tinyVASTcontrol {tinyVAST} | R Documentation |
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,
get_rsr = FALSE,
extra_reporting = FALSE,
use_anisotropy = FALSE
)
Arguments
nlminb_loops |
Integer number of times to call |
newton_loops |
Integer number of Newton steps to do after running
|
eval.max |
Maximum number of evaluations of the objective function
allowed. Passed to |
iter.max |
Maximum number of iterations allowed. Passed to |
getsd |
Boolean indicating whether to call |
silent |
Disable terminal output for inner optimizer? |
trace |
Parameter values are printed every |
verbose |
Output additional messages about model steps during fitting? |
profile |
Parameters to profile out of the likelihood (this subset will be appended to |
tmb_par |
list of parameters for starting values, with shape identical
to |
tmb_map |
input passed to TMB::MakeADFun as argument |
gmrf_parameterization |
Parameterization to use for the Gaussian Markov
random field, where the default |
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 |
calculate_deviance_explained |
whether to calculate proportion of deviance
explained. See |
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 |
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
|
use_anisotropy |
Whether to estimate two parameters representing geometric anisotropy |
Value
An object (list) of class tinyVASTcontrol
, containing either default or
updated values supplied by the user for model settings