.
`output_stocks`	List of `g3_stock`s that maturing `stock` should move into.
`output_ratios`	Vector of proportions for how to distribute into `output_stocks`, summing to 1, default evenly spread.
`run_f`	formula specifying a condition for running this action, default always runs.
`run_at`	Integer order that actions will be run within model, see `g3_action_order`.
`transition_at`	Integer order that transition actions will be run within model, see `g3_action_order`.

Details

Generally you would use g3a_growmature, which does both growth and maturity at the same time.

A model can have any number of g3a_mature actions, so long as the calling arguments are different. For instance, run_f = ~age == 5 and run_f = ~age == 7.

Value

g3a_mature_continuous

A formula object representing

m_0 * (\alpha \Delta{L} + \beta \Delta{t})^\top

m_0: The g3a_mature_constant formula, as defined below, using parameters supplied to g3a_mature_continuous
\Delta{L}: Vector of all possible changes in length, as per current growth matrix (see g3a_grow_impl_bbinom)
\Delta{t}: Length of the current timestep

g3a_mature_constant

A formula object with the following equation

\frac{1}{ 1 + e^{-\alpha(l - l_{50}) -\beta(a - a_{50}) -\gamma(k - k_{50})}}

l: length of stock
l_{50}: length of stock when 50% are mature
a: age of stock
a_{50}: age of stock when 50% are mature
k: weight of stock
k_{50}: weight of stock when 50% are mature

g3a_mature

An action (i.e. list of formula objects) that will, for the given stock...

Move any maturing individuals into temporary storage, stock__transitioning_num / stock__transitioning_wgt
Move the contents of the temporary storage into output_stocks

Examples

ling_imm <- g3_stock('ling_imm', seq(20, 156, 4))
ling_mat <- g3_stock('ling_mat', seq(20, 156, 4))

# Maturity for immature ling
maturity_action <- g3a_mature(ling_imm,
    maturity_f = g3a_mature_continuous(),
    output_stocks = list(ling_mat))

[Package gadget3 version 0.12-1 Index]