BinaryReplicates: Dealing with Binary Replicates

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.

Version:	1.0.0
Depends:	R (≥ 3.5.0)
Imports:	methods, Rcpp (≥ 0.12.0), RcppParallel (≥ 5.0.1), rstan (≥ 2.18.1), rstantools (≥ 2.4.0), dplyr (≥ 0.8.0), magrittr (≥ 1.5)
LinkingTo:	BH (≥ 1.66.0), Rcpp (≥ 0.12.0), RcppEigen (≥ 0.3.3.3.0), RcppParallel (≥ 5.0.1), rstan (≥ 2.18.1), StanHeaders (≥ 2.18.0)
Suggests:	knitr, rmarkdown, tidyverse
Published:	2026-01-23
DOI:	10.32614/CRAN.package.BinaryReplicates
Author:	Pierre Pudlo [aut, cre], Manuela Royez-Carenzi [aut], Hadrien Lorenzo [aut]
Maintainer:	Pierre Pudlo <pierre.pudlo at univ-amu.fr>
BugReports:	https://github.com/pierrepudlo/BinaryReplicates/issues
License:	GPL (≥ 3)
URL:	https://github.com/pierrepudlo/BinaryReplicates
NeedsCompilation:	yes
SystemRequirements:	GNU make
Materials:	README
CRAN checks:	BinaryReplicates results

Documentation:

Reference manual:	BinaryReplicates.html , BinaryReplicates.pdf
Vignettes:	Get started with BinaryReplicates (source, R code)

Downloads:

Package source:	BinaryReplicates_1.0.0.tar.gz
Windows binaries:	r-devel: BinaryReplicates_1.0.0.zip, r-release: BinaryReplicates_1.0.0.zip, r-oldrel: BinaryReplicates_1.0.0.zip
macOS binaries:	r-release (arm64): BinaryReplicates_1.0.0.tgz, r-oldrel (arm64): BinaryReplicates_1.0.0.tgz, r-release (x86_64): BinaryReplicates_1.0.0.tgz, r-oldrel (x86_64): BinaryReplicates_1.0.0.tgz

Linking:

Please use the canonical form https://CRAN.R-project.org/package=BinaryReplicates to link to this page.