R Observatory: Metrics for VBphenoR version 1.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

VBphenoR

1.1.0Package record

Variational Bayes for Latent Patient Phenotypes in EHR

0packages depend

3.1Kdownloads / year

65.0%test coverage

13/13flavors OK

Overview

About

Maintained by Brian BuckleyCRAN page ↗GitHub ↗Issues ↗

Identification of Latent Patient Phenotype from Electronic Health Records (EHR) Data using Variational Bayes Gaussian Mixture Model for Latent Class Analysis and Variational Bayes regression for Biomarker level shifts, both implemented by Coordinate Ascent Variational Inference algorithms. Variational methods are used to enable Bayesian analysis of very large Electronic Health Records data. For VB GMM details see Bishop (2006,ISBN:9780-387-31073-2). For Logistic VB see Jaakkola and Jordan (2000) doi:10.1023/A:1008932416310. Please see preprint of JSS-submitted paper doi:10.48550/arXiv.2512.14272.

Changes in 1.1.0

Vignette changed to preprint paper on arxiv (https://doi.org/10.48550/arXiv.2512.14272) and submitted to Journal of Statistical Software.

From NEWS.md in the release

Install

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

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

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

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("buckleybrian/VBphenoR")

Development version from buckleybrian/VBphenoR. Installs pak first if it is not already available.

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-vbphenor

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-VBphenoR

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-VBphenoR

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: 2.0 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-09-08
ERROR12 OK, 1 ERROR2026-09-07
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.1.0

READMEYes · 180 wordsVignettesNoNEWSYes · 67% structured · mentions 1.1.0Citation fileNo

Help pages: 9 (1 internal)includes a package overview page
Examples that run: 0%3 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 11%

How these are measured

Downloads

3.1K

CRAN downloads in the past year

Rank #20,099 · ~8/day · ~258/mo

Releases R versions

Daily download trend is not available in this view yet.

26430 days

65790 days

3.1K1 year

Compare downloads with other packages →

Also on73 r2u6 autocran

How downloads are counted

Repository

buckleybrian/vbphenor ↗Account: buckleybrian

0Stars

0Forks

2Open issues

0Open PRs

0Releases

Last activity 2025-12-17

Responsiveness

not measured

How these are measured

PracticesBeta

2 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/buckleybrian/vbphenor on 2026-10-18.

Docs source (1)

GitHub Pages site last deployed 2025-12-17

CRAN release process (1)

cran-comments.md

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

8 external dependencies (excludes base and recommended)

Installing VBphenoR adds 28 packages (13 with compiled code, 26 MB of source tarballs). Heaviest: ggplot2 6.0 MB, data.table 5.7 MB, dbscan 3.8 MB.

Depends (1)

R >= 3.5.0

Imports (8)

statsCholWishart pracma knitrutilsdbscan data.table ggplot2

LinkingTo (0)

none

Suggests (2)

rmarkdown testthat

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 (3)

Brian Buckley

Marie Galligan

Author

Co-author

Adrian O'Hagan

Author

Co-author

Releases (2)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.1.0Latest
record
2025-12-18 · current release · diff ↗
1.0.0
record
2025-09-15
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-09-15
Total releases: 2 / 1 yrs
License: MIT + file LICENCE OSI
Minimum R: ≥ 3.5.0
Bundled data: 971 KB / 1 file
Download size: 1.0 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("VBphenoR")

Format

Buckley, B., Galligan, M., & O'Hagan, A. (2025). VBphenoR: Variational Bayes for Latent Patient Phenotypes in EHR (Version 1.1.0) [Computer software]. https://doi.org/10.32614/CRAN.package.VBphenoR

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 VBphenoR version 1.1.0 [Data set]. HJJB, LLC. Data release v2026-10-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

Report a problem with this page →