R Observatory: Metrics for CPBayes version 1.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

CPBayes

1.1.0Package record

Bayesian Meta Analysis for Studying Cross-Phenotype Genetic Associations

0packages depend

3.5Kdownloads / year

72.0%test coverage

11/13flavors OK

Overview

About

Maintained by Arunabha MajumdarCRAN page ↗GitHub ↗Issues ↗

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.

Changes in 1.1.0

Fifth version of CPBayes R-package

New features

None.

Bug fixes and minor improvements

The default choices of the burn in period and the MCMC sample size are modified. Computational runtime is reduced significantly.

From NEWS.md in the release

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. 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-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). 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

2NOTE11OK

Check messages

NOTECRAN incoming feasibilityr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Maintainer: ‘Arunabha Majumdar <statgen.arunabha@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Arunabha",
                      family = "Majumdar",
                      role = c("aut", "cre"),
                      email = "statgen.arunabha@gmail.com"),
               person(given = "Tanushree",
                      family = "Haldar",
                      role = "aut",
                      email = "tanushree.haldar@gmail.com"),
               person(given = "John",
                      family = "Witte",
                      role = "ctb"))
as necessary.

CRAN check page ↗

Slowest check: 1.9 min · r-oldrel-windows-x86_64

Status changes

NOTE11 OK, 2 NOTENow
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.1.0

READMEYes · 1,782 wordsVignettesYes · 1 · dynamicNEWSYes · 67% structured · mentions 1.1.0Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 11includes a package overview page
Examples that run: 100%10 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 73%

Vignettes (1)

CPBayes (Bayesian meta analysis for studying cross-phenotype genetic associations) package

How these are measured

Downloads

3.5K

CRAN downloads in the past year

Rank #10,560 · ~10/day · ~295/mo

Releases R versions

Daily download trend is not available in this view yet.

33830 days

98790 days

3.5K1 year

Compare downloads with other packages →

Also on113 r2u9 autocran104 c2d4u

How downloads are counted

Repository

arunabhacodes/cpbayes ↗Account: ArunabhaCodes

3Stars

1Forks

2Open issues

0Open PRs

3Releases

65Commits

2Commit identities

65 commits · Last activity 2020-12-01

Responsiveness

not measured

Stars over time

2024-09-05 · 32026-07-07 · 3

How these are measured

PracticesBeta

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

Checks run against github.com/arunabhacodes/cpbayes on 2026-10-21.

Continuous integration (1)

Travis CI (config file)

Docs source (1)

README.Rmd

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Installing CPBayes adds 12 packages (9 with compiled code, 6.3 MB of source tarballs). Heaviest: forestplot 1.9 MB, mvtnorm 1.0 MB, vctrs 1.0 MB.

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.

How these are counted

Code & Tests

Datasets

People & History

People (from the free-text Author field) (3)

Arunabha Majumdar

Author, Maintainer since 0.1.0 (2017)

Tanushree Haldar

Author

John Witte

Contributor

Releases (5)

Pick two releases to compare their code metrics.

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
record
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
record
2019-01-12 · diff ↗ ·
added 2 exports
analytic_locFDR_BF_cor, analytic_locFDR_BF_uncor
R
R 3.5.0 released · 2018-04-23
0.3.0
record
2018-02-23 · diff ↗
R
R 3.4.0 released · 2017-04-21
0.2.0
record
2017-04-06 · diff ↗ ·
added 1 export
forest_cpbayes
0.1.0
record
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

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 v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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