action_predate.RdAdd predation to a g3 model
g3a_predate_catchability_totalfleet(E)
g3a_predate_catchability_numberfleet(E)
g3a_predate_catchability_linearfleet(E)
g3a_predate_catchability_effortfleet(catchability_fs, E)
g3a_predate_catchability_quotafleet(quota_table, E,
sum_stocks = list(),
recalc_f = NULL)
g3a_predate_fleet(fleet_stock, prey_stocks, suitabilities, catchability_f,
overconsumption_f = quote(
logspace_add_vec(stock__consratio * -1e3, 0.95 * -1e3) / -1e3 ),
run_f = ~TRUE, run_at = g3_action_order$predate)
# NB: Deprecated interface, use g3a_predate_fleet with g3a_predate_catchability_totalfleet
g3a_predate_totalfleet(fleet_stock, prey_stocks, suitabilities, amount_f,
overconsumption_f = quote(
logspace_add_vec(stock__consratio * -1e3, 0.95 * -1e3) / -1e3 ),
run_f = ~TRUE, run_at = g3_action_order$predate)g3_stock that describes the harvesting fleet.
List of g3_stocks that maturing stock should move into.
Either a list of stock names to formula objects, with an optional unnamed default option, or a formula object (which is always used).
Each formula should define suitability of a stock, for example
by using g3_suitability_exponentiall50.
A formula generated by one of the g3a_predate_catchability_* functions,
which define the total biomass a fleet is able to catch.
A formula defining total catch a fleet can harvest at the current time/area (totalfleet/numberfleet), or a scaling factor used to define the stock caught (linearfleet/effortfleet/quotafleet).
Either a list of stock names to formula objects, with an optional unnamed default option, or a formula object (which is always used).
A data.frame with 'biomass' and 'quota' columns,
'biomass' a numeric column, an upper bound for total biomass amount, the final value always being Inf.
'quota' being a list of formulas, defining the quota for each, e.g. with g3_parameterized.
Either a list of g3_stock objects to sum when choosing a value from quote_table,
or NULL, in which case choose the quota based on the current prey.
A formula denoting when to recalculate the current quota. For example ~cur_step == 1
will ensure the quota is only recalculated at the beginning of the year.
Equivalent to E passed to g3a_predate_catchability_totalfleet.
Overconsumption rule, a formula that should cap all values in stock__consratio to <= 95
formula specifying a condition for running this action, default always runs.
Integer order that actions will be run within model, see g3_action_order.
g3a_predate_fleet will, given a g3_fleet "predator" and g3_stock prey,
add predation into a model. The behaviour is driven by 2 parameters:
Defines a predator's preference within a prey stock, normally one of the suitability functions, e.g. g3_suitability_exponentiall50
Defines a predator's overall requirements, set with one of the catchability functions, e.g. g3a_predate_catchability_totalfleet
For the definition of each catchability function, see the values section below.
The actions will define the following stock instance variables for each given fleet_stock and prey_stock:
Suitability of (prey_stock) for (fleet_stock), in a prey array. i.e. the result of calculating the formula in suitabilities for the current state of the prey
Biomass of (prey_stock) caught by (fleet_stock), in a prey array
Biomass of all prey caught by (fleet stock), in a fleet array
Biomass of total consumed (prey_stock), in a prey array
Ratio of prey_stock__totalpredate / (current biomass), capped by overconsumption_f
A model can have any number of g3a_predate_* actions, so long as the
calling arguments are different. For instance, run_f = ~age == 5 and
run_f = ~age == 7.
A formula that defines a fleet's desired catch by total biomass (e.g. landings data): $$ \frac{E N_{sl} W_{sl}}{\displaystyle \sum_{\it stocks} \sum_{\it lengths} N_{sl} W_{sl}} $$
E argument, biomass caught by fleet. Generally a g3_timeareadata table containing landings data, with year/step/area/weight columns
Number of stock in length cell
Mean weight of stock in length cell
A formula that defines a fleet's desired catch by total number of stock landed (not the biomass): $$ \frac{E N_{sl}}{\displaystyle \sum_{\it stocks} \sum_{\it lengths} N_{sl}} $$
E argument, numbers caught by fleet. Generally a g3_timeareadata table containing landings data, or a constant quota
Number of stock in length cell
A formula object that defines a linear relationship between desired catch and available biomass: $$ E \Delta t N_{sl} W_{sl} $$
E argument, scaling factor for the stock that is to be caught, per month
length of current timestep in months
Number of stock in length cell
Mean weight of stock in length cell
This is a multi-species extension to linearfleet, allowing differently-parameterized catchability per-stock. Returns a formula object that defines: $$ c_{s} E \Delta t N_{sl} W_{sl} $$
catchability_fs argument for the current stock
E argument, scaling factor for the stock that is to be caught, per month
length of current timestep in months
Number of stock in length cell
Mean weight of stock in length cell
A formula onject that defines catch based on the available biomass of the stock multiplied by a scaling factor set according to a simple harvest control rule: $$ q E \Delta t N_{sl} W_{sl} $$
quota selected from quota_table, corresponding to the total biomass of sum_stocks.
For example, given data.frame(biomass = c(10000, Inf), quota = I(list(g3_parameterized('quota.low'), g3_parameterized('quota.high')))),
'quota.low' will be chosen when total biomass is less than 10000, otherwise 'quota.high' will be used.
E argument, scaling factor for the stock that is to be caught, per month
length of current timestep
Number of stock in length cell
Mean weight of stock in length cell
...if recalc_f is set, this will only be recaculated when true. Any other step will use the previous value.
An action (i.e. list of formula objects) that will...
Zero fleet and prey catch counters
For each prey, collect maximum desired by fleet for all prey, into a prey_stock__predby_predstock variable
After all fleet consumption is done, scale consumption using catchability_f, sum into prey_stock__totalpredate
After all consumption is done, temporarily convert prey_stock__predby_predstock to a proprotion of prey_stock__totalpredate
Calculate prey_stock__consratio (ratio of consumed to available), capping using overconsumption_f. Update prey_stock__num
Recalculate prey_stock__predby_predstock, fleet_stock__catch, post-overconsumption
library(magrittr)
areas <- c(a = 1, b = 2)
ling_imm <- g3_stock(c(species = 'ling', 'imm'), seq(20, 156, 4)) %>% g3s_age(3, 10)
ling_mat <- g3_stock(c(species = 'ling', 'mat'), seq(20, 156, 4)) %>% g3s_age(5, 15)
lln <- g3_fleet('lln') %>% g3s_livesonareas(areas[c('a', 'b')])
# Invent a lln_landings table
lln_landings <- expand.grid(
year = 1999:2000,
step = c(1, 2),
area = areas[c('a', 'b')])
lln_landings$total_weight <- floor(runif(nrow(lln_landings), min=100, max=999))
# g3a_predate_catchability_totalfleet(): Set catch accordings to landings data
predate_action <- g3a_predate_fleet(
lln,
list(ling_imm, ling_mat),
suitabilities = g3_suitability_exponentiall50(by_stock = 'species'),
catchability_f = g3a_predate_catchability_totalfleet(
g3_timeareadata('lln_landings', lln_landings, "total_weight") ))
# g3a_predate_catchability_numberfleet(): Fixed quota of 1000 fish
predate_action <- g3a_predate_fleet(
lln,
list(ling_imm, ling_mat),
suitabilities = g3_suitability_exponentiall50(by_stock = 'species'),
catchability_f = g3a_predate_catchability_numberfleet(
g3_parameterized(
'quota',
value = 1000,
by_predator = TRUE,
scale = 0.5,
optimise = FALSE) ))
attr(suppressWarnings(g3_to_r(list(predate_action))), 'parameter_template')
#> $ling.lln.alpha
#> [1] 0
#>
#> $ling.lln.l50
#> [1] 0
#>
#> $lln.quota
#> [1] 1000
#>