Multiplicity of Infection and Allele Frequency Recovery from Noisy Polyallelic Genetics Data

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Documentation for package ‘moire’ version 3.7.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

calculate_he	Calculate the expected heterozygosity from allele frequencies
calculate_med_allele_freqs	Calculate the geometric median of the posterior distribution of allele frequencies
calculate_naive_allele_frequencies	Calculate naive allele frequencies
calculate_naive_coi	Calculate naive COI
calculate_naive_coi_offset	Calculate naive COI offset
load_delimited_data	Load delimited data
load_long_form_data	Load long form data
mcmc_results	MCMC results from using the packaged simulated data and calling 'run_mcmc()'
namibia_data	Genetic and epidemiological data from Namibia
plot_chain_swaps	Plot chain swap acceptance rates
rdirichlet	Dirichlet distribution
regional_allele_frequencies	Allele frequencies for different regions
run_mcmc	Sample from the target distribution using MCMC
simulated_data	Simulated genotyping data
simulate_allele_frequencies	Simulate allele frequencies
simulate_data	Simulate data generated according to the assumed model
simulate_observed_allele	Simulates the observation process
simulate_observed_genotype	Simulate observed genotypes
simulate_sample_coi	Simulate sample COI
simulate_sample_genotype	Simulate sample genotype
summarize_allele_freqs	Summarize allele frequencies
summarize_allele_freq_fn	Summarize Function of Allele Frequencies
summarize_coi	Summarize COI
summarize_effective_coi	Summarize effective COI
summarize_epsilon_neg	Summarize epsilon_neg
summarize_epsilon_pos	Summarize epsilon_pos
summarize_he	Summarize locus heterozygosity
summarize_relatedness	Summarize relatedness