Gadget3 maturity action

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...

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))