set_F: Specify configuration for fully-selected fishing mortality
In timjmiller/wham: Woods Hole Assessment Model (WHAM)

set_F

R Documentation

Specify configuration for fully-selected fishing mortality

Description

Specify configuration for fully-selected fishing mortality

Usage

set_F(input, F_opts = NULL)

Arguments

input

list containing data, parameters, map, and random elements (output from wham::prepare_wham_input)

F_opts

(optional) named list of initial values for annual fully-selected fishing mortality and configuration method for estimation.

F_opts specifies a few as well as the effect on the population. Environmental covariate data need not span the same years as the fisheries data. It can be NULL if no environmental data are to be fit. Otherwise, it must be a named list with the following components:

$F: matrix (n_years x n_fleets) of (initial) values for fully-selected fishing morality.
$F_config: integer 1: (default) configure F parameters (on log scale) as an F in the initial year and then deviations from one year to the next, or 2: configure F parameters as (log) annual values.
$F_map: matrix (n_years x n_fleets) of (initial) values for fully-selected fishing morality.
$map_F: Specify whether to fix any fully-selected F parameters, corresponds to map$F_pars. integer matrix (n_years x n_fleets). Use NA to fix parameters and common integers will make those parameters equal. E.g., for a given column (fleet) values NA,1,2,... will fix the first year and estimate other years. Use unique values for all distinct parameters for each year and fleet.