strataG (version 1.0.3)

gelato: GELATo - Group ExcLusion and Assignment Test

Description

Run a GELATo test to evaluate assignment likelihoods of groups of samples.

Usage

gelato(g, unknown.strata, nrep = 1000, min.sample.size = 5, num.cores = 1)
gelatoPlot(gelato.result, unknown, main = NULL)

Arguments

g

a gtypes object.

unknown.strata

a character vector listing to assign. Strata must occur in g.

nrep

number of permutation replicates for Fst distribution.

min.sample.size

minimum number of samples to use to characterize knowns. If the known sample size would be smaller than this after drawing an equivalent number of unknowns for self-assignment, then the comparison is not done.

num.cores

number of CPU cores to use. Value is passed to mclapply.

gelato.result

the result of a call to gelato.

unknown

the name of an unknown stratum in the x$likelihoods element.

main

main label for top of plot.

Value

• A list with the following elements: ll{ assign.prob a data.frame of assignment probabilities. likelihoods a list of likelihoods. }

References

O'Corry-Crowe, G., W. Lucey, F.I. Archer, and B. Mahoney. 2015. The genetic ecology and population origins of the beluga whales of Yakutat Bay. Marine Fisheries Review.

Examples

data(msats.g)
stratify(msats.g, "fine")

gelato.fine <- gelato(msats.g, unk = "Offshore.South", nrep = 10)

gelatoPlot(gelato.fine, "Offshore.South")