tinyVASTcontrol: Control parameters for tinyVAST

Description

Control parameters for tinyVAST

Usage

tinyVASTcontrol(
  nlminb_loops = 1,
  newton_loops = 0,
  eval.max = 1000,
  iter.max = 1000,
  getsd = TRUE,
  silent = getOption("tinyVAST.silent", TRUE),
  trace = getOption("tinyVAST.trace", 0),
  verbose = getOption("tinyVAST.verbose", FALSE),
  profile = c(),
  tmb_par = NULL,
  tmb_map = NULL,
  gmrf_parameterization = c("separable", "projection"),
  reml = FALSE,
  getJointPrecision = FALSE,
  calculate_deviance_explained = TRUE,
  run_model = TRUE,
  suppress_nlminb_warnings = TRUE,
  suppress_user_warnings = FALSE,
  get_rsr = FALSE,
  extra_reporting = FALSE,
  use_anisotropy = FALSE,
  sar_adjacency = "queen"
)

Value

An object (list) of class tinyVASTcontrol, containing either default or updated values supplied by the user for model settings

Arguments

nlminb_loops: Integer number of times to call stats::nlminb().
newton_loops: Integer number of Newton steps to do after running stats::nlminb().
eval.max: Maximum number of evaluations of the objective function allowed. Passed to control in stats::nlminb().
iter.max: Maximum number of iterations allowed. Passed to control in stats::nlminb().
getsd: Boolean indicating whether to call TMB::sdreport()
silent: Disable terminal output for inner optimizer?
trace: Parameter values are printed every trace iteration for the outer optimizer. Passed to control in stats::nlminb().
verbose: Output additional messages about model steps during fitting?
profile: Parameters to profile out of the likelihood (this subset will be appended to random with Laplace approximation disabled).
tmb_par: list of parameters for starting values, with shape identical to tinyVAST(...)$internal$parlist
tmb_map: input passed to TMB::MakeADFun as argument map, over-writing the version tinyVAST(...)$tmb_inputs$tmb_map and allowing detailed control over estimated parameters (advanced feature)
gmrf_parameterization: Parameterization to use for the Gaussian Markov random field, where the default separable constructs a full-rank and separable precision matrix, and the alternative projection constructs a full-rank and IID precision for variables over time, and then projects this using the inverse-cholesky of the precision, where this projection allows for rank-deficient covariance.
reml: Logical: use REML (restricted maximum likelihood) estimation rather than maximum likelihood? Internally, this adds the fixed effects to the list of random effects to integrate over.
getJointPrecision: whether to get the joint precision matrix. Passed to sdreport.
calculate_deviance_explained: whether to calculate proportion of deviance explained. See deviance_explained()
run_model: whether to run the model of export TMB objects prior to compilation (useful for debugging)
suppress_nlminb_warnings: whether to suppress uniformative warnings from nlminb arising when a function evaluation is NA, which are then replaced with Inf and avoided during estimation
suppress_user_warnings: whether to suppress warnings from package author regarding dangerous or non-standard options
get_rsr: Experimental option, whether to report restricted spatial regression (RSR) adjusted estimator for covariate responses
extra_reporting: Whether to report a much larger set of quantities via obj$env$report()
use_anisotropy: Whether to estimate two parameters representing geometric anisotropy
sar_adjacency: Whether to use queen or rook adjacency when defining a Simultaneous Autoregressive spatial precision from a sfc_GEOMETRY (default is queen)