R Observatory: Metrics for CPBayes version 1.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

CPBayes

1.1.0

Bayesian Meta Analysis for Studying Cross-Phenotype Genetic Associations

0packages depend

3.3Kdownloads / year

72.0%test coverage

11/13checks pass

Overview

About

Maintained by Arunabha MajumdarFirst published 2017-01-235 releasesCRAN page ↗GitHub ↗

A Bayesian meta-analysis method for studying cross-phenotype genetic associations. It uses summary-level data across multiple phenotypes to simultaneously measure the evidence of aggregate-level pleiotropic association and estimate an optimal subset of traits associated with the risk locus. CPBayes is based on a spike and slab prior. The methodology is available from: A Majumdar, T Haldar, S Bhattacharya, JS Witte (2018) doi:10.1371/journal.pgen.1007139.

Install

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

install.packages("CPBayes", 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("ArunabhaCodes/CPBayes")

Development version from ArunabhaCodes/CPBayes. 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-cpbayes

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-CPBayes

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-CPBayes

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

2NOTE11OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc

Slowest check: 2.0 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.21

72.0%

Coverage · measured lines

100%

Documentation · exports

6

Dependencies · direct

Check history

NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 1,782 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 67% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 73%

Downloads

3.3K

CRAN downloads in the past year

Rank #11,824 · ~9/day · ~278/mo

Releases R versions

Daily download trend is not available in this view yet.

22030 days

84690 days

3.3K1 year

Compare downloads with other packages →

Also on139 r2u16 autocran56 c2d4u

Repository

GitHub ↗ arunabhacodes/cpbayes

3Stars

1Forks

2Open issues

0Open PRs

3Releases

65Commits

2Contributors

65 commits · Last activity 2020-12-01

Stars over time

2024-09-05 · 32026-07-07 · 3

Repository practices

Upstream repositoryBeta

4 development-tooling and community-health practices detected across 4 families in the upstream repository

Checks run against github.com/arunabhacodes/cpbayes on 2026-08-09.

Continuous integration (1)

Travis CI

CRAN release process (1)

cran-comments.md

Docs source (1)

README.Rmd

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.2.0

Imports (6)

MASSstatsforestplotgrDevicespurrr mvtnorm

LinkingTo (0)

none

Suggests (3)

testthat knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (0)

Author records are not tracked yet for this package.

Listed in earlier versions (3)

Tanushree Haldar

no longer listed · 0.1.0 to 1.1.0

Arunabha Majumdar

no longer listed · 0.1.0 to 1.1.0

John Witte

no longer listed · 0.1.0 to 1.1.0

Package Timeline

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

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
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
1.1.0Latest
2020-12-02 · current release · diff ↗
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
1.0.0
2019-01-12 · diff ↗
R
R 3.5.0 released · 2018-04-23
0.3.0
2018-02-23 · diff ↗
R
R 3.4.0 released · 2017-04-21
0.2.0
2017-04-06 · diff ↗
0.1.0
2017-01-23
R
R 3.3.0 released · 2016-05-03

Package metadata

First published: 2017-01-23
Total releases: 5 / 9 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.2.0
Bundled data: 1.2 KB / 3 files
Download size: 60 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Bayesian Inference Meta-Analysis

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("CPBayes")

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 CPBayes version 1.1.0 [Data set]. HJJB, LLC. Data release v2026-08-15. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-15, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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