stock: Gadget3 stock storage

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

Gadget3 stock storage

Description

Define multi-dimensional storage for use in models, mostly to contain state about stocks.

Usage

g3_stock(var_name, lengthgroups, open_ended = TRUE)

g3_stock_instance(stock, init_value = NA, desc = "")

g3_fleet(var_name)

g3_stock_def(stock, name)

g3s_clone(inner_stock, var_name)

g3_is_stock(stock)

Arguments

var_name	Prefix used for all instance variables of this stock. Can have multiple parts that will be concatentated together, see example.
lengthgroups	Vector defining length groups, each entry defining the minimum value.
open_ended	If TRUE, final lengthgroups value defines a group x:Inf. If FALSE, final lengthgroups value is the upper bound for the previous group.
inner_stock	A g3_stock or g3_fleet object to clone.
stock	A g3_stock or g3_fleet. For g3_stock_def, can also be a list of stock objects.
init_value	Intially the array will be filled with this constant, e.g. 1, 0 or NaN
desc	Description of the array that will be included in models
name	Name of definition to extract, e.g. "minlen".

Value

g3_stock

A g3_stock with length groups

g3_stock_instance

An array with dimensions matching the stock.

g3_fleet

A g3_stock without length groups

g3_stock_def

The definition of the given variable in the stock. If stock is a list, then a list with the definition of each will be returned.

g3s_clone

A g3_stock with identical dimensions to inner_stock but with a new name.

g3_is_stock

TRUE iff stock is a g3_stock object.

Examples

# Define a stock with 3 lengthgroups
stock <- g3_stock('name', c(1, 10, 100))

# Define a stock with a multi-part name. We can then dig out species name
stock <- g3_stock(c(species = 'ling', 'imm'), c(1, 10, 100))
stopifnot( stock$name == 'ling_imm' )
stopifnot( stock$name_parts[['species']] == 'ling' )

# Use stock_instance define storage for mean weight of stock,
# has dimensions matching what was defined above.
g3_stock_instance(stock, 1, "Mean weight")

# Can get definitions for multiple stocks in one go
stocks <- list(
  imm = g3_stock(c('st', 'imm'), 1:10),
  mat = g3_stock(c('st', 'mat'), 1:10) )
g3_stock_def(stocks, 'minlen')

# Retrieve the upperlen for the stock
g3_stock_def(stock, 'upperlen')

# Define a stock, not-open-ended. Now only 2 groups long
stock <- g3_stock('name', c(1, 10, 100), open_ended = FALSE)

# Use stock_instance to see what the array would look like
g3_stock_instance(stock)

# Fleets don't have lengthgroups
stock <- g3_fleet('name') %>% g3s_livesonareas(1)

# Use stock_instance to see what the array would look like
g3_stock_instance(stock)

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