dev_ermod_bin_cov_functions {BayesERtools} | R Documentation |
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()),
prior = rstanarm::default_prior_coef(stats::binomial()),
prior_intercept = rstanarm::default_prior_intercept(stats::binomial()),
prior_aux = rstanarm::exponential(autoscale = TRUE)
)
.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
)
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. |
prior , prior_intercept , prior_aux |
|
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
Value
.dev_ermod_refmodel()
: The reference model object that can be used
for variable selection.
.select_cov_projpred()
: The selected variables