The function propShared computes the proportion of
shared alleles in a set of genotypes (i.e. from a genind
object). Current implementation works for any level of ploidy.
Usage
propShared(obj)
Arguments
obj
a genind object.
Details
Computations of the numbers of shared alleles are done in C.
Proportions are computed from all available data, i.e. proportion can
be computed as far as there is at least one typed locus in common
between two genotypes.
## Not run:
## make a small object
data(microbov)
obj <- microbov[1:5, loc = locNames(microbov)[1:2]]
## verify results
propShared(obj)
genind2df(obj,sep="|")
## Use this similarity measure inside a PCoA
## ! This is for illustration only !
## the distance should be rendered Euclidean before
## (e.g. using cailliez from package ade4).
matSimil <- propShared(microbov)
matDist <- exp(-matSimil)
D <- cailliez(as.dist(matDist))
pcoa1 <- dudi.pco(D,scannf=FALSE,nf=3)
s.class(pcoa1$li,microbov$pop,lab=popNames(microbov))
## End(Not run)