CalcFractionsMultiLoglik: Calculates the loglikelihood for placing a sample 100 percent...
In OriGen: Fast Spatial Ancestry via Flexible Allele Frequency Surfaces

Description Usage Arguments Value Author(s) References See Also Examples

This function takes the UnknownDataArray which contains allelelic information for individuals WITHIN a single sample site and calculates the resulting fraction loglikelihood for placing all individuals 100 percent back into their site

1	CalcFractionsMultiLoglik(UnknownDataArray,LambdaParameter=100)

`UnknownDataArray`	An array showing the unknown individuals genetic data. It lists the two allele numbers of the unknown data. The dimension of this array is [NumberUnknowns,2,NumberLoci].
`LambdaParameter`	This is a real precision parameter weighting the admixture fractions algorithm. For the most part, this does not need to be changed as it seems to only affect the time to convergence. Default is 100.

An array giving the penalized loglikelihood resulting from placing each unknown individual 100 percent back into his own sample site. The length of this array is [NumberUnknowns].

John Michael Ranola, John Novembre, and Kenneth Lange

Ranola J, Novembre J, Lange K (2014) Fast Spatial Ancestry via Flexible Allele Frequency Surfaces. Bioinformatics, in press.

FitMultinomialAdmixedModelFindUnknowns for getting loglikelihoods of unknown individuals placed into chosen regions.

#Data generation
NumberUnknowns = 50
NumberLoci = 10
TestUnknownDataArray=array(sample(1:5,2*NumberUnknowns*NumberLoci,replace=TRUE)
	,dim=c(NumberUnknowns,2,NumberLoci))

CalcFractionsMultiLoglik(TestUnknownDataArray)