expsnps: Distribution of genetic distances

In seedy: Simulation of Evolutionary and Epidemiological Dynamics

Description

For any pair of epidemiologically linked individuals, returns the distribution of genetic distance separating randomly drawn samples.

Usage

expsnps(x, m.rate, c.rate, tau)

Arguments

x	Vector of (non-negative integer) quantiles.
m.rate	Mutation rate (per genome per generation).
c.rate	Rate of coalescence prior to lineage divergence (constant).
tau	Total time from lineage divergence to observations.

Details

A pair of genomes sampled during an outbreak will have an epidemiological and an evolutionary relationship with each other. 'Lineage divergence' is defined to be the time at which the lineages ceased to exist within the same host (or, the latest possible time of coalescence). Mutations may arise in two distinct time periods: (a) the time between coalescence and lineage divergence, and (b) the time between lineage divergence and observation. The latter follows a Poisson distribution with mean equal to the mutation rate multiplied by the total time between lineage divergence and observations (two branches). The former is not Poisson distributed, since the time to coalescence is typically unknown (but follows an exponential distribution with a constant effective population size). It follows that, with a constant effective population size (and therefore coalescent rate), the number of mutations follows a geometric distribution. Therefore, the total number of SNPs between two samples is a geometric-Poisson mixture distribution, which this function returns.

Value

Returns the probability density for given genetic distances.

See Also

estcoaltime

Examples

expsnps(3, m.rate=0.003, c.rate=1/10000, tau=1000)
  
plot(expsnps(0:100, m.rate=0.003, c.rate=1/2000, tau=5000), type="h")

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