BinaryReplicates

1.0.0

Dealing with Binary Replicates

0packages depend

1.6Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Pierre PudloFirst published 2026-01-231 releasesCRAN page ↗GitHub ↗

Statistical methods for analyzing binary replicates, which are noisy binary measurements of latent binary states. Provides scoring functions (average, median, likelihood-based, and Bayesian) to estimate the probability that an individual is in the positive state. Includes maximum a posteriori estimation via the EM algorithm and full Bayesian inference via Stan. Supports classification with inconclusive decisions and prevalence estimation.

Install

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

install.packages("BinaryReplicates", 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("pierrepudlo/BinaryReplicates")

Development version from pierrepudlo/BinaryReplicates. 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-binaryreplicates

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

# 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-BinaryReplicates

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

Health

CRAN checks

13OK

Slowest check: 6.8 min · r-oldrel-windows-x86_64

Check history

OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-04-22
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
10 OK · 3 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE

Show 1 earlier snapshots

NOTE2026-03-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

Documentation signals are not tracked yet for this package.

Downloads

1.6K

CRAN downloads in the past year

Rank #14,101 · ~4/day · ~135/mo

BinaryReplicates Releases R versions

Daily download trend is not available in this view yet.

35030 days

75890 days

1.6K1 year

Compare downloads with other packages →

Also on207 r2u45 autocran

Repository

GitHub ↗ pierrepudlo/binaryreplicates

1Stars

0Forks

0Open issues

0Open PRs

0Releases

70Commits

2Contributors

License GPL-3.0 · 70 commits · Last activity 2026-02-02

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/pierrepudlo/binaryreplicates on 2026-07-19.

Continuous integration (1)

GitHub Actions

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

15 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (7)

methodsRcpp RcppParallel rstan (>= 2.18.1)rstantools dplyr magrittr (>= 1.5)

LinkingTo (6)

BH Rcpp RcppEigen RcppParallel rstan StanHeaders (>= 2.18.0)

Suggests (3)

knitr rmarkdown tidyverse

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (3)

Maintainer (1)

Pierre Pudlo

Author, Maintainer

Authors (3)

Pierre Pudlo

Author, Maintainer

Hadrien Lorenzo

Author

Manuela Royez-Carenzi

Author

Package Timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
1.0.0Latest
2026-03-10 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2026-01-23
Total releases: 1 / 1 yrs
License: GPL (>= 3) OSI
Download size: 44 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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