Gadget3 renewal actions

Add renewal / initialconditions to a g3 model

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(stock, num_f, wgt_f, run_f = ~cur_time == 0L,
        run_at = g3_action_order$initial)

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(stock, num_f, wgt_f, run_f = ~TRUE,
        run_at = g3_action_order$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 <= total_steps ),
        run_at = g3_action_order$initial)

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

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).(age).init

\(M\)

M argument, by default model parameter named (stock).(age).M

\(F_{0}\)

init_F argument, by default model parameter named (stock).(age).M

\(a_{0}\)

recage argument, by default model parameter named recage

p

proportion argument, by default 1

g3a_initialconditions / g3a_renewal / 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

As g3a_initialconditions / g3a_renewal, but the following formulae 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

As g3a_initialconditions / g3a_renewal, but the following formulae are used to calculate abundance (\(N\)) and mean weight (\(W\)):

$$n = e^{-(\frac{L - \mu}{\mu * {CV}})^2 / 2}$$ $$N = F 10000 \frac{n}{\sum n}$$ $$W = \alpha L^{\beta}$$

\(L\)

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

See also

https://gadget-framework.github.io/gadget2/userguide/chap-stock.html#sec:stockinitial, https://gadget-framework.github.io/gadget2/userguide/chap-stock.html#sec:stockrenew, https://gadget-framework.github.io/gadget2/userguide/chap-other.html#chap-other, g3_stock

Examples

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",]))