suit_formulas: Functions to assemble suitability function lines for writing...

In inspktrgadget/gadgetSim: Create Gadget replicates for use in simulation studies

Description

To specify consumption for either prey or fleets Gadget requires suitability information to be displayed in a certain manner (see Section 4.9 in Gadget User Guide). These functions will output the correct format for each respective suitability type. These functions are meant to be used in conjunction when putting together Gadget stocks or fleets.

Usage

make_constant_suit(fleet, stock, params = list("alpha"), param_names = NULL)

make_straightline_suit(fleet, stock, params = list("alpha", "beta"),
  param_names = NULL)

make_exponential_suit(fleet, stock, params = list("alpha", "beta", "gamma",
  "delta"), param_names = NULL)

make_exponentiall50_suit(fleet, stock, params = list("alpha", "l50"),
  param_names = NULL)

make_richards_suit(fleet, stock, params = as.list(paste0("p", 0:4)),
  param_names = NULL)

make_andersen_suit(fleet, stock, params = as.list(paste0("p", 0:4)),
  param_names = NULL)

make_andersenfleet_suit(fleet, stock, params = as.list(paste0("p", 0:5)),
  param_names = NULL)

make_gamma_suit(fleet, stock, params = list("alpha", "beta", "gamma"),
  param_names = NULL)

make_fleet_suit(fleet = "comm", stock = NULL, fun = "exponentiall50",
  params = NULL, param_names = NULL)

Arguments

fleet	Character. The name of the fleet. Used to name switches for suitability parameters
stock	Character. The name of the stock to serve as the prey
params	Optional. List of parameter names as either character vectors or numbers. If character values are given, switches will be returned as function parameters. If numbers are given, then the respective arguments to the functions will be fixed.
param_names	Optional. Character to use to name the params. This is of use if there is more than one stock for the fleet, but the same selectivity curve is desired

Value

A character vector of function information pasted together in a format ready for writing to Gadget file.

Examples

make_exponential_suit("comm", "cod")
make_gamma_suit("spr", "cod")

# include multiple stocks
make_exponential_suit("comm", stock = c("immature", "mature"))
# fix a function
make_constant_suit("spr", "cod", params = 1)

# or more generally
make_fleet_suit("comm", "cod", fun = "exponentiall50",
                params = list("alpha", "l50"))

inspktrgadget/gadgetSim documentation built on May 10, 2019, 9:51 a.m.