Package: openEBGM 0.9.1
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.
Authors:
openEBGM_0.9.1.tar.gz
openEBGM_0.9.1.zip(r-4.5)openEBGM_0.9.1.zip(r-4.4)openEBGM_0.9.1.zip(r-4.3)
openEBGM_0.9.1.tgz(r-4.4-any)openEBGM_0.9.1.tgz(r-4.3-any)
openEBGM_0.9.1.tar.gz(r-4.5-noble)openEBGM_0.9.1.tar.gz(r-4.4-noble)
openEBGM_0.9.1.tgz(r-4.4-emscripten)openEBGM_0.9.1.tgz(r-4.3-emscripten)
openEBGM.pdf |openEBGM.html✨
openEBGM/json (API)
NEWS
# Install 'openEBGM' in R: |
install.packages('openEBGM', repos = c('https://johnihrie.r-universe.dev', 'https://cloud.r-project.org')) |
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 1 years agofrom:6e6885cc87. Checks:OK: 3 NOTE: 4. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Oct 09 2024 |
R-4.5-win | NOTE | Oct 09 2024 |
R-4.5-linux | NOTE | Oct 09 2024 |
R-4.4-win | NOTE | Oct 09 2024 |
R-4.4-mac | NOTE | Oct 09 2024 |
R-4.3-win | OK | Oct 09 2024 |
R-4.3-mac | OK | Oct 09 2024 |
Exports:autoHyperautoSquashebgmebScoresexploreHypershyperEMnegLLnegLLsquashnegLLzeronegLLzeroSquashprocessRawQnquantBisectsquashData
Dependencies:clicolorspacedata.tablefansifarverggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigR6RColorBrewerrlangscalestibbleutf8vctrsviridisLitewithr
Empirical Bayes Metrics with openEBGM
Rendered fromvignette04-posteriorCalculation.Rmd
usingknitr::rmarkdown
on Oct 09 2024.Last update: 2023-09-15
Started: 2023-09-15
Hyperparameter Estimation with openEBGM
Rendered fromvignette03-hyperparameterEstimation.Rmd
usingknitr::rmarkdown
on Oct 09 2024.Last update: 2023-09-15
Started: 2023-09-15
Introduction to openEBGM
Rendered fromvignette01-introAndDataPrep.Rmd
usingknitr::rmarkdown
on Oct 09 2024.Last update: 2023-09-15
Started: 2023-09-15
openEBGM Objects and Class Functions
Rendered fromvignette05-openEBGMObject.Rmd
usingknitr::rmarkdown
on Oct 09 2024.Last update: 2023-09-15
Started: 2023-09-15
Processing Raw Data with openEBGM
Rendered fromvignette02-rawDataProcessing.Rmd
usingknitr::rmarkdown
on Oct 09 2024.Last update: 2023-09-15
Started: 2023-09-15
Readme and manuals
Help Manual
Help page | Topics |
---|---|
Semi-automated hyperparameter estimation | autoHyper |
Automated data squashing | autoSquash |
Dietary supplement reports and products | caers |
Raw CAERS data | caers_raw |
Calculate EBGM scores | ebgm |
Construct an openEBGM object | ebScores |
Explore various hyperparameter estimates | exploreHypers |
Estimate hyperparameters using an EM algorithm | hyperEM |
Likelihood without zero counts | negLL |
Likelihood with data squashing and no zero counts | negLLsquash |
Likelihood with zero counts | negLLzero |
Likelihood with data squashing & zero counts | negLLzeroSquash |
Plot an openEBGM object | plot.openEBGM |
Print an openEBGM object | print.openEBGM |
Process raw data | processRaw |
Calculate Qn | Qn |
Find quantiles of the posterior distribution | quantBisect |
Squash data for hyperparameter estimation | squashData |
Summarize an openEBGM object | summary.openEBGM |