Package index

All functions

RG_inference()

Computes the likelihood of all relationship graphs

RG_to_igraph()

Converts relationship graph to an igraph object

compatible_rstrs()

Find all vectors of recurrence states compatible with relationship graph

compute_posterior()

Compute posterior probabilities of P. vivax recurrent states

determine_MOIs()

Determine MOIs from unphased data

enumerate_CPs()

Enumerate clonal partitions

enumerate_IPs_RG()

Enumerate IBD partitions consistent with a given relationship graph

enumerate_RGs()

Enumerate relationship graphs

enumerate_alleles()

Find all allele assignments for genotypes within the same infection

enumerate_halfsib_alleles()

List all allelic draws for three half siblings

fs_VHX_BPD

Allele frequencies computed from example Plasmodium vivax data

hash.IP()

Convert IBD partition to a unique string for hashing

locus_type_summary()

Summarise locus-wise data types

maxima

Upper bounds on posterior probabilities

msg_progress_bar-class msg_progress_bar

Message progress bar

plot_RG()

Plot a relationship graph (RG)

plot_data()

Plots the data

plot_simplex()

Plots a 2D simplex

prep_data()

Pre-process data to remove repeats and NAs

project2D()

Project 3D probability coordinates onto 2D simplex coordinates

recombine_parent_ids()

Generate parental allocations for a meiotic tetrad

sample_RG()

Sample a transitive relationship graph

split_two()

Partition a vector into at most two subvectors

ys_VHX_BPD

Example Plasmodium vivax data