tests/testthat/helper-functionbuild.R

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

root_dir <- normalizePath(system.file("testdata", package = "spatq"))

spec_design <- spatq_simstudyspec("qdevscaling",
  repl = 1,
  opmod = 6,
  estmod = "design",
  root_dir = root_dir
)
setup_design <- spatq_simsetup(
  study = "qdevscaling",
  repl = 1,
  opmod = 6,
  estmod = "design",
  root_dir = root_dir,
  max_T = 15
)
obj_design <- spatq_obj(setup_design)
fit_design <- fit_spatq(obj_design)
rep_design <- report_spatq(obj_design)
sdr_design <- sdreport_spatq(obj_design)

estd <- specify_estimated(
  beta = TRUE, gamma = FALSE,
  omega = TRUE, epsilon = TRUE,
  lambda = TRUE, eta = FALSE,
  phi = FALSE, psi = FALSE
)
obj <- make_sim_adfun(
  study = "qdevscaling",
  repl = 1,
  opmod = 6,
  sub_df = data.frame(
    vessel_idx = 2,
    n = 500
  ),
  root_dir = normalizePath(
    system.file("testdata", package = "spatq")
  ),
  max_T = 15,
  spec_estd = estd,
  index_step = 5,
  runSymbolicAnalysis = TRUE,
  normalize = TRUE,
  silent = TRUE
)

## Fixed-effect only model
estd_f <- specify_estimated()
obj_f <- make_sim_adfun(
  study = "qdevscaling",
  repl = 1,
  opmod = 6,
  estmod = NULL,
  root_dir = normalizePath(
    system.file("testdata", package = "spatq")
  ),
  max_T = 15,
  spec_estd = estd_f,
  index_step = 5,
  ## Can't use Metis if no random effects
  runSymbolicAnalysis = FALSE,
  normalize = TRUE,
  silent = TRUE
)

## Tweedie with fixed effects
twf_estd <- specify_estimated(
  beta = TRUE, lambda = TRUE,
  obs_lik = 1L
)
twf_setup <- spatq_simsetup(
  study = "qdevscaling",
  repl = 1,
  opmod = 6,
  root_dir = normalizePath(
    system.file("testdata", package = "spatq")
  ),
  max_T = 5,
  index_step = 50,
  spec_estd = twf_estd
)
twf_obj <- spatq_obj(twf_setup)
twf_fit <- fit_spatq(twf_obj)

## Tweedie with random effects
tw_estd <- specify_estimated(
  beta = TRUE, gamma = FALSE,
  omega = TRUE, epsilon = TRUE,
  lambda = TRUE, eta = FALSE,
  phi = TRUE, psi = FALSE,
  kappa_map = c(1, NA, 1, NA, 1, NA, NA, NA),
  aniso = TRUE,
  obs_lik = 1L
)
tw_setup <- spatq_simsetup(
  study = "qdevscaling",
  repl = 1,
  opmod = 6,
  root_dir = normalizePath(
    system.file("testdata", package = "spatq")
  ),
  max_T = 15,
  index_step = 5,
  spec_estd = tw_estd,
  init_fixef = TRUE
)
tw_obj <- spatq_obj(tw_setup)