self_test: Perform self-test simulation and estimation of a fitted WHAM...

In timjmiller/wham: Woods Hole Assessment Model (WHAM)

Perform self-test simulation and estimation of a fitted WHAM model

Description

Generate simulated data from fitted model and refit the model to the simulated data

Usage

self_test(
  fit_RDS = NULL,
  n = 10,
  seeds = NULL,
  which_seeds = NULL,
  conditional = TRUE,
  map_change = NULL,
  do_parallel = TRUE,
  n_cores = NULL,
  res_dir = NULL,
  wham_location = NULL,
  test_dir = NULL,
  save_inputs = FALSE
)

Arguments

fit_RDS	(required) location of RDS file with fitted WHAM model.
n	the number of simulated data sets to create and fit. Default = 10.
seeds	(optional) vector of seeds to use to generate each simulated data set.
which_seeds	(optional) which seeds to use for simualted data set. Useful if doing self test in stages.
conditional	T/F whether to fix rather than simulate estimated random effects. Deafult = TRUE.
map_change	(optional) list of input$map elements for altering mapping assumptions of fitted model.
do_parallel	T/F whether to do self-test fits in parallel. Requires snowfall and parallel packages to be installed. Default = TRUE.
n_cores	(optional) the number of cores to use for parallel fitting.
res_dir	directory where to save individual files for each self test fit. Useful if doing self test in stages. If not provided, no files will be saved.
wham_location	(optional) location of WHAM package. Useful if not using the WHAM installation in the standard library location.
test_dir	(optional) directory for package repository. To be used when the function is being called during package testing rather than an installed version of WHAM.
save_inputs	T/F whether to save the simulated inputs in res_dir. Default = FALSE.

Value

a list of two elements. First is the results which is a list (length = n) of lists with 6 elements: minimized negative log-likelihood, MLEs, gradient, SSB, F, abundance at age. Second element is the vector of seeds used for self-test simulations.

See Also

fit_wham

timjmiller/wham documentation built on Feb. 4, 2025, 10:31 p.m.