prepare_pars: Prepare parameter list

In jkbest2/spatq: Use spatially varying catchability to standardize fishery-dependent data

Prepare parameter list

Description

Prepare a list of parameters of appropriate dimension. Otherwise uninitialized parameter starting values are set to zeros except kappa and tau, which use a correlation range of 50 (half the domain) and marginal variance of 1, tranformed to the kappa and tau parameterization. Initial estimates of fixed effects can be estimated using GLMs with the init_fixef = TRUE argument. This is recommended.

Usage

prepare_pars(data, mesh, init_fixef = FALSE)

Arguments

data	Data list, as from prepare_data
mesh	SPDE mesh
init_fixef	Use GLMs to estimate fixed effect parameters for abundance and catchability in both numbers density and weight per group processes

Value

List with scalar, vector, or matrices of zeros as starting values for optimization

Author(s)

John Best

jkbest2/spatq documentation built on Sept. 22, 2022, 3:22 a.m.