Add maturity actions to a g3 model

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,
        bounded = TRUE,
        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.

bounded

Should the maturity ratio be bounded to 0..1? Set TRUE if maturity is producing negative numbers of individuals.

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_stocks 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 current step as a proportion of the year, e.g. 0.25. See cur_step_size in g3a_time

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...

  1. Move any maturing individuals into temporary storage, stock__transitioning_num / stock__transitioning_wgt

  2. 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))