ancJNmp:

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

Usage

ancJNmp(x1, y1, x2, y2, regfun = qreg, p.crit = NULL, DEEP = FALSE, plotit = TRUE, xlab = "X1", ylab = "X2", null.value = 0, FRAC = 0.5, cov1 = FALSE, SMM = TRUE, alpha = 0.05, nreps = 1000, MC = FALSE, pts = NULL, SEED = TRUE, nboot = 100, xout = FALSE, outfun = out, ...)

Arguments

x1
y1
x2
y2
regfun
p.crit
DEEP
plotit
xlab
ylab
null.value
FRAC
cov1
SMM
alpha
nreps
MC
pts
SEED
nboot
xout
outfun
...

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, regfun = qreg, p.crit = NULL, DEEP = FALSE, 
    plotit = TRUE, xlab = "X1", ylab = "X2", null.value = 0, 
    FRAC = 0.5, cov1 = FALSE, SMM = TRUE, alpha = 0.05, nreps = 1000, 
    MC = FALSE, pts = NULL, SEED = TRUE, nboot = 100, xout = FALSE, 
    outfun = out, ...) 
{
    if (SEED) 
        set.seed(2)
    x1 = as.matrix(x1)
    x2 = as.matrix(x2)
    if (ncol(x1) != ncol(x2)) 
        stop("x1 and x2 have a different number of columns")
    p = ncol(x1)
    p1 = p + 1
    m1 = elimna(cbind(x1, y1))
    x1 = m1[, 1:p]
    y1 = m1[, p1]
    m2 = elimna(cbind(x2, y2))
    x2 = m2[, 1:p]
    y2 = m2[, p1]
    if (xout) {
        m <- cbind(x1, y1)
        flag <- outfun(x1, plotit = FALSE, ...)$keep
        m <- m[flag, ]
        x1 <- m[, 1:p]
        y1 <- m[, p1]
        m <- cbind(x2, y2)
        flag <- outfun(x2, plotit = FALSE, ...)$keep
        m <- m[flag, ]
        x2 <- m[, 1:p]
        y2 <- m[, p1]
    }
    n1 = length(y1)
    n2 = length(y2)
    nv = c(n1, n2)
    if (cov1) {
        pts = x1
        if (alpha == 0.05) 
            p.crit = 0.00676
    }
    if (DEEP) 
        pts = NULL
    if (!is.null(pts[1])) {
        p.crit = NULL
        DEEP = FALSE
    }
    if (is.null(pts[1])) {
        if (!DEEP) {
            x1 <- as.matrix(x1)
            pts <- ancdes(unique(rbind(x1, x2)))
            p.crit = NULL
        }
        if (DEEP) {
            pts = ancov2COV(x1, y1, x2, y2, DETAILS = TRUE, cr = 0.27, 
                pr = FALSE, FRAC = FRAC)$all.points.used[, 1:2]
        }
    }
    pts <- as.matrix(pts)
    ntests = nrow(pts)
    mat <- matrix(NA, ntests, 8)
    dimnames(mat) <- list(NULL, c("Est 1", "Est 2", "DIF", "TEST", 
        "se", "ci.low", "ci.hi", "p.value"))
    sqsd1 = regYvar(x1, y1, pts = pts, regfun = regfun, nboot = nboot, 
        SEED = FALSE, xout = FALSE, outfun = outfun, ...)
    sqsd2 = regYvar(x2, y2, pts = pts, regfun = regfun, nboot = nboot, 
        SEED = FALSE, xout = FALSE, outfun = outfun, ...)
    est1 = regYhat(x1, y1, regfun = regfun, xr = pts, xout = FALSE, 
        outfun = outfun, ...)
    est2 = regYhat(x2, y2, regfun = regfun, xr = pts, xout = FALSE, 
        outfun = outfun, ...)
    mat[, 1] = est1
    mat[, 2] = est2
    est = est1 - est2
    mat[, 3] = est
    sd = sqrt(sqsd1 + sqsd2)
    mat[, 5] = sd
    tests = (est1 - est2)/sd
    mat[, 4] = tests
    pv = 2 * (1 - pnorm(abs(tests)))
    mat[, 8] = pv
    crit = NULL
    if (!cov1) {
        if (!DEEP) {
            if (ntests == 1) 
                crit = qnorm(1 - alpha/2)
            if (length(pts) > 1) {
                if (ntests <= 28) {
                  if (alpha == 0.05) 
                    crit <- smmcrit(Inf, ntests)
                  if (alpha == 0.01) 
                    crit <- smmcrit01(Inf, ntests)
                }
                if (ntests > 28 || is.null(crit)) 
                  crit = smmvalv2(dfvec = rep(Inf, nrow(pts)), 
                    alpha = alpha)
            }
        }
    }
    if (cov1) {
        if (!DEEP) {
            if (alpha == 0.05) 
                p.crit = 0.00676
            if (alpha != 0.05) 
                p.crit = ancJNmpcp(n1, n2, alpha = alpha, regfun = regfun, 
                  nreps = nreps, MC = MC, cov1 = cov1, DEEP = FALSE)$pc.est
            crit = qnorm(1 - p.crit/2)
        }
    }
    if (DEEP) {
        if (p == 2) {
            p.crit = 0.012
            if (alpha != 0.05) 
                p.crit = ancJNmpcp(n1, n2, alpha = alpha, regfun = regfun, 
                  nreps = nreps, MC = MC, cov1 = cov1, DEEP = TRUE)$pc.est
            crit = qnorm(1 - p.crit/2)
        }
        if (p > 2) {
            if (length(pts) > 1) {
                if (SMM) {
                  if (ntests <= 28) {
                    if (alpha == 0.05) 
                      crit <- smmcrit(Inf, ntests)
                    if (alpha == 0.01) 
                      crit <- smmcrit01(Inf, ntests)
                  }
                  if (ntests > 28 || is.null(crit)) 
                    crit = smmvalv2(dfvec = rep(Inf, nrow(pts)), 
                      alpha = alpha)
                }
                if (!SMM) {
                  p.crit = ancJNmpcp(n1, n2, alpha = alpha, regfun = regfun, 
                    nreps = nreps, MC = MC, cov1 = FALSE)
                  crit = qnorm(1 - p.crit/2)
                }
            }
        }
    }
    mat[, 6] = est - crit * sd
    mat[, 7] = est + crit * sd
    flag = rep(FALSE, nrow(mat))
    flag.chk1 = as.logical(mat[, 6] > null.value)
    flag.chk2 = (mat[, 7] < null.value)
    flag.chk = (flag.chk1 + flag.chk2 > 0)
    num.sig = sum(flag.chk)
    if (p == 2) {
        if (plotit) {
            plot(pts[, 1], pts[, 2], xlab = xlab, ylab = ylab, 
                type = "n")
            flag[flag.chk] = TRUE
            points(pts[!flag, 1], pts[!flag, 2], pch = "*")
            points(pts[flag, 1], pts[flag, 2], pch = "+")
        }
    }
    list(n = nv, num.sig = num.sig, p.crit = p.crit, points = pts, 
        output = mat)
  }

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