ancovampG:

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

Usage

ancovampG(x1, y1, x2, y2, fr1 = 1, fr2 = 1, est = tmean, alpha = 0.05, pts = NULL, SEED = TRUE, test = yuen, DH = FALSE, FRAC = 0.5, cov.fun = skip.cov, pr = FALSE, q = 0.5, plotit = FALSE, pv = FALSE, theta = 50, xlab = " ", ylab = " ", SCAT = FALSE, zlab = " ", ...)

Arguments

x1
y1
x2
y2
fr1
fr2
est
alpha
pts
SEED
test
DH
FRAC
cov.fun
pr
q
plotit
pv
theta
xlab
ylab
SCAT
zlab
...

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 (x1, y1, x2, y2, fr1 = 1, fr2 = 1, est = tmean, alpha = 0.05, 
    pts = NULL, SEED = TRUE, test = yuen, DH = FALSE, FRAC = 0.5, 
    cov.fun = skip.cov, pr = FALSE, q = 0.5, plotit = FALSE, 
    pv = FALSE, theta = 50, xlab = " ", ylab = " ", SCAT = FALSE, 
    zlab = " ", ...) 
{
    x1 = as.matrix(x1)
    p = ncol(x1)
    p1 = p + 1
    m1 = elimna(cbind(x1, y1))
    x1 = m1[, 1:p]
    y1 = m1[, p1]
    x2 = as.matrix(x2)
    p = ncol(x2)
    p1 = p + 1
    m2 = elimna(cbind(x2, y2))
    x2 = m2[, 1:p]
    y2 = m2[, p1]
    if (is.null(pts[1])) {
        x1 <- as.matrix(x1)
        pts <- ancdes(x1, DH = DH, FRAC = FRAC)
    }
    pts <- as.matrix(pts)
    n1 <- 1
    n2 <- 1
    vecn <- 1
    mval1 <- cov.fun(x1)
    mval2 <- cov.fun(x2)
    for (i in 1:nrow(pts)) {
        n1[i] <- length(y1[near3d(x1, pts[i, ], fr1, mval1)])
        n2[i] <- length(y2[near3d(x2, pts[i, ], fr2, mval2)])
    }
    flag <- rep(TRUE, nrow(pts))
    for (i in 1:nrow(pts)) if (n1[i] < 10 || n2[i] < 10) 
        flag[i] <- F
    flag = as.logical(flag)
    pts <- pts[flag, ]
    if (sum(flag) == 1) 
        pts <- t(as.matrix(pts))
    dd = NULL
    if (sum(flag) == 0) {
        print("No comparable design points found, might increase span.")
        pts = NULL
        mat = NULL
        dd = NULL
    }
    if (sum(flag) > 0) {
        mat <- matrix(NA, nrow(pts), 6)
        mat[, 5] = 0
        dimnames(mat) <- list(NULL, c("n1", "n2", "p.value", 
            "crit.p.value", "Sig", "est.dif"))
        output = list()
        for (i in 1:nrow(pts)) {
            g1 <- y1[near3d(x1, pts[i, ], fr1, mval1)]
            g2 <- y2[near3d(x2, pts[i, ], fr2, mval2)]
            g1 <- g1[!is.na(g1)]
            g2 <- g2[!is.na(g2)]
            if (identical(test, qcomhd)) 
                temp = qcomhd(g1, g2, q = q, plotit = FALSE)
            if (!identical(test, qcomhd)) 
                temp = test(g1, g2, ...)
            if (is.null(temp$p.value)) 
                print("Apparently argument test is a function that does not return a p-value")
            mat[i, 3] = temp$p.value
            output[[i]] = temp
            mat[i, 1] <- length(g1)
            mat[i, 2] <- length(g2)
            mat[i, 6] = est(g1) - est(g2)
            if (length(g1) <= 5) 
                print(paste("Warning, there are", length(g1), 
                  " points corresponding to the design point X=", 
                  pts[i, ]))
            if (length(g2) <= 5) 
                print(paste("Warning, there are", length(g2), 
                  " points corresponding to the design point X=", 
                  pts[i, ]))
        }
        npt = nrow(pts)
        dvec = alpha/c(1:npt)
        temp2 <- order(0 - mat[, 3])
        sigvec <- (mat[temp2, 3] >= dvec)
        dd = 0
        if (sum(sigvec) < npt) 
            dd <- npt - sum(sigvec)
        mat[temp2, 4] = dvec
        flag = mat[, 3] <= mat[, 4]
        if (sum(flag) > 0) 
            mat[flag, 5] = 1
    }
    if (SCAT) 
        plotit = FALSE
    if (DH) {
        if (ncol(x1) == 2) {
            if (plotit) {
                if (pv) 
                  lplot(pts, mat[, 3], xlab = xlab, ylab = ylab, 
                    ticktype = "det", zlab = zlab, theta = theta)
                if (!pv) 
                  lplot(pts, mat[, 6], xlab = xlab, ylab = ylab, 
                    ticktype = "det", zlab = zlab, theta = theta)
            }
            if (SCAT) {
                chk = mat[, 5] == 1
                plot(pts[!chk, 1], pts[!chk, 2], xlab = xlab, 
                  ylab = ylab)
                points(pts[chk, 1], pts[chk, 2], pch = "*")
            }
        }
    }
    list(points = pts, results = mat, num.sig = dd)
  }

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