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#' @rdname cor.matrix
#' @encoding UTF-8
#' @export
pro.matrix<-function (mx1, mx2, x, my1 = NULL, my2 = NULL, y, permute.my2 = FALSE, permutations = 999,
norm = FALSE, norm.y = FALSE, strata = NULL, seqpermutation = NULL,
parallel = NULL, newClusters = TRUE, CL = NULL)
{
if(!is.null(seqpermutation)){
if(dim(seqpermutation)[1] != permutations){
stop("\n seqpermutation must be the dimension of permutations\n")
}
}
x <- cbind(x)
if(permute.my2){
my1 <- as.matrix(my1)
my2 <- as.matrix(my2)
}
y <- cbind(y)
correlation <- procrustes.syncsa(x,y)
N <- nrow(mx2)
if(is.null(seqpermutation)){
seqpermutation <- permut.vector(N, strata = strata, nset = permutations)
}
if(!is.null(CL)){
parallel <- length(CL)
}
ptest <- function(samp, mx1, mx2, my1, my2, y, permute.my2, norm, norm.y){
# x.permut <- mx1 %*% mx2[samp, , drop = FALSE]
x.permut <- matmult.syncsa(mx1, mx2[samp, , drop = FALSE])
if (norm) {
matrix.permut <- apply(x.permut^2, 2, sum)
x.permut <- sweep(x.permut, 2, sqrt(matrix.permut), "/")
}
if(permute.my2){
# y.permut <- my1 %*% my2[samp, , drop = FALSE]
y.permut <- matmult.syncsa(my1, my2[samp, , drop = FALSE])
if (norm.y) {
matrix.permut <- apply(y.permut^2, 2, sum)
y.permut <- sweep(y.permut, 2, sqrt(matrix.permut), "/")
}
}
if(!permute.my2){
res <- SYNCSA::procrustes.syncsa(x.permut, y)
}
if(permute.my2){
res <- SYNCSA::procrustes.syncsa(x.permut, y.permut)
}
return(res)
}
if(is.null(parallel)){
value <- matrix(NA, nrow = permutations, ncol = 1)
for (i in 1: permutations) {
value[i,] <- ptest(samp = seqpermutation[i,], mx1 = mx1, mx2 = mx2, my1 = my1, my2 = my2, y = y, permute.my2 = permute.my2, norm = norm, norm.y = norm.y)
}
} else {
if (newClusters) {
CL <- parallel::makeCluster(parallel, type = "PSOCK")
}
value <- cbind(parallel::parRapply(CL, seqpermutation, ptest, mx1 = mx1, mx2 = mx2, my1 = my1, my2 = my2, y = y, permute.my2 = permute.my2, norm = norm, norm.y = norm.y))
if (newClusters){
parallel::stopCluster(CL)
}
}
sig <- (sum(value >= correlation) + 1)/(permutations + 1)
return(list(Obs = correlation, p = sig))
}
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