R Observatory: Metrics for BayesPIM version 2.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

BayesPIM

2.0

Bayesian Prevalence-Incidence Mixture Model

0packages depend

1.2Kdownloads / year

84.1%test coverage

13/13checks pass

Overview

About

Maintained by Thomas KlauschFirst published 2026-05-083 releasesCRAN page ↗GitHub ↗

Models time-to-event data from interval-censored screening studies. It accounts for latent prevalence at baseline and incorporates misclassification due to imperfect test sensitivity. For usage details, see the package vignette "BayesPIM_intro". Further details can be found in Klausch, Lissenberg-Witte and Coupé (2026) doi:10.1002/sim.70433.

Install

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

install.packages("BayesPIM", 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("thomasklausch2/BayesPIM")

Development version from thomasklausch2/BayesPIM. 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-bayespim

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-BayesPIM

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-BayesPIM

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

Health

CRAN checks

13OK

Slowest check: 4.1 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.34

84.1%

Coverage · measured lines

100%

Documentation · exports

14

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-05-09
9 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 161 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 67% structuredCode of conductNoContributing guideNo

Examples that run: 91%
Documented parameters: 100%
Return-value docs: 100%
References docs: 25%

Downloads

1.2K

CRAN downloads in the past year

Rank #14,458 · ~3/day · ~101/mo

Releases R versions

Daily download trend is not available in this view yet.

23130 days

73190 days

1.2K1 year

Compare downloads with other packages →

Also on413 r2u67 autocran

Repository

GitHub ↗ thomasklausch2/bayespim

0Stars

0Forks

0Open issues

0Open PRs

2Releases

25Commits

1Contributors

25 commits · Last activity 2026-08-21

Releases over time

2026-05-07 · 12026-08-22 · 2

Repository practices

Upstream repositoryBeta

3 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/thomasklausch2/bayespim on 2026-08-23.

CRAN release process (1)

cran-comments.md

Docs source (1)

README.Rmd

Git structural (1)

.gitattributes

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

Dependencies

Declared dependencies

11 external dependencies (excludes base and recommended)

Depends (2)

R >= 3.5.0coda

Imports (13)

RcppMASSdoParallel foreachparallelactuar posteriorsurvivalflexsurvgraphicsgrDevicesstatsutils

LinkingTo (1)

Rcpp

Suggests (3)

knitr rmarkdown bookdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (1)

Maintainer (1)

Thomas Klausch

Author, Maintainer

Authors (1)

Thomas Klausch

Author, Maintainer

Package Timeline

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

2.0Latest
2026-08-21 · current release · diff ↗
1.0.1
2026-05-08 · diff ↗
unarchivedReturned to CRAN
2026-05-08
R
R 4.6.0 released · 2026-04-24
archivedRemoved from CRAN
2026-01-30
policy violation On simultaneous use of CPUs
R
R 4.5.0 released · 2025-04-11
1.0.0
2025-03-22
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2026-05-08
Total releases: 3 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.5.0
Bundled data: 409 KB / 1 file
Download size: 2.1 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("BayesPIM")

Format

Klausch, T. (2026). BayesPIM: Bayesian Prevalence-Incidence Mixture Model (Version 2.0) [Computer software]. https://doi.org/10.32614/CRAN.package.BayesPIM

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

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 BayesPIM version 2.0 [Data set]. HJJB, LLC. Data release v2026-08-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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