set_L: Specify model and parameter configuration for "extra"...

In timjmiller/wham: Woods Hole Assessment Model (WHAM)

Specify model and parameter configuration for "extra" mortality not directly attributed to natural mortality

Description

Specify model and parameter configuration for "extra" mortality not directly attributed to natural mortality

Usage

set_L(input, L)

Arguments

input

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

L

(optional) list specifying "extra" mortality options: model, random effects, initial values, and parameters to fix (see details) L specifies estimation options for "extra" mortality. If NULL, This mortality source is not used. L is a list with the following entries: $model length = n_regions. "extra" mortality model options are: "none" (default) no extra mortality for this region. "constant" estimate a single mean mortality for the region shared across all ages "iid_re" estimate independent random effects over years, for the region "ar1_re" estimate random effect correlated over years, for the region $initial_means Initial/mean L-at-region $sigma_vals Initial standard deviation by region value to use for the L random effects. Values are not used if L$model = "none". $cor_vals Initial correlation values to use for the L random effects. If unspecified all initial values are 0

timjmiller/wham documentation built on June 10, 2025, 7:09 p.m.