dev_ermod_bin_cov_functions: Internal functions for developing an ER model with covariates for binary endpoint

Description

These functions are not intended to be used directly by users.

Usage

.dev_ermod_refmodel(
  data,
  var_resp,
  var_exposure,
  var_cov_candidates,
  verbosity_level = 1,
  chains = 4,
  iter = 2000,
  fun_family = quote(stats::binomial())
)
.select_cov_projpred(
  refm_obj,
  var_exposure,
  var_cov_candidates,
  nterms_max = NULL,
  cv_method = c("LOO", "kfold"),
  k = 5,
  .reduce_obj_size = TRUE,
  validate_search = FALSE,
  verbosity_level = 1
)

Value

.dev_ermod_refmodel(): The reference model object that can be used for variable selection.

.select_cov_projpred(): The selected variables

Arguments

data: Input data for E-R analysis
var_resp: Response variable name in character
var_exposure: Exposure variable names in character
var_cov_candidates: Candidate covariate names in character vector
verbosity_level: Verbosity level. 0: No output, 1: Display steps, 2: Display progress in each step, 3: Display MCMC sampling.
chains: Number of chains for Stan.
iter: Number of iterations for Stan.
fun_family: Family function for the model. Default is binomial.
refm_obj: Reference model object used for variable selection
nterms_max: Maximum number of terms to consider in the model. Default is NULL (all terms are considered).
cv_method: Cross-validation method. Default is "LOO" (recommended). Use "kfold" if you see warnings on Pareto k estimates.
k: Number of folds for kfold CV. Only used if cv_method is "kfold".
.reduce_obj_size: Whether to reduce object size by removing some elements from projpred outputs that are not necessary for the functionality of this package.
validate_search: Whether to validate the search. Default is FALSE. Recommend to set to TRUE for kfold CV. Do not use for LOO (run time would become too long).

Details

.dev_ermod_refmodel() is used to fit the refmodel (full reference model) necessary for projpred

.select_cov_projpred() is used to select variables with projpred package