moire: Multiplicity of Infection and Allele Frequency Recovery from Noisy Polyallelic Genetics Data
A Markov Chain Monte Carlo (MCMC) based approach to Bayesian estimation of individual level multiplicity of infection, within host relatedness, and population allele frequencies from polyallelic genetic data. Implements the model described in Murphy and Greenhouse (2024) <doi:10.1093/bioinformatics/btae619>.
| Version: | 3.7.0 |
| Depends: | R (≥ 4.1.0) |
| Imports: | Rcpp, RcppProgress, RcppParallel, dplyr, tidyr, stats, parallel, purrr, rlang, ggplot2 |
| LinkingTo: | Rcpp, RcppProgress, RcppParallel, BH |
| Suggests: | knitr, rmarkdown, forcats, testthat (≥ 3.0.0), parallelly |
| Published: | 2026-09-26 |
| DOI: | 10.32614/CRAN.package.moire (may not be active yet) |
| Author: | Maxwell Murphy 
[aut, cre],
Bryan Greenhouse
[aut, ths] |
| Maintainer: | Maxwell Murphy <mm at maxmurphy.dev> |
| BugReports: | https://github.com/EPPIcenter/moire/issues |
| License: | GPL (≥ 3) |
| URL: | https://github.com/EPPIcenter/moire, https://eppicenter.github.io/moire/, https://eppicenter.ucsf.edu/resources |
| NeedsCompilation: | yes |
| SystemRequirements: | C++17, GNU make |
| Citation: | moire citation info |
| Materials: | README, NEWS |
| CRAN checks: | moire results |
Documentation:
| Reference manual: | moire.html , moire.pdf |
| Vignettes: |
MCMC Demonstration (source, R code) Application to Namibia (source, R code) |
Downloads:
| Package source: | moire_3.7.0.tar.gz |
| Windows binaries: | r-devel: not available, r-release: not available, r-oldrel: not available |
| macOS binaries: | r-release (arm64): moire_3.7.0.tgz, r-oldrel (arm64): moire_3.7.0.tgz, r-release (x86_64): moire_3.7.0.tgz, r-oldrel (x86_64): moire_3.7.0.tgz |
Linking:
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