Package: moire 3.5.0

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.

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

moire_3.5.0.tar.gz
moire_3.5.0.zip(r-4.7)moire_3.5.0.zip(r-4.6)moire_3.5.0.zip(r-4.5)
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moire_3.5.0.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

4.29 score 7 stars 28 scripts 24 exports 33 dependencies

Last updated from:656dcfbb82. Checks:13 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK210
linux-devel-x86_64OK222
source / vignettesOK251
linux-release-arm64OK205
linux-release-x86_64OK245
macos-release-arm64OK214
macos-release-x86_64OK359
macos-oldrel-arm64OK214
macos-oldrel-x86_64OK526
windows-develOK185
windows-releaseOK190
windows-oldrelOK210
wasm-releaseOK193

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

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

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

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: 2023-12-19
Started: 2020-08-24

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