ancJN:

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

Usage

ancJN(x1, y1, x2, y2, pts = NULL, regfun = tsreg, fr1 = 1, fr2 = 1, SCAT = TRUE, pch1 = "*", pch2 = "+", alpha = 0.05, plotit = TRUE, xout = FALSE, outfun = out, nboot = 100, SEED = TRUE, xlab = "X", ylab = "Y", ...)

Arguments

x1
y1
x2
y2
pts
regfun
fr1
fr2
SCAT
pch1
pch2
alpha
plotit
xout
outfun
nboot
SEED
xlab
ylab
...

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, pts = NULL, regfun = tsreg, fr1 = 1, 
    fr2 = 1, SCAT = TRUE, pch1 = "*", pch2 = "+", alpha = 0.05, 
    plotit = TRUE, xout = FALSE, outfun = out, nboot = 100, SEED = TRUE, 
    xlab = "X", ylab = "Y", ...) 
{
    if (identical(outfun, boxplot)) 
        stop("Use outfun=outbox")
    if (SEED) 
        set.seed(2)
    FLAG = pts
    xy = elimna(cbind(x1, y1))
    if (ncol(xy) > 2) 
        stop("Only one covariate is allowed. Use ancJNmp")
    x1 = xy[, 1]
    y1 = xy[, 2]
    xy = elimna(cbind(x2, y2))
    if (ncol(xy) > 2) 
        stop("Only one covariate is allowed. Use ancJNmp")
    x2 = xy[, 1]
    y2 = xy[, 2]
    if (xout) {
        m <- cbind(x1, y1)
        p1 = ncol(m)
        p = p1 - 1
        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]
    }
    if (is.null(pts[1])) {
        npt <- 5
        isub <- c(1:5)
        test <- c(1:5)
        xorder <- order(x1)
        y1 <- y1[xorder]
        x1 <- x1[xorder]
        xorder <- order(x2)
        y2 <- y2[xorder]
        x2 <- x2[xorder]
        n1 <- 1
        n2 <- 1
        vecn <- 1
        for (i in 1:length(x1)) n1[i] <- length(y1[near(x1, x1[i], 
            fr1)])
        for (i in 1:length(x1)) n2[i] <- length(y2[near(x2, x1[i], 
            fr2)])
        for (i in 1:length(x1)) vecn[i] <- min(n1[i], n2[i])
        sub <- c(1:length(x1))
        isub[1] <- min(sub[vecn >= 12])
        isub[5] <- max(sub[vecn >= 12])
        isub[3] <- floor((isub[1] + isub[5])/2)
        isub[2] <- floor((isub[1] + isub[3])/2)
        isub[4] <- floor((isub[3] + isub[5])/2)
        mat <- matrix(NA, 5, 9)
        dimnames(mat) <- list(NULL, c("X", "Est1", "Est2", "DIF", 
            "TEST", "se", "ci.low", "ci.hi", "p.value"))
        pts = x1[isub]
        mat[, 1] = pts
        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, xr = pts, regfun = regfun, xout = FALSE, 
            outfun = outfun, ...)
        est2 = regYhat(x2, y2, xr = pts, regfun = regfun, xout = FALSE, 
            outfun = outfun, ...)
        mat[, 2] = est1
        mat[, 3] = est2
        est = est1 - est2
        mat[, 4] = est
        sd = sqrt(sqsd1 + sqsd2)
        mat[, 6] = sd
        tests = (est1 - est2)/sd
        mat[, 5] = tests
        pv = 2 * (1 - pnorm(abs(tests)))
        mat[, 9] = pv
        crit <- smmcrit(Inf, 5)
        mat[, 7] = est - crit * sd
        mat[, 8] = est + crit * sd
    }
    if (!is.null(FLAG)) {
        n1 = NA
        n2 = NA
        for (i in 1:length(pts)) {
            n1[i] <- length(y1[near(x1, pts[i], fr1)])
            n2[i] <- length(y2[near(x2, pts[i], fr2)])
        }
        mat <- matrix(NA, length(pts), 9)
        dimnames(mat) <- list(NULL, c("X", "Est1", "Est2", "DIF", 
            "TEST", "se", "ci.low", "ci.hi", "p.value"))
        mat[, 1] <- pts
        sqsd1 = regYvar(x1, y1, regfun = regfun, pts = pts, nboot = nboot, 
            SEED = FALSE, xout = FALSE, outfun = outfun, ...)
        sqsd2 = regYvar(x2, y2, regfun = regfun, pts = pts, 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[, 2] = est1
        mat[, 3] = est2
        est = est1 - est2
        mat[, 4] = est
        sd = sqrt(sqsd1 + sqsd2)
        mat[, 6] = sd
        tests = (est1 - est2)/sd
        mat[, 5] = tests
        pv = 2 * (1 - pnorm(abs(tests)))
        mat[, 9] = pv
        crit <- smmcrit(Inf, length(pts))
        mat[, 7] = est - crit * sd
        mat[, 8] = est + crit * sd
    }
    reg1 = regfun(x1, y1, ...)$coef
    reg2 = regfun(x2, y2, ...)$coef
    if (plotit) {
        if (xout) {
            flag <- outfun(x1, ...)$keep
            x1 <- x1[flag]
            y1 <- y1[flag]
            flag <- outfun(x2, ...)$keep
            x2 <- x2[flag]
            y2 <- y2[flag]
        }
        plot(c(x1, x2), c(y1, y2), type = "n", xlab = xlab, ylab = ylab)
        if (SCAT) {
            points(x1, y1, pch = pch1)
            points(x2, y2, pch = pch2)
        }
        abline(reg1)
        abline(reg2, lty = 2)
    }
    list(intercept.slope.group1 = reg1, intercept.slope.group2 = reg2, 
        output = mat)
  }

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