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#' @rdname cor.matrix
#' @encoding UTF-8
#' @export
cor.procrustes <- function (x, y, permutations = 999, strata = NULL, na.rm = FALSE, seqpermutation = NULL,
parallel = NULL, newClusters = TRUE, CL = NULL)
{
if(!is.null(seqpermutation)){
if(dim(seqpermutation)[1] != permutations){
stop("\nThe seqpermutation must be the same dimension of permutations\n")
}
}
correlation <- procrustes.syncsa(x, y)
N <- nrow(x)
if(is.null(seqpermutation)){
seqpermutation <- permut.vector(N, strata = strata, nset = permutations)
}
if(!is.null(CL)){
parallel <- length(CL)
}
ptest <- function(samp, x, y){
res <- SYNCSA::procrustes.syncsa(x, y[samp, ,drop=FALSE])
return(res)
}
if(is.null(parallel)){
value <- matrix(NA, nrow = permutations, ncol = 1)
for (i in 1: permutations) {
value[i,] <- ptest(samp = seqpermutation[i,], x = x, y = y)
}
} else {
if (newClusters) {
CL <- parallel::makeCluster(parallel, type = "PSOCK")
}
value <- cbind(parallel::parRapply(CL, seqpermutation, ptest, x = x, y = y))
if (newClusters){
parallel::stopCluster(CL)
}
}
signific <- (sum(abs(value) >= abs(correlation)) + 1)/(permutations + 1)
res <- list(Obs = correlation, p = signific)
return(res)
}
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