Package: pvEBayes 0.3.0

Yihao Tan

pvEBayes: Empirical Bayes Methods for Pharmacovigilance

A suite of empirical Bayes methods to use in pharmacovigilance. Contains various model fitting and post-processing functions. For more details see Tan et al. (2025) <doi:10.1002/sim.70195>, <doi:10.48550/arXiv.2512.01057>; Koenker and Mizera (2014) <doi:10.1080/01621459.2013.869224>; Efron (2016) <doi:10.1093/biomet/asv068>.

Authors:Yihao Tan [aut, cre], Marianthi Markatou [aut], Saptarshi Chakraborty [aut], Raktim Mukhopadhyay [aut]

pvEBayes_0.3.0.tar.gz
pvEBayes_0.3.0.zip(r-4.7)pvEBayes_0.3.0.zip(r-4.6)pvEBayes_0.3.0.zip(r-4.5)
pvEBayes_0.3.0.tgz(r-4.6-x86_64)pvEBayes_0.3.0.tgz(r-4.6-arm64)pvEBayes_0.3.0.tgz(r-4.5-x86_64)pvEBayes_0.3.0.tgz(r-4.5-arm64)
pvEBayes_0.3.0.tar.gz(r-4.7-arm64)pvEBayes_0.3.0.tar.gz(r-4.7-x86_64)pvEBayes_0.3.0.tar.gz(r-4.6-arm64)pvEBayes_0.3.0.tar.gz(r-4.6-x86_64)
pvEBayes_0.3.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
pvEBayes/json (API)

# Install 'pvEBayes' in R:

install.packages('pvEBayes', repos = c('https://ropensci.r-universe.dev', 'https://cloud.r-project.org'))

Reviews:rOpenSci Software Review #760

Bug tracker:https://github.com/ropensci/pvebayes/issues

Pkgdown/docs site:https://docs.ropensci.org

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

faers_opioid_mental - FDA opioid dataset with 243 mental-related adverse events
gbca2025 - FDA GBCA dataset with 1328 adverse events
gbca2025_69 - FDA GBCA dataset with 69 adverse events
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
vigi_opioid_mental - VigiBase opioid dataset with 100 mental-related adverse events

On CRAN:

pharmacovigilance cpp

4.98 score 3 scripts 612 downloads 11 exports 55 dependencies

Last updated from:c8b5cd8925 (on main). Checks:2 FAIL, 12 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	FAIL	463
linux-devel-x86_64	FAIL	497
pkgdown docs	OK	255
source / vignettes	OK	232
linux-release-arm64	OK	192
linux-release-x86_64	OK	174
macos-release-arm64	OK	103
macos-release-x86_64	OK	256
macos-oldrel-arm64	OK	120
macos-oldrel-x86_64	OK	219
windows-devel	OK	193
windows-release	OK	166
windows-oldrel	OK	166
wasm-release	OK	192

Exports:%>%estimate_null_expected_count extract_all_fitted_models eyeplot_pvEBayes generate_contin_table get_posterior_prob heatmap_pvEBayes posterior_draws pvEBayes pvEBayes_tune summary_table_pvEBayes

Dependencies:backports checkmate clarabel cli commonmark cpp11 curl CVXR data.table distributional farver generics ggdist ggfittext ggplot2 glue gmp gridtext gtable highs isoband jpeg labeling lattice lifecycle litedown magrittr markdown Matrix numDeriv osqp pillar pkgconfig png quadprog R6 RColorBrewer Rcpp RcppEigen rlang S7 scales scs shades slam stringi stringr tibble utf8 vctrs viridisLite wacolors withr xfun xml2

Introduction to pvEBayes

Rendered frompvEBayes-introduction.Rmdusingknitr::rmarkdown

Last update: 2026-05-03
Started: 2025-11-19

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
A suite of empirical Bayes methods to use in pharmacovigilance.	pvEBayes-package
Obtain Akaike Information Criterion (AIC) for a pvEBayes object	AIC.pvEBayes
Obtain Bayesian Information Criterion (BIC) for a pvEBayes object	BIC.pvEBayes
Estimate expected null baseline count based on reference row and column	estimate_null_expected_count
Extract all fitted models from a tuned pvEBayes Object	extract_all_fitted_models
Generate an eyeplot showing the distribution of posterior draws for selected drugs and adverse events	eyeplot_pvEBayes
FDA opioid dataset with 243 mental-related adverse events	faers_opioid_mental
FDA GBCA dataset with 1328 adverse events	gbca2025
FDA GBCA dataset with 69 adverse events	gbca2025_69
Generate random contingency tables based on a reference table embedded signals,and possibly with zero inflation	generate_contin_table
Obtain posterior probability of being a signal	get_posterior_prob
Generate a heatmap plot visualizing posterior probabilities for selected drugs and adverse events	heatmap_pvEBayes
Extract log marginal likelihood for a pvEBayes object	logLik.pvEBayes
Plotting method for a pvEBayes object	plot.pvEBayes
Generate posterior draws for each AE-drug combination	posterior_draws
Print method for a pvEBayes object	print.pvEBayes
Fit a general-gamma, GPS, K-gamma, KM or efron model for a contingency table.	pvEBayes
Select hyperparameter and obtain the optimal general-gamma or efron model based on AIC and BIC	pvEBayes_tune
FDA statin dataset with 5119 adverse events	statin2025
FDA statin dataset with 44 adverse events	statin2025_44
FDA statin dataset with 42 adverse events	statin42
Obtain a summary table for a pvEBayes object	summary_table_pvEBayes
Summary method for a pvEBayes object	summary.pvEBayes
VigiBase opioid dataset with 100 mental-related adverse events	vigi_opioid_mental