specify_estimated: Specify which parameters to estimate

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

Specify which parameters to estimate

Description

Indicate which parameters should be estimated; conversely, which should be mapped to their initial values. Each argument can be logical, indicating whether both the numbers density, weight per group, and their hyperparameters should be estimated. A list specifying whether the numbers density, weight per group, and hyperparameters (potentially nested inside each specific process).

Usage

specify_estimated(
  beta = TRUE,
  gamma = FALSE,
  omega = FALSE,
  epsilon = FALSE,
  lambda = TRUE,
  eta = FALSE,
  phi = FALSE,
  psi = FALSE,
  kappa_map = NULL,
  aniso = FALSE,
  obs_lik = 0L
)

Arguments

beta	Abundance fixed effects
gamma	Abundance iid random effects
omega	Abundance spatial effects
epsilon	Abundance spatiotemporal effects
lambda	Catchability fixed effects
eta	Catchability iid random effects
phi	Catchability spatial effects
psi	Catchability spatiotemporal effects
kappa_map	Factor vector of length 8 specifying the map for kappa parameters
obs_lik	Observation likelihood. Current options are 0: Poisson-link log-normal and 1: Tweedie

Value

A list with elements for each random effect process and parameter in the spatq model, each with a logical indicating whether it is (TRUE) or is not (FALSE) estimated.

Author(s)

John Best

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