openEBGM

0.9.1

EBGM Disproportionality Scores for Adverse Event Data Mining

0packages depend

7.4Kdownloads / year

68.0%test coverage

0/13checks pass

Overview

About

Maintained by John IhrieFirst published 2017-05-0512 releasesCRAN page ↗

An implementation of DuMouchel's (1999) doi:10.1080/00031305.1999.10474456 Bayesian data mining method for the market basket problem. Calculates Empirical Bayes Geometric Mean (EBGM) and posterior quantile scores using the Gamma-Poisson Shrinker (GPS) model to find unusually large cell counts in large, sparse contingency tables. Can be used to find unusually high reporting rates of adverse events associated with products. In general, can be used to mine any database where the co-occurrence of two variables or items is of interest. Also calculates relative and proportional reporting ratios. Builds on the work of the 'PhViD' package, from which much of the code is derived. Some of the added features include stratification to adjust for confounding variables and data squashing to improve computational efficiency. Includes an implementation of the EM algorithm for hyperparameter estimation loosely derived from the 'mederrRank' package.

Install

R (CRAN)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("openEBGM", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-openebgm

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-openEBGM

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-openEBGM

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13NOTE

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc
NOTE r-devel-linux-x86_64-fedora-clang
NOTE r-devel-linux-x86_64-fedora-gcc
NOTE r-devel-windows-x86_64
NOTE r-oldrel-macos-arm64
NOTE r-oldrel-macos-x86_64
NOTE r-oldrel-windows-x86_64
NOTE r-patched-linux-x86_64
NOTE r-release-linux-x86_64
NOTE r-release-macos-arm64
NOTE r-release-macos-x86_64
NOTE r-release-windows-x86_64

Slowest check: 5.8 min · r-devel-windows-x86_64

Code health

Yes

Tests · ratio 0.43

68.0%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-03-10
0 OK · 14 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 70%

Downloads

7.4K

CRAN downloads in the past year

Rank #6,025 · ~20/day · ~614/mo

Releases R versions

Daily download trend is not available in this view yet.

53830 days

1.5K90 days

7.4K1 year

Compare downloads with other packages →

Also on99 r2u89 bioconda101 c2d4u

Dependencies

Declared dependencies

8 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.2.3

Imports (3)

data.table ggplot2stats

LinkingTo (0)

none

Suggests (6)

DEoptim dplyr knitr rmarkdown testthat tidyr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (6)

Maintainer (1)

John Ihrie

Maintainer, Author

Authors (2)

John Ihrie

Maintainer, Author

Travis Canida

Author

Contributors (4)

Ismaïl Ahmed

Contributor

Jessica Myers

Contributor · added in 0.5.0

Antoine Poncet

Contributor

Sergio Venturini

Contributor · added in 0.4.0

Package Timeline

12 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
0.9.1Latest
2023-09-15 · current release · diff ↗
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
0.8.3
2020-03-02 · diff ↗
R
R 3.6.0 released · 2019-04-26
0.8.2
2019-04-25 · diff ↗
0.8.1
2019-02-28 · diff ↗
0.8.0
2019-01-30 · diff ↗
0.7.0
2018-08-16 · diff ↗
0.6.0
2018-05-21 · diff ↗
R
R 3.5.0 released · 2018-04-23

Show 6 earlier events

0.5.0
2018-04-02 · diff ↗
0.4.0
2018-03-09 · diff ↗
0.3.0
2017-11-15 · diff ↗
0.2.0
2017-07-31 · diff ↗
0.1.0
2017-05-05
R
R 3.4.0 released · 2017-04-21

Package metadata

First published: 2017-05-05
Total releases: 12 / 9 yrs
License: GPL-2 | GPL-3 OSI
Minimum R: ≥ 3.2.3
Bundled data: 106 KB / 2 files
Download size: 289 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Bayesian Inference

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