Package index • moire

MCMC

run_mcmc(): Sample from the target distribution using MCMC

Simulate

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

rdirichlet(): Dirichlet distribution

Summaries

summarize_allele_freq_fn(): Summarize Function of Allele Frequencies

summarize_allele_freqs(): Summarize 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

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

Utilities

load_delimited_data(): Load delimited data

load_long_form_data(): Load long form data

plot_chain_swaps(): Plot chain swap acceptance rates

Data

simulated_data: Simulated genotyping data

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