Nothing
"mantl" <-
function(x, y, method = "pearson", permutations = 1000, sub = NULL, loop = FALSE, ...){
p <- permutations
x <- as.matrix(x)
y <- as.matrix(y)
sel <- row(x)>col(x)
if(!is.null(sub)){ sel <- (sel+sub)==2 }
stat <- cor(x[sel], y[sel], method = method, ...)
if(loop){
when <- seq(0, permutations, floor(permutations/10))
perms <- rep(NA, permutations)
for(i in c(1:permutations)){
py <- sample(c(1:nrow(x)))
perms[i] <- cor(x[sel], y[py,py][sel], method = method, ...)
if(sum(when==i)==1) cat(".",sep="")
}
}
else{
permsy <- lapply(1:p, function(z) sample(c(1:nrow(x))))
perms <- sapply(permsy, function(z) cor(x[sel], y[z,z][sel], method = method, ...))
}
if (stat >= 0) {
signif <- sum(perms >= stat)/p
}
else {
signif <- sum(perms <= stat)/p
}
N <- length(x[sel])
res <- list(call=match.call(), method=method, statistic=stat, signif=signif, n=N, permutations=p, perms=perms)
class(res) <-"permcor"
res
}
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