meansnps: Mean diversity within a single population

In seedy: Simulation of Evolutionary and Epidemiological Dynamics

Description

Calculates the expected pairwise genetic distance (number of SNPs) between two randomly sampled genomes in a population.

Usage

meansnps(strain.log, freq.log, libr, nuc, key)

Arguments

strain.log	Vector of unique genotype IDs in population
freq.log	Vector of counts of genotypes in population, corresponding to strain.log.
libr	Library object from simulation functions. A list in which each entry represents a unique genotype, and is a vector of mutated nucleotide positions relative to the reference seqeunce.
nuc	Nucleotide database from simulation functions. A list (corresponding to libr) in which each entry represents a unique genotype, and is a vector of mutated nucleotides relative to the reference sequence.
key	Vector of genotype IDs corresponding to the libr and nuc objects.

Examples

data(withinhost)
meansnps(withinhost$obs.strain, rep(1, 10), withinhost$libr, withinhost$nuc, 
         withinhost$librstrains)

seedy documentation built on May 29, 2017, 10:58 a.m.