sumstat_four_gamete: A Summary Statistic based on the Four-Gamete-Condition
Description
The Four-Gamete-Condition for two SNPs is violated if all four combinations
of derived and ancestral alleles at the SNPs are observed in a gamete/a
haplotype. Under an Infinite-Sites mutation model, a violation indicates that
there must have been at least one recombination event between the SNPs.
This summary statistic calculates the percentage of certain pairs of SNPs
that violate the Four-Gamete-Condition.
It is sensitive for recombination and particularly useful when estimating
recombination rates.
Usage
sumstat_four_gamete(name = "four_gamete", population = 1)
Arguments
name
The name of the summary statistic. When simulating a model,
the value of the statistics are written to an entry of the returned list
with this name. Summary statistic names must be unique in a model.
population
The population for which the statistic is calculated.
Details
The statistic generates a matrix where each row represents one locus, and the
columns give the statistic for different classes of pairs of SNPs: