Package index

Model fitting and tuning

Functions for fitting empirical Bayes models, tuning hyperparameters, and preparing contingency-table inputs.

pvEBayes(): Fit a general-gamma, GPS, K-gamma, KM or efron model for a contingency table.
pvEBayes_tune(): Select hyperparameter and obtain the optimal general-gamma or efron model based on AIC and BIC
estimate_null_expected_count(): Estimate expected null baseline count based on reference row and column
generate_contin_table(): Generate random contingency tables based on a reference table embedded signals,and possibly with zero inflation

Functions for generating posterior draws, computing posterior signal probabilities, and extracting fitted models.

posterior_draws(): Generate posterior draws for each AE-drug combination
get_posterior_prob(): Obtain posterior probability of being a signal
extract_all_fitted_models(): Extract all fitted models from a tuned pvEBayes Object

S3 methods and helper functions for summarizing fitted pvEBayes objects and comparing fitted models.

summary(<pvEBayes>): Summary method for a pvEBayes object
summary_table_pvEBayes(): Obtain a summary table for a pvEBayes object
print(<pvEBayes>): Print method for a pvEBayes object
logLik(<pvEBayes>): Extract log marginal likelihood for a pvEBayes object
AIC(<pvEBayes>): Obtain Akaike Information Criterion (AIC) for a pvEBayes object
BIC(<pvEBayes>): Obtain Bayesian Information Criterion (BIC) for a pvEBayes object

Functions for visualizing fitted pvEBayes models, posterior draws, and posterior signal probabilities.

plot(<pvEBayes>): Plotting method for a pvEBayes object
eyeplot_pvEBayes(): Generate an eyeplot showing the distribution of posterior draws for selected drugs and adverse events
heatmap_pvEBayes(): Generate a heatmap plot visualizing posterior probabilities for selected drugs and adverse events

Example spontaneous reporting system datasets included with the package.

statin2025: FDA statin dataset with 5119 adverse events
statin2025_44: FDA statin dataset with 44 adverse events
statin42: FDA statin dataset with 42 adverse events
gbca2025: FDA GBCA dataset with 1328 adverse events
gbca2025_69: FDA GBCA dataset with 69 adverse events
faers_opioid_mental: FDA opioid dataset with 243 mental-related adverse events
vigi_opioid_mental: VigiBase opioid dataset with 100 mental-related adverse events

pvEBayes-package: A suite of empirical Bayes methods to use in pharmacovigilance.