action_renewal: Gadget3 renewal actions

Description

Add renewal / initialconditions to a g3 model

Usage

g3a_renewal_vonb_recl(
        Linf = g3_parameterized('Linf', value = 1, by_stock = by_stock),
        K = g3_parameterized('K', value = 1, by_stock = by_stock),
        recl = g3_parameterized('recl', by_stock = by_stock),
        recage = g3_parameterized('recage', by_stock = FALSE, optimise = FALSE),
        by_stock = TRUE)
g3a_renewal_vonb_t0(
        Linf = g3_parameterized('Linf', value = 1, by_stock = by_stock),
        K = g3_parameterized('K', value = 1, by_stock = by_stock),
        t0 = g3_parameterized('t0', by_stock = by_stock),
        by_stock = TRUE)
g3a_renewal_initabund(
    scalar = g3_parameterized('init.scalar', value = 1, by_stock = by_stock),
    init = g3_parameterized('init', value = 1, by_stock = by_stock, by_age = TRUE),
    M = g3_parameterized('M', by_stock = by_stock, by_age = TRUE),
    init_F = g3_parameterized('init.F', by_stock = by_stock_f),
    recage = g3_parameterized('recage', by_stock = FALSE, optimise = FALSE),
    proportion_f = ~1,
    by_stock = TRUE,
    by_stock_f = FALSE)
############################# g3a_initialconditions
g3a_initialconditions_normalparam(
        stock,
        factor_f = g3a_renewal_initabund(by_stock = by_stock),
        mean_f = g3a_renewal_vonb_t0(by_stock = by_stock),
        stddev_f = g3_parameterized('init.sd', value = 10,
            by_stock = by_stock, by_age = by_age),
        alpha_f = g3_parameterized('walpha', by_stock = wgt_by_stock),
        beta_f = g3_parameterized('wbeta', by_stock = wgt_by_stock),
        age_offset = quote( cur_step_size ),
        by_stock = TRUE,
        by_age = FALSE,
        wgt_by_stock = TRUE,
        run_f = ~cur_time == 0L,
        run_at = g3_action_order$initial)
g3a_initialconditions_normalcv(
        stock,
        factor_f = g3a_renewal_initabund(by_stock = by_stock),
        mean_f = g3a_renewal_vonb_t0(by_stock = by_stock),
        cv_f = g3_parameterized('lencv', by_stock = by_stock, value = 0.1,
            optimise = FALSE),
        alpha_f = g3_parameterized('walpha', by_stock = wgt_by_stock),
        beta_f = g3_parameterized('wbeta', by_stock = wgt_by_stock),
        age_offset = quote( cur_step_size ),
        by_stock = TRUE,
        by_age = FALSE,
        wgt_by_stock = TRUE,
        run_f = ~cur_time == 0L,
        run_at = g3_action_order$initial)
############################# g3a_renewal
g3a_renewal_normalparam(
        stock,
        factor_f = g3_parameterized('rec',
            by_stock = by_stock,
            by_year = TRUE,
            scale = g3_parameterized(
                name = 'rec.scalar',
                by_stock = by_stock),
            ifmissing = g3_parameterized(
                name = 'rec.proj',
                optimise = FALSE,
                by_stock = by_stock )),
        mean_f = g3a_renewal_vonb_t0(by_stock = by_stock),
        stddev_f = g3_parameterized('rec.sd', value = 10, by_stock = by_stock),
        alpha_f = g3_parameterized('walpha', by_stock = wgt_by_stock),
        beta_f = g3_parameterized('wbeta', by_stock = wgt_by_stock),
        by_stock = TRUE,
        wgt_by_stock = TRUE,
        run_age = quote(stock__minage),
        run_projection = TRUE,
        run_step = 1,
        run_f = NULL,
        run_at = g3_action_order$renewal)
g3a_renewal_normalcv(
        stock,
        factor_f = g3_parameterized('rec',
            by_stock = by_stock,
            by_year = TRUE,
            scale = g3_parameterized(
                name = 'rec.scalar',
                by_stock = by_stock),
            ifmissing = g3_parameterized(
                name = 'rec.proj',
                optimise = FALSE,
                by_stock = by_stock )),
        mean_f = g3a_renewal_vonb_t0(by_stock = by_stock),
        cv_f = g3_parameterized('lencv', by_stock = by_stock, value = 0.1,
            optimise = FALSE),
        alpha_f = g3_parameterized('walpha', by_stock = wgt_by_stock),
        beta_f = g3_parameterized('wbeta', by_stock = wgt_by_stock),
        by_stock = TRUE,
        wgt_by_stock = TRUE,
        run_age = quote(stock__minage),
        run_projection = TRUE,
        run_step = 1,
        run_f = NULL,
        run_at = g3_action_order$renewal)
############################# g3a_otherfood
g3a_otherfood(
        stock,
        num_f = g3_parameterized('of_abund', by_year = TRUE, by_stock = by_stock,
            scale = g3_parameterized(
                'of_abund.step', value = 1, by_step = TRUE, by_stock = by_stock),
            ifmissing = "of_abund.proj" ),
        wgt_f = g3_parameterized('of_meanwgt', by_stock = by_stock),
        by_stock = TRUE,
        force_lengthvector = !any(grepl("__midlen$", all.vars(num_f))),
        run_f = quote( cur_time <= total_steps="" ),="" run_at="g3_action_order$initial)
g3a_otherfood_normalparam(
        stock,
        factor_f = g3_parameterized(
            'of_abund', by_year = TRUE, by_stock = by_stock,
            scale = g3_parameterized(
                'of_abund.step', value = 1, by_step = TRUE, by_stock = by_stock),
            ifmissing = "of_abund.proj" ),
        mean_f = g3a_renewal_vonb_t0(by_stock = by_stock),
        stddev_f = g3_parameterized('init.sd', value = 10,
            by_stock = by_stock, by_age = by_age),
        alpha_f = g3_parameterized('walpha', by_stock = wgt_by_stock),
        beta_f = g3_parameterized('wbeta', by_stock = wgt_by_stock),
        by_stock = TRUE,
        by_age = FALSE,
        wgt_by_stock = TRUE,
        run_f = quote( cur_time <= total_steps="" ),="" run_at="g3_action_order$initial)
g3a_otherfood_normalcv(
        stock,
        factor_f = g3_parameterized(
            'of_abund', by_year = TRUE, by_stock = by_stock,
            scale = g3_parameterized(
                'of_abund.step', value = 1, by_step = TRUE, by_stock = by_stock),
            ifmissing = "of_abund.proj" ),
        mean_f = g3a_renewal_vonb_t0(by_stock = by_stock),
        cv_f = g3_parameterized('lencv', by_stock = by_stock, value = 0.1,
            optimise = FALSE),
        alpha_f = g3_parameterized('walpha', by_stock = wgt_by_stock),
        beta_f = g3_parameterized('wbeta', by_stock = wgt_by_stock),
        by_stock = TRUE,
        by_age = FALSE,
        wgt_by_stock = TRUE,
        run_f = quote( cur_time

Value

g3a_renewal_vonb_recl

A formula object representing $$ L_{\infty} (1 - e^{-\kappa (a - a_{0} + \frac{\log(1 - L_{0}/L_{\infty})}{\kappa} )}) $$

$L_{\infty}$: Linf argument, by default model parameter named (stock).Linf
$\kappa$: K argument, by default model parameter named (stock).K
$L_{0}$: recl argument, by default model parameter named (stock).recl
$a_{0}$: recage argument, by default model parameter named recage

NB: g3a_initialconditions_normalparam will replace $a$ with $a - \Delta{t}$, see age_offset

g3a_renewal_vonb_t0

A formula object representing $$ L_{\infty} (1 - e^{-\kappa (a - t_{0}) }) $$

$L_{\infty}$: Linf argument, by default model parameter named (stock).Linf
$\kappa$: K argument, by default model parameter named (stock).K
$t_{0}$: t0 argument, by default model parameter named (stock).t0

NB: g3a_initialconditions_normalparam will replace $a$ with $a - \Delta{t}$, see age_offset

g3a_renewal_vonb

An alias for g3a_renewal_vonb_recl()

g3a_renewal_initabund

A formula object representing $$ p s_{0} s_{a} e^{-1 (M + F_{0}) (a - a_{0})} $$

$s_{0}$: scalar argument, by default model parameter named (stock).init.scalar
$s_{a}$: init argument, by default model parameter named (stock).init.(age)
$M$: M argument, by default model parameter named (stock).M.(age)
$F_{0}$: init_F argument, by default model parameter named init.F
$a_{0}$: recage argument, by default model parameter named recage
p: proportion argument, by default 1

g3a_otherfood

An action (i.e. list of formula objects) that will, for the given stock, iterate over each area/age/etc. combination, and generate a lengthgroup vector of new individuals and weights using num_f and wgt_f.

renewal will add fish to the existing stock, whereas initialconditions & otherfood will replace any previous values.

g3a_initialconditions_normalparam / g3a_renewal_normalparam / g3a_otherfood_normalparam

An action (i.e. list of formula objects) that will, for the given stock, iterate over each area/age/etc. combination, and generate new individuals.

The following formulas are used to calculate abundance ($N$) and mean weight ($W$):

$$n = {dnorm}(L, \mu, \sigma)$$ $$N = F 10000 \frac{n}{\sum n}$$ $$W = \alpha L^{\beta}$$

$L$: Midlength of all length groups for current area/age/...
$F$: factor_f argument, by default output of g3a_renewal_initabund
$\mu$: mean_f argument, by default output of g3a_renewal_vonb_t0
$\sigma$: stddev_f argument, by default model parameter named (stock).(init|rec).sd
$\alpha$: alpha_f argument, by default model parameter named (stock).walpha
$\beta$: beta_f argument, by default model parameter named (stock).wbeta

g3a_initialconditions_normalcv / g3a_renewal_normalcv / g3a_otherfood_normalcv

An action (i.e. list of formula objects) that will, for the given stock, iterate over each area/age/etc. combination, and generate new individuals.

The following formulas are used to calculate abundance ($N$) and mean weight ($W$):

$$n = {dnorm}(L, \mu, \mu * {CV})$$ $$N = F 10000 \frac{n}{\sum n}$$ $$W = \alpha L^{\beta}$$

$L$: Midlength of all length groups for current area/age/...
$F$: factor_f argument, by default output of g3a_renewal_initabund
$\mu$: mean_f argument, by default output of g3a_renewal_vonb_t0
$CV$: cv_f argument, by default model parameter named (stock).lencv
$\alpha$: alpha_f argument, by default model parameter named (stock).walpha
$\beta$: beta_f argument, by default model parameter named (stock).wbeta

Arguments

stock: The g3_stock to apply to
num_f: formula that produces a lengthgroup vector of number of individuals for the current age/area/... length group.
wgt_f: formula that produces a lenghgroup vector of mean weight for the current age/area/... length group.
run_at: Integer order that actions will be run within model, see g3_action_order.
factor_f,mean_f,stddev_f,alpha_f,beta_f: formula substituted into normalparam calcuations, see below.
cv_f: formula substituted into normalcv calcuations, basically stddev_f = mean_f * cv_f, see below.
age_offset: Replace age with age - age_offset in mean_f. Used to simulate initialconditions at time "-1".
force_lengthvector: Should we assume that num_f is a constant, and needs repeating enough times to turn into a length vector?
run_age: Age to run renewals for, used as age == (run_age) into default run_f
run_projection: Boolean. Run renewal in projection years? If false adds !cur_year_projection into default run_f
run_step: Which step to perform renewal in, or NULL for continuous renewal. Adds cur_step == (run_step) into default run_f
run_f: formula specifying a condition for running this action, For initialconditions defaults to first timestep. For renewal, the default is a combination of run_age, run_step & run_projection. For otherfood, the default is to always run, apart from when the model is ending.
Linf,K,t0,recl: formula substituted into vonb calcuations, see below.
recage: formula substituted into initial abundance and vonb calcuations, see below.
proportion_f,scalar,init,M,init_F: formula substituted into initial abundance calcuations, see below.
by_stock,wgt_by_stock,by_stock_f,by_age: Controls how parameters are grouped, see g3_parameterized

Details

All of the following actions will renew stock in a model. The differences are when and what they apply to by default:

g3a_initialconditions_*: Will run at the start of the model, building an inital state of all ages
g3a_renewal_*: Will run at every step but only for the minimal age, adding new recruits as an alternative to g3a_spawn()
g3a_otherfood_*: Will run at every step, replacing the previous state, creating a non-dynamic stock for predators to consume

Specifying the quantities and mean-weights in each case works identically.

A model can have any number of g3a_renewal_* actions, so long as the calling arguments are different. For instance, run_f = ~age == 5 and run_f = ~age == 7.

The g3a_renewal_* actions will define the following stock instance variables for stock:

stock__renewalnum: Extra individuals added to the stock
stock__renewalwgt: Mean weight of added individuals

Examples

Run this code

library(magrittr)
stocks <- list(
    imm = g3_stock(c('ling', maturity = "imm"), seq(10, 100, 10)) %>% g3s_age(3, 7),
    mat = g3_stock(c('ling', maturity = "mat"), seq(10, 100, 10)) %>% g3s_age(5, 10) )

actions <- list(
    g3a_time(2000, 2000),
    g3a_initialconditions_normalcv(stocks$imm),
    g3a_initialconditions_normalcv(stocks$mat),
    NULL)
model_fn <- g3_to_r(c(actions, list(
    g3a_report_detail(actions) )))
attr(model_fn, 'parameter_template') |>
    g3_init_val("init.F", 0.4) |>
    g3_init_val("ling_imm.Linf", 80) |>
    g3_init_val("ling_mat.Linf", 160) |>
    g3_init_val("ling_*.K", 90) |>
    g3_init_val("ling_*.t0", 0) |>
    g3_init_val("ling_*.lencv", 0.1) |>
    g3_init_val("ling_imm.init.#", 3:7 * 100) |>
    g3_init_val("ling_mat.init.#", 5:10 * 200) |>
    g3_init_val("ling_*.init.scalar", 200) |>
    g3_init_val("ling_*.walpha", 2.275e-06) |>
    g3_init_val("ling_*.wbeta", 3.2020) |>
    g3_init_val("ling_*.M.#", 0.15) |>
    identity() -> params.in
r <- model_fn(params.in)

g3_array_plot(attr(r, "dstart_ling_imm__num")[,,time=1])
g3_array_plot(attr(r, "dstart_ling_mat__num")[,,time=1])

## Plots
par(mar = c(4,2,2,1), cex.main = 1)
curve(g3_eval(g3a_renewal_vonb_t0(Linf = 20, K = 0.8, t0 = 0), age = x),
    0, 10, col = 2, xlab = "age", main = "g3a_renewal_vonb_t0(Linf = 20, K = 0.8..1.4, t0 = 0)")
curve(g3_eval(g3a_renewal_vonb_t0(Linf = 20, K = 1.0, t0 = 0), age = x),
    0, 10, col = 1, add = TRUE)
curve(g3_eval(g3a_renewal_vonb_t0(Linf = 20, K = 1.2, t0 = 0), age = x),
    0, 10, col = 3, add = TRUE)
curve(g3_eval(g3a_renewal_vonb_t0(Linf = 20, K = 1.4, t0 = 0), age = x),
    0, 10, col = 4, add = TRUE)

## Otherfood
# "Otherfood" stocks are defined in a similar manner to any other stock
# Note that _normalparam & _normalcv need both length & age dimensions
other_wgt <- g3_stock('other_wgt', 0)
other_cv <- g3_stock('other_cv', seq(50, 100, by = 10)) %>% g3s_age(5,10)

actions <- list(
    g3a_time(2000, 2010),
    # Will get other_wgt.of_abund.1998.1, other_wgt.of_meanwgt parameters
    g3a_otherfood(other_wgt),
    # Use standard vonB parameters (Linf/K/t0) to define abundance
    g3a_otherfood_normalcv(other_cv),
    NULL)
model_fn <- g3_to_r(c(actions, list(
    g3a_report_detail(actions) )))
attr(model_fn, 'parameter_template') |>
    g3_init_val("other_cv.Linf", 80) |>
    g3_init_val("other_cv.K", 90) |>
    g3_init_val("other_cv.t0", 0) |>
    g3_init_val("other_cv.of_abund.#", 100:110) |>
    g3_init_val("other_wgt.of_abund.#", 100:110) |>
    g3_init_val("other_wgt.of_abund.step.#", 1) |>
    g3_init_val("other_cv.of_abund.proj", 80) |>
    g3_init_val("other_wgt.of_abund.proj", 70) |>
    g3_init_val("project_years", 5) |>
    identity() -> params.in
r <- model_fn(params.in)

g3_array_plot(t(attr(r, "dstart_other_wgt__num")))
g3_array_plot(t(attr(r, "dstart_other_cv__num")[,age="age7",]))

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