R Observatory: Metrics for openEBGM version 0.10.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

openEBGM

0.10.0Package record

EBGM Disproportionality Scores for Adverse Event Data Mining

0packages depend

7.9Kdownloads / year

75.7%test coverage

13/13flavors OK

Overview

About

Maintained by John IhrieCRAN 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.

Changes in 0.10.0

Improved numerical stability of hyperparameter calculations.
Now requires 'numDeriv' package for calculating Hessian matrices.
Removed 'param_lower' and 'param_upper' arguments from hyperEM().
Added 'transformed' argument to the likelihood functions to allow for optimization on the log & logit scales.
Added 'min_theta' & 'max_theta' arguments to Qn(), ebgm(), quantBisect(), & ebScores(). Alpha values now must also be between one half & twice the value of the corresponding beta values. Values outside these ranges are replaced by the limits.
Updates to vignettes, data, examples, etc.
Fixed NOTES regarding documentation.

From NEWS.md in the release

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. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 6.7 min · r-release-windows-x86_64

Status changes

OK13 OK2026-09-10
NOTE14 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.10.0

READMENoVignettesYes · 5 · dynamicNEWSYes · 100% structured · mentions 0.10.0Citation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Cites an R Journal article

Help pages: 20 (1 internal)includes a package overview page
Examples that run: 100%12 run in a plain check
Exported functions with examples: 79%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 70%

Vignettes (5)

How these are measured

Downloads

7.9K

CRAN downloads in the past year

Rank #3,426 · ~22/day · ~659/mo

Releases R versions

Daily download trend is not available in this view yet.

1.6K30 days

3.1K90 days

7.9K1 year

Compare downloads with other packages →

Also on196 r2u1 autocran132 bioconda171 c2d4u

How downloads are counted

Dependencies

Declared dependencies

9 external dependencies (excludes base and recommended)

Installing openEBGM adds 19 packages (8 with compiled code, 19 MB of source tarballs). Heaviest: ggplot2 6.0 MB, data.table 5.7 MB, isoband 1.5 MB.

Depends (1)

R >= 3.5.0

Imports (4)

data.table ggplot2 numDerivstats

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.

How these are counted

Code & Tests

Datasets

People & History

People (6)

John Ihrie

Maintainer since 0.1.0 (2017), Author

Travis Canida

Author

Ismaïl Ahmed

Contributor

author of 'PhViD' package (derived code)

Jessica Myers

Contributor · added in 0.5.0

author of 'mederrRank'

Antoine Poncet

Contributor

author of 'PhViD'

Sergio Venturini

Contributor · added in 0.4.0

author of 'mederrRank' package (derived code)

Releases (13)

Pick two releases to compare their code metrics.

0.10.0Latest
record
2026-09-03 · current release · diff ↗
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
0.9.1
record
2023-09-15 · 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
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2020-03-02 · diff ↗
R
R 3.6.0 released · 2019-04-26
0.8.2
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2019-04-25 · diff ↗
0.8.1
record
2019-02-28 · diff ↗
0.8.0
record
2019-01-30 · diff ↗
0.7.0
record
2018-08-16 · diff ↗ ·
added 1 export
autoSquash
0.6.0
record
2018-05-21 · diff ↗

Show 7 earlier eventsHide 7 earlier events

R
R 3.5.0 released · 2018-04-23
0.5.0
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2018-04-02 · diff ↗
0.4.0
record
2018-03-09 · diff ↗ ·
added 1 export
hyperEM
0.3.0
record
2017-11-15 · diff ↗
0.2.0
record
2017-07-31 · diff ↗
0.1.0
record
2017-05-05
R
R 3.4.0 released · 2017-04-21

Package metadata

First published: 2017-05-05
Total releases: 13 / 9 yrs
License: GPL-2 | GPL-3 OSI
Minimum R: ≥ 3.5.0
Bundled data: 90 KB / 2 files
Download size: 283 KB

Appears in task views

Bayesian Inference

Cite

Cite this package

Run in R for the authors' entry:

citation("openEBGM")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.32614/rj-2017-063.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for openEBGM version 0.10.0 [Data set]. HJJB, LLC. Data release v2026-10-21. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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