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 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,
wwhich gives (3-1) + (3-1) (for each loci). Note, because we consider self comparisons, the
denominator is always less than the true COI.
get_within_ibd(swf, host_index = NULL)result of forwards simulation using the function sim_swf()
a vector of target hosts. Defaults to all hosts
double of within-host IBD
Function limited to a single host per "realization"