Gadget3 stock storage — stock • gadget3

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

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")
#> length
#>    1:10  10:100 100:Inf 
#>       1       1       1 
#> attr(,"desc")
#> [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')
#> $imm
#>    1:2    2:3    3:4    4:5    5:6    6:7    7:8    8:9   9:10 10:Inf 
#>      1      2      3      4      5      6      7      8      9     10 
#> attr(,"class")
#> [1] "force_vector" "integer"     
#> 
#> $mat
#>    1:2    2:3    3:4    4:5    5:6    6:7    7:8    8:9   9:10 10:Inf 
#>      1      2      3      4      5      6      7      8      9     10 
#> attr(,"class")
#> [1] "force_vector" "integer"     
#> 

# Retrieve the upperlen for the stock
g3_stock_def(stock, 'upperlen')
#> [1] Inf

# 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)
#> length
#>   1:10 10:100 
#>     NA     NA 

# 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)
#> area
#> area1 
#>    NA