[adegenet-forum] seqTrack max(prot

[Joseph Hughes]

Dear all,


I am trying to understanding how seqTrack uses the proximity matrix in the
code and I am a bit confused about the following section (line 106 in
seqTrack.R):

        ## Choose the most connected ancestor, given prox.mat
        if(!is.null(prox.mat)){ # if we've got no other info
            toKeep <- test.equal(max(prox.mat[ances,idx]),
prox.mat[ances,idx])
            ances <- ances[toKeep]
        }

It seems to me that the ancestor that has the maximum distance to the
progenitor, is being kept. Is this correct?

Also how was the threshold in the following chosen and how would this
influence a study looking at spread over very short distance:

    ## AUXILIARY FUNCTIONS ##
    ## test equality in floats
    test.equal <- function(val,vec){
        return(abs(val-vec) < 1e-12)
    }


Kind regards,

Joseph Hughes
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