spatq_simsetup: Construct a spatq_setup from a simulated data set

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

Construct a spatq_setup from a simulated data set

Description

Convenience constructor when data follows simulation study directory structure. See also new_spatq_setup.

Usage

spatq_simsetup(
  study,
  repl,
  opmod,
  estmod = NULL,
  sub_df = NULL,
  spec_estd = NULL,
  root_dir = ".",
  max_T = NULL,
  index_step = 5,
  mesh_resolution = "coarse",
  init_fixef = TRUE,
  ...
)

Arguments

study	Simulation study name
repl	Replicate number
opmod	Operating model
estmod	Estimation model
sub_df	Data frame indicating subsampling strategy; see subsample_catch
spec_estd	List of logicals indicating which parameters are to be estimated, as output specify_estimated
root_dir	Directory to load data from
max_T	Last year of data to include
index_step	Step for the index grid
mesh_resolution	Mesh resolution to pass to generate_mesh. Must be "coarse", "medium", or "fine".
init_fixef	Use parameter estimates from model with only fixed effects as initial values?
...	Additional arguments to pass to init_fixef, which are then passed to spatq_fit for the fixed effect model fit

Value

A list with elements data, parameters, map, and random, ready to be used as the arguments to prepare_adfun or passed to spatq_obj

Author(s)

John K Best

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