new_spatq_setup: Set up inputs for spatq model

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

Set up inputs for spatq model

Description

Checks that data, parameters, and map are consistent then puts them in a list for use by prepare_adfun

Usage

new_spatq_setup(data, parameters, map, random)

spatq_setup(
  catch_df,
  spatq_spec,
  index_step,
  init_fixef = TRUE,
  mesh_resolution = "coarse",
  ...
)

Arguments

data	Data for spatq model, as produced by prepare_data
parameters	Parameter list as from prepare_pars
map	Map list as from prepare_map
random	Random vector as from prepare_random
catch_df	Data frame with catch observations, as from read_catch
spatq_spec	Model specification from specify_estimated
index_step	Index grid step size create_index_df
init_fixef	Use parameter estimates from model with only fixed effects as initial values?
mesh_resolution	Mesh resolution to pass to generate_mesh. Must be "coarse", "medium", or "fine".
...	Additional arguments to pass to init_fixef, which are then passed to spatq_fit for the fixed effect model fit

Value

A spatq_setup object ready to be used to construct a spatq objective function

Functions

• spatq_setup: Convenient constructor for model setups

Author(s)

John K Best

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