Package index • BayesERtools

Step 1: Develop ER models

Linear model

dev_ermod_bin() dev_ermod_lin(): Develop linear ER model for binary or continuous endpoint

dev_ermod_bin_exp_sel() dev_ermod_lin_exp_sel(): Exposure metrics selection for linear ER models

dev_ermod_bin_cov_sel() dev_ermod_lin_cov_sel(): Perform covariate selection for linear ER model

Emax model

dev_ermod_emax() dev_ermod_bin_emax(): Develop Emax model for continuous and binary endpoint

dev_ermod_emax_exp_sel() dev_ermod_bin_emax_exp_sel(): Exposure metrics selection for Emax models

Step 2: Simulate responses

sim_er(): Simulate from ER model

sim_er_new_exp() sim_er_curve(): Simulate from ER model at specified exposure values

sim_er_new_exp_marg() sim_er_curve_marg(): Calculate marginal expected response for specified exposure values

calc_ersim_med_qi(): Calculate median and quantile intervals from ersim object

Step 3: Plot ER

plot_er(): Plot ER model simulations

plot_er_gof(): Default GOF plot for ER model

plot_er_exp_sel(): Plot exposure metric selection comparison

Step 4: Model evaluation

eval_ermod(): Evaluate exposure-response model prediction performance

loo(): Efficient approximate leave-one-out cross-validation (LOO)

kfold() extract_kfold_loo(): Run k-fold cross-validation

Other post-processing functions

Covariate selection

plot_submod_performance() plot_var_ranking(): Plot variable selection performance

Covariate effect forest plot

build_spec_coveff(): Build specifications for covariate effect simulation/visualization

build_spec_coveff_one_variable() replace_spec_coveff(): Customize specifications for covariate effect simulations/visualizations

sim_coveff(): Perform simulation of covariate effects for ER model

plot_coveff(): Visualize the covariate effects for ER model

print_coveff(): Format the covariate effect simulation results for printing

Others

as_draws() as_draws_list() as_draws_array() as_draws_df() as_draws_matrix() as_draws_rvars(): Transform to draws objects

prior_summary(): Summarize the priors used for linear or linear logistic regression models

p_direction(<ermod_bin>): Probability of Direction (pd)

Utility functions

extract_data() extract_mod() extract_var_resp() extract_var_exposure() extract_var_cov() extract_exp_sel_list_model() extract_exp_sel_comp() extract_var_selected(): Extract elements from S3 objects

extract_coef_exp_ci(): Extract credible interval of the exposure coefficient

Data

d_sim_binom_cov d_sim_binom_cov_hgly2: Sample simulated data for exposure-response with binary endpoint.

d_sim_lin: Sample simulated data for exposure-response with continuous endpoint using linear model.

d_sim_emax: Sample simulated data for Emax exposure-response models with covariates.

S3 methods

print(<ermod>) plot(<ermod_bin>) coef(<ermod>) summary(<ermod>): S3 methods for the classes ermod_*

plot(<ersim>) plot(<ersim_med_qi>): S3 methods for the classes ersim_* and ersim_med_qi_*

print(<ermod_exp_sel>) plot(<ermod_exp_sel>): S3 methods for the classes ermod_exp_sel

print(<ermod_cov_sel>) plot(<ermod_cov_sel>): S3 methods for the classes ermod_bin_cov_sel