Package: moire 3.7.0

Maxwell Murphy

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>.

Authors:Maxwell Murphy [aut, cre], Bryan Greenhouse [aut, ths]

moire_3.7.0.tar.gz
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moire_3.7.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
moire/json (API)

# Install 'moire' in R:
install.packages('moire', repos = c('https://eppicenter.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/eppicenter/moire/issues

Pkgdown/docs site:https://eppicenter.github.io

Uses libs:
  • c++– GNU Standard C++ Library v3
  • openmp– GCC OpenMP (GOMP) support library
Datasets:

On CRAN:

Conda:

genomicsmalariamcmccppopenmp

5.81 score 8 stars 27 scripts 439 downloads 24 exports 33 dependencies

Last updated from:6ae03862fe. Checks:15 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK194
linux-devel-x86_64OK191
source / vignettesOK261
linux-release-arm64OK180
linux-release-x86_64OK179
macos-release-arm64OK161
macos-release-x86_64OK399
macos-oldrel-arm64OK205
macos-oldrel-x86_64OK420
windows-devel-arm64OK297
windows-devel-x86_64OK206
windows-release-arm64OK285
windows-release-x86_64OK189
windows-oldrel-x86_64OK198
wasm-releaseOK150

Exports:calculate_hecalculate_med_allele_freqscalculate_naive_allele_frequenciescalculate_naive_coicalculate_naive_coi_offsetload_delimited_dataload_long_form_dataplot_chain_swapsrdirichletrun_mcmcsimulate_allele_frequenciessimulate_datasimulate_observed_allelesimulate_observed_genotypesimulate_sample_coisimulate_sample_genotypesummarize_allele_freq_fnsummarize_allele_freqssummarize_coisummarize_effective_coisummarize_epsilon_negsummarize_epsilon_possummarize_hesummarize_relatedness

Dependencies:BHclicpp11dplyrfarvergenericsggplot2gluegtableisobandlabelinglifecyclemagrittrpillarpkgconfigpurrrR6RColorBrewerRcppRcppParallelRcppProgressrlangS7scalesstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithr

MCMC Demonstration
Simulation and MCMC | Estimating COI | Estimating effective COI | What is effective COI? | Estimating Relatedness | Estimating allele frequencies | Estimating expected heterozygosity
Rendered frommcmc_demo.Rmdusingknitr::rmarkdown

Last update: 2026-09-10
Started: 2020-08-24

Application to Namibia
Running MOIRE on Namibia data
Rendered fromnamibia.Rmdusingknitr::rmarkdown

Last update: 2024-08-01
Started: 2024-03-18

Readme and manuals

Help Manual

Help pageTopics
Calculate the expected heterozygosity from allele frequenciescalculate_he
Calculate the geometric median of the posterior distribution of allele frequenciescalculate_med_allele_freqs
Calculate naive allele frequenciescalculate_naive_allele_frequencies
Calculate naive COIcalculate_naive_coi
Calculate naive COI offsetcalculate_naive_coi_offset
Load delimited dataload_delimited_data
Load long form dataload_long_form_data
MCMC results from using the packaged simulated data and calling 'run_mcmc()'mcmc_results
Genetic and epidemiological data from Namibianamibia_data
Plot chain swap acceptance ratesplot_chain_swaps
Dirichlet distributionrdirichlet
Allele frequencies for different regionsregional_allele_frequencies
Sample from the target distribution using MCMCrun_mcmc
Simulate allele frequenciessimulate_allele_frequencies
Simulate data generated according to the assumed modelsimulate_data
Simulates the observation processsimulate_observed_allele
Simulate observed genotypessimulate_observed_genotype
Simulate sample COIsimulate_sample_coi
Simulate sample genotypesimulate_sample_genotype
Simulated genotyping datasimulated_data
Summarize Function of Allele Frequenciessummarize_allele_freq_fn
Summarize allele frequenciessummarize_allele_freqs
Summarize COIsummarize_coi
Summarize effective COIsummarize_effective_coi
Summarize epsilon_negsummarize_epsilon_neg
Summarize epsilon_possummarize_epsilon_pos
Summarize locus heterozygositysummarize_he
Summarize relatednesssummarize_relatedness