Mpca:

In musto101/wilcox_R: What the package does (short line)

Usage

Mpca(x, N1 = 3, N2 = 2, tol = 0.001, N2p = 10, Nran = 50, Nkeep = 10, SEED = TRUE, op.pro = 0.1, SCORES = FALSE, pval = NULL)

Arguments

x
N1
N2
tol
N2p
Nran
Nkeep
SEED
op.pro
SCORES
pval

Examples

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

## The function is currently defined as
function (x, N1 = 3, N2 = 2, tol = 0.001, N2p = 10, Nran = 50, 
    Nkeep = 10, SEED = TRUE, op.pro = 0.1, SCORES = FALSE, pval = NULL) 
{
    scores <- NULL
    wt.cov <- NULL
    x <- elimna(x)
    if (SEED) 
        set.seed(2)
    m <- ncol(x)
    n <- nrow(x)
    bot <- marpca(x, p = 0, N1 = N1, N2 = N2, tol = tol, N2p = N2p, 
        Nran = Nran, Nkeep = Nkeep, SEED = SEED)
    bot <- bot$var.op
    mn1 <- m - 1
    rat <- 1
    it <- 0
    ratval <- NULL
    if (is.null(pval)) {
        ratval <- matrix(nrow = mn1, ncol = 2)
        dimnames(ratval) <- list(NULL, c("p", "pro.unex.var"))
        ratval[, 1] <- c(1:mn1)
        for (it in 1:mn1) {
            if (rat > op.pro) {
                temp <- marpca(x, p = it, N1 = N1, N2 = N2, tol = tol, 
                  N2p = N2p, Nran = Nran, Nkeep = Nkeep, SEED = SEED)
                rat <- temp$var.op/bot
                ratval[it, 2] <- rat
            }
        }
    }
    if (!is.null(pval)) {
        if (pval >= m) 
            stop("This method assumes pval<ncol(x)")
        temp <- marpca(x, p = pval, N1 = N1, N2 = N2, tol = tol, 
            N2p = N2p, Nran = Nran, Nkeep = Nkeep, SEED = SEED)
        wt.cov <- temp$wt.cov
        ratval <- temp$var.op/bot
    }
    if (SCORES) {
        if (is.null(pval)) 
            stop("When computing scores, need to specify pval")
        temp2 <- marpca(x, ncol(x))
        ev <- eigen(temp2$wt.cov)
        ord.val <- order(ev$values)
        mn1 <- m - pval + 1
        Bp <- ev$vectors[, ord.val[mn1:m]]
        xmmu <- x
        for (j in 1:m) xmmu[, j] <- x[, j] - temp2$wt.mu[j]
        scores <- matrix(ncol = pval, nrow = n)
        for (i in 1:n) scores[i, ] <- t(Bp) %*% as.matrix(xmmu[i, 
            ])
    }
    list(B = temp$B, a = temp$a, var.op = temp$var.op, unexplained.pro.var = ratval, 
        scores = scores, wt.cov = wt.cov)
  }

musto101/wilcox_R documentation built on May 23, 2019, 10:52 a.m.