mRatio: M ratio

In EricArcher/strataG: Summaries and Population Structure Analyses of Genetic Data

M ratio

Description

Calculate Garza-Williamson M ratio (bottleneck) statistic for microsattelite data.

Usage

mRatio(g, by.strata = FALSE, rpt.size = 8:2)

Arguments

g	a gtypes object.
by.strata	calculate ratio for each stratum separately?
rpt.size	set of values to check for allele repeat size. Function will use the largest common denominator found in this vector or return NA.

Note

The function will only compute the metric for microastellite loci, which is defined as loci with allele labels that can be converted to numeric values in their entirety and have a fixed repeat size. NA is returned for all loci that do not have all numeric alleles. NA will also be returned if a locus is monomorphic, the locus has no genotypes, or a minimum repeat size cannot be found for all alleles at a locus.

Author(s)

Eric Archer [e-mail]

References

Garza, J.C. and E.G. Williamson. 2001. Detection of reduction in population size using data form microsatellite loci. Molecular Ecology 10(2):305-318.

Examples

data(msats.g)

m.by.strata <- mRatio(msats.g, TRUE)
m.by.strata

m.overall <- mRatio(msats.g, FALSE)
m.overall

EricArcher/strataG documentation built on Feb. 12, 2023, 4:11 a.m.