VBphenoR

1.1.0

Variational Bayes for Latent Patient Phenotypes in EHR

0packages depend

3.1Kdownloads / year

65.0%test coverage

13/13checks pass

Overview

About

Maintained by Brian BuckleyFirst published 2025-09-152 releasesCRAN page ↗GitHub ↗

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.

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.

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).

Health

CRAN checks

13OK

Slowest check: 2.1 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 3.40

65.0%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 180 wordsVignettesNopkgdown siteNoNEWSYes · 67% structuredCode of conductNoContributing guideNo

Examples that run: 0%
Documented parameters: 100%
Return-value docs: 100%
References docs: 11%

Downloads

3.1K

CRAN downloads in the past year

Rank #23,045 · ~9/day · ~260/mo

Releases R versions

Daily download trend is not available in this view yet.

16030 days

49590 days

3.1K1 year

Compare downloads with other packages →

Also on69 r2u31 autocran

Repository

GitHub ↗ buckleybrian/vbphenor

0Stars

0Forks

2Open issues

0Open PRs

0Releases

Last activity 2025-12-17

Repository practices

Upstream repositoryBeta

1 development-tooling and community-health practice detected across 1 family in the upstream repository

Checks run against github.com/buckleybrian/vbphenor on 2026-07-19.

CRAN release process (1)

cran-comments.md

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

8 external dependencies (excludes base and recommended)

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.

Code & Tests

Code Composition

Other 3,003 (59%)R 1,328 (26%)Rd 744 (15%)

Code characteristics

Object systems

S31

Cyclomatic complexity: 4.0 median / 21 max
Test cases: 11 / 3.40 per code line

Test coverage

Line coverage

65%

Expression

67.1%

Tests / Examples

65.0% / 0% ex

Functions

11 3 exported

Complexity

5.6 avg / 21 max

Call network

11 nodes / 12 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

11 functions

Function	Cyclo	Coverage
run_Model exp	4	0%
logDiagnostics	1	0%
print.vbphenor	2	0%
VB_GMM_Init	7	55%
vb_gmm_cavi exp	21	69%
logsumexp	4	70%

People & History

People (3)

Maintainer (1)

Brian Buckley

Author, Maintainer, Copyright holder

Authors (3)

Brian Buckley

Author, Maintainer, Copyright holder

Marie Galligan

Author

Adrian O'Hagan

Author

Brian Buckley

Author, Maintainer, Copyright holder

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
1.1.0Latest
2025-12-18 · current release · diff ↗
1.0.0
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
Installed size: not tracked yet
With dependencies: not tracked yet

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