get_within_ibd: Calculate Within-Host IBD

In nickbrazeau/polySimIBD: Structured Wright Fisher Simulator for Malaria Genetics

Calculate Within-Host IBD

Description

The within-host IBD is calculated as the number of strains that have coalesced within the tlim at each loci divided by the original (i.e. not effective) COI. As an example, consider that there are three strains (i.e. parasites) within a host and that the parasite genome has ten equidistant loci with a single recombination breakpoint at loci 5 (i.e.). Within this framework, we consider at loci 1:5 if 2/3 strains have coalesced, the within-host IBD for this section is 2/3. Next, for loci 6:10 if no strains have coalesced the within-host IBD is 0. Combining these results with-weighting for respective length/portion of the genome (weights here are equal and therefore negligible) the overall within-host IBD is:

\frac{2 + 0}{Host_{COI} - 1}

, where one is subtracted from the Host-COI for self-comparison, which gives (3-1) + (3-1) (for each loci). Note, because we consider self comparisons, the denominator is always less than the true COI.

Usage

get_within_ibd(swf, host_index = NULL)

Arguments

swf	result of forwards simulation using the function sim_swf()
host_index	a vector of target hosts. Defaults to all hosts

Details

Function limited to a single host per "realization"

Value

double of within-host IBD

nickbrazeau/polySimIBD documentation built on Sept. 26, 2024, 5:29 p.m.