openEBGM: EBGM Disproportionality Scores for Adverse Event Data Mining

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.

Version:	0.9.1
Depends:	R (≥ 3.2.3)
Imports:	data.table (≥ 1.10.0), ggplot2 (≥ 2.2.1), stats (≥ 3.2.3)
Suggests:	DEoptim (≥ 2.2), dplyr (≥ 0.5.0), knitr (≥ 1.15.1), rmarkdown (≥ 1.2), testthat (≥ 1.0.2), tidyr (≥ 0.6.0)
Published:	2023-09-14
DOI:	10.32614/CRAN.package.openEBGM
Author:	John Ihrie [cre, aut], Travis Canida [aut], Ismaïl Ahmed [ctb] (author of 'PhViD' package (derived code)), Antoine Poncet [ctb] (author of 'PhViD'), Sergio Venturini [ctb] (author of 'mederrRank' package (derived code)), Jessica Myers [ctb] (author of 'mederrRank')
Maintainer:	John Ihrie <John.Ihrie at fda.hhs.gov>
License:	GPL-2 | GPL-3
URL:	https://journal.r-project.org/archive/2017/RJ-2017-063/index.html
NeedsCompilation:	no
Citation:	openEBGM citation info
Materials:	NEWS
In views:	Bayesian
CRAN checks:	openEBGM results

Documentation:

Reference manual:	openEBGM.html , openEBGM.pdf
Vignettes:	Introduction to openEBGM (source, R code) Processing Raw Data with openEBGM (source, R code) Hyperparameter Estimation with openEBGM (source, R code) Empirical Bayes Metrics with openEBGM (source, R code) openEBGM Objects, Class Functions and Individual Calculations (source, R code)

Downloads:

Package source:	openEBGM_0.9.1.tar.gz
Windows binaries:	r-devel: openEBGM_0.9.1.zip, r-release: openEBGM_0.9.1.zip, r-oldrel: openEBGM_0.9.1.zip
macOS binaries:	r-release (arm64): openEBGM_0.9.1.tgz, r-oldrel (arm64): openEBGM_0.9.1.tgz, r-release (x86_64): openEBGM_0.9.1.tgz, r-oldrel (x86_64): openEBGM_0.9.1.tgz
Old sources:	openEBGM archive

Reverse dependencies:

Reverse imports:

faers

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