R/get_results.R
get_effective_coi.RdFrom a single host in a SWF Simulation, extract the effective COI
for loci within the ARG. Effective COI is defined as the number of non-coalesced genomes
at the end of tlim. For example, if a host contains five strains (i.e. five parasites),
then at loci 1 we can determine "mini" coalescent trees have occurred. If the effective COI is
2, then three strains have formed one coalescent tree and two strains have formed a separate
coalescent tree. Notably, this framework is independent for each recombination event
(versus loci which are just genetic markers). This means, if loci 10 is located within a different
recombination block than loci 1 - and therefore is a separate entry in the ARG - we expect the
effective COI to be (potentially) different.
get_effective_coi(swf, host_index = NULL)result of forwards simulation using the function sim_swf()
a vector of target hosts. Defaults to all hosts
vector of effective COI by loci
Function limited to a single host per "realization"