stock_areas.RdAdd area dimensions to g3_stock classes
g3_areas(area_names)
g3s_livesonareas(inner_stock, areas)
g3s_areagroup(inner_stock, areagroups)A character vector of area names to use in the model
A g3_stock that we extend with an area dimension
A vector of numeric areas that the stock is part of
A list mapping names to vectors of numeric areas the stock is part of
g3s_livesonareas breaks up a stock by area.
Within a model, areas are only referred to by integer, however if these are named
then that name will be used for report output.
Each area will be defined as a variable in your model as area_x,
allowing you to use names in formulas, e.g. run_f = quote( area == area_x ).
g3_areas is a helper to map a set of names to an integer
Inside a model each area will only be referred to by integer.
g3s_areagroup allows areas to be combined, this is mostly used internally
by g3l_catchdistribution.
A g3_stock with an additional 'area' dimension.
When iterating over the stock, iterate over each area in turn, area will be set to the current integer area.
When intersecting with another stock, only do anything if area is also part of our list of areas.
A g3_stock with an additional 'area' dimension.
When iterating over the stock, iterate over each areagroup in turn, area will be set to the first area in the group.
When intersecting with another stock, only do anything if area is part of one of the groups.
library(magrittr)
# Make a lookup so we can refer to areas by name
area_names <- g3_areas(c('a', 'b', 'c', 'd', 'e'))
stopifnot(area_names == c(a=1, b=2, c=3, d=4, e=5))
# Define a stock with 3 lengthgroups and 3 areas
stock <- g3_stock('name', c(1, 10, 100)) %>%
g3s_livesonareas(area_names[c('a', 'b', 'c')])
# Area variables will be defined, so you can refer to them in formulas:
g3a_migrate(stock, g3_parameterized("migrate_spring"),
run_f = ~area == area_b && cur_step == 2)
#> $`002:name :001`
#> ~{
#> debug_trace("Clear name migration matrix")
#> name__migratematrix[] <- NaN
#> }
#> <environment: 0x55977c88bfd0>
#>
#> $`002:name :002:f43e386b07dca64199ee`
#> ~{
#> debug_label("g3a_migrate: Migration of name")
#> name__postmigratenum[] <- 0
#> name__postmigratewgt[] <- 0
#> for (name__area_idx in seq_along(name__areas)) g3_with(`:=`(area,
#> name__areas[[name__area_idx]]), if (area == area_b &&
#> cur_step == 2) {
#> debug_trace("Fill in any gaps in the migration matrix")
#> if (any(is.nan(name__migratematrix[, name__area_idx]))) {
#> for (name__destarea_idx in seq_along(name__areas)) g3_with(`:=`(dest_area,
#> name__areas[[name__destarea_idx]]), name__migratematrix[[name__destarea_idx,
#> name__area_idx]] <- g3_param("migrate_spring"))
#> name__migratematrix[, name__area_idx] <- g3a_migrate_normalize(name__migratematrix[,
#> name__area_idx], name__area_idx, 1)
#> }
#> debug_trace("Apply migration matrix to current stock")
#> for (name__destarea_idx in seq_along(name__areas)) g3_with(`:=`(dest_area,
#> name__areas[[name__destarea_idx]]), `:=`(migrate_prop,
#> name__migratematrix[[name__destarea_idx, name__area_idx]]),
#> {
#> name__postmigratewgt[, name__destarea_idx] <- ratio_add_vec(name__postmigratewgt[,
#> name__destarea_idx], name__postmigratenum[,
#> name__destarea_idx], name__wgt[, name__area_idx],
#> migrate_prop * name__num[, name__area_idx])
#> name__postmigratenum[, name__destarea_idx] <- name__postmigratenum[,
#> name__destarea_idx] + migrate_prop * name__num[,
#> name__area_idx]
#> })
#> }
#> else {
#> debug_trace("Copy not-migrating stocks")
#> name__postmigratewgt[, name__area_idx] <- name__postmigratewgt[,
#> name__area_idx] + name__wgt[, name__area_idx]
#> name__postmigratenum[, name__area_idx] <- name__postmigratenum[,
#> name__area_idx] + name__num[, name__area_idx]
#> })
#> debug_trace("Switch around __postmigratenum and __num")
#> name__num <- name__postmigratenum
#> name__wgt <- name__postmigratewgt
#> }
#> <environment: 0x5597798ab1a8>
#>
# Use stock_instance to see what the array would look like
g3_stock_instance(stock)
#> area
#> length a b c
#> 1:10 NA NA NA
#> 10:100 NA NA NA
#> 100:Inf NA NA NA
# Define a stock that groups areas into "north" and "south"
stock <- g3_stock('name', c(1, 10, 100)) %>%
g3s_areagroup(list(
north = area_names[c('a', 'b', 'c')],
south = area_names[c('d', 'e')]))
# Use stock_instance to see what the array would look like
g3_stock_instance(stock)
#> area
#> length north south
#> 1:10 NA NA
#> 10:100 NA NA
#> 100:Inf NA NA