likelihood_understocking: Gadget3 likelihood understocking action

In lentinj/gadget3: Globally-Applicable Area Disaggregated General Ecosystem Toolbox V3

Gadget3 likelihood understocking action

Description

Add rates of understocking in a g3 model to nll

Usage

g3l_understocking(
        prey_stocks,
        power_f = ~2,
        nll_breakdown = FALSE,
        weight = 1e+08,
        run_at = g3_action_order$likelihood)

Arguments

prey_stocks	A list of g3_stock objects to collect catch data for
power_f	A formula representing power coefficient p to use.
nll_breakdown	Should the nll report be broken down by time? TRUE / FALSE
weight	Weighting applied to this likelihood component.
run_at	Integer order that actions will be run within model, see g3_action_order.

Details

The model report will contain nll_understocking__wgt, the results of the formula below. If nll_breakdown is TRUE, this will be an array with one entry per timestep.

Value

g3l_distribution_understocking

An action (i.e. list of formula objects) that will...

1. Sum the total biomass adjustment due to overstocking for each prey according to the formula

   \ell = \sum_{\it time}\sum_{\it areas} \Big(\sum_{\it prey\_stocks} U_{trs} \Big)^p

   Where p is the power coefficient from power_f, U_{trs} is the total biomass adjustment to predator consumtion due to overconsumtion.

Examples

ling_imm <- g3_stock('ling_imm', seq(20, 156, 4)) %>% g3s_age(3, 10)
ling_mat <- g3_stock('ling_mat', seq(20, 156, 4)) %>% g3s_age(5, 15)
lln <- g3_fleet('lln')

likelihood_actions <- list(
  g3l_understocking(list(ling_imm, ling_mat)))

lentinj/gadget3 documentation built on June 12, 2025, 5:46 a.m.