gelato: GELATo - Group ExcLusion and Assignment Test
In strataG: Summaries and Population Structure Analyses of Genetic Data

Description Usage Arguments Value Author(s) References Examples

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

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

gelatoPlot(gelato.result, unknown = NULL, main = NULL)

`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`	The number of cores to use to distribute replicates over. If set to `NULL`, the value will be what is reported by `detectCores - 1`.
`gelato.result`	the result of a call to `gelato`.
`unknown`	the names of the unknown strata in the `x$likelihoods` element to create plots. If `NULL` one plot for each stratum is created.
`main`	main label for top of plot.#'

A list with the following elements:

`assign.prob`	a data.frame of assignment probabilities.
`likelihoods`	a list of likelihoods.

Eric Archer eric.archer@noaa.gov

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 77(1):47-58

## Not run: 
data(msats.g)

# Run GELATo analysis
gelato.fine <- gelato(msats.g, unk = "Offshore.South", nrep = 20, num.cores = 2)
gelato.fine

# Plot results
gelatoPlot(gelato.fine, "Offshore.South")

## End(Not run)