pairwiseTest update

[avancise]

It would be useful to add a value to the pairwiseTest function output, reporting how many loci were used to calculate differentiation between each pair of strata.

[EricArcher]

Although I can see that this would be handy, I've elected not to implement this because it would actually involve adding the code to each individual metric algorithm (e.g., statPHIst, statFst, statChi2, etc.), and that would cause an overhead, especially in the permutation test parts.

You can get the number of samples missing at each locus in each each stratum with:

sapply(strataSplit(msats.g), numMissing)

By extension, you can get the number of samples without missing data at each locus in each stratum with:

sapply(strataSplit(msats.g), function(x) nInd(x) - numMissing(x))

Looking at the cells with 0's in this latter matrix with tell you where that locus is unavailable for use in a pairwise context and some further processing of this matrix would tell you which loci and how many were used in each test.

[avancise]

Thanks Eric! Make sense. Happy Memorial Day!

Cheers,
Amy

<)))>< <)))>< <)))>< <)))>< <)))>< <)))>< <)))>< <)))><

Amy Van Cise
PhD Candidate
NSF Graduate Research Fellow
https://amyvancise.wordpress.com

Scripps Institution of Oceanography
Ritter Hall 117
781-686-6753
avancise@ucsd.edu

NOAA Southwest Fisheries Science Center
8901 La Jolla Shores Drive
858-546-5648
avancise@gmail.com

On Mon, May 30, 2016 at 10:55 AM, Eric Archer notifications@github.com
wrote:

Closed #1 #1.

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