Nothing
"haplodata" <-
function(dat){
if (!is.matrix(dat)) dat <- as.matrix(dat)
nloci <- ncol(dat)
P.obj <- allelefreqs(dat)
if (!P.obj$all.polym)
cat(c("\nSome loci (", P.obj$non.polym, ") are not polymorphic.\n\n"))
P <- P.obj$freqs
Q <- qnorm(P)
C <- cor(dat)
null.mat <- matrix(0, nrow=nloci,ncol=nloci)
vmat <- .C("covariance", as.integer(nloci),as.double(C),as.double(P),as.double(Q),
rlt=as.double(null.mat), PACKAGE="hapsim")$rlt
V <- matrix(vmat, nrow=nloci, ncol=nloci)
if (!checkpd(V)) V <- makepd(V)
D <- divlocus(dat)
return(list(freqs=P, cor=C, cov=V, div=D))
}
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