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:
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NEWS
| # Install 'moire' in R: |
| install.packages('moire', repos = c('https://plasmogenepi.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/eppicenter/moire/issues
Pkgdown site:https://eppicenter.github.io
- mcmc_results - MCMC results from using the packaged simulated data and calling 'run_mcmc()'
- namibia_data - Genetic and epidemiological data from Namibia
- regional_allele_frequencies - Allele frequencies for different regions
- simulated_data - Simulated genotyping data
Last updated 3 months agofrom:656dcfbb82. Checks:3 OK, 6 NOTE. Indexed: no.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Jan 05 2025 |
| R-4.5-win-x86_64 | OK | Jan 05 2025 |
| R-4.5-linux-x86_64 | OK | Jan 05 2025 |
| R-4.4-win-x86_64 | NOTE | Jan 05 2025 |
| R-4.4-mac-x86_64 | NOTE | Jan 05 2025 |
| R-4.4-mac-aarch64 | NOTE | Jan 05 2025 |
| R-4.3-win-x86_64 | NOTE | Jan 05 2025 |
| R-4.3-mac-x86_64 | NOTE | Jan 05 2025 |
| R-4.3-mac-aarch64 | NOTE | Jan 05 2025 |
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:BHclicolorspacecpp11dplyrfansifarvergenericsggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigpurrrR6RColorBrewerRcppRcppParallelRcppProgressrlangscalesstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithr
