msmed:

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

Usage

msmed(x, y = NA, con = 0, alpha = 0.05)

Arguments

x
y
con
alpha

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, y = NA, con = 0, alpha = 0.05) 
{
    if (!is.na(y[1])) {
        xx <- list()
        xx[[1]] <- x
        xx[[2]] <- y
        if (is.matrix(x) || is.list(x)) 
            stop("When y is speficied, x should not have list mode or be a matrix")
        x <- xx
    }
    if (is.matrix(x)) 
        x <- listm(x)
    if (!is.list(x)) 
        stop("Data must be stored in a matrix or in list mode.")
    con <- as.matrix(con)
    J <- length(x)
    h <- vector("numeric", J)
    w <- vector("numeric", J)
    xbar <- vector("numeric", J)
    for (j in 1:J) {
        xx <- !is.na(x[[j]])
        val <- x[[j]]
        if (sum(duplicated(val) > 0)) {
            print(paste("Warning: Group", j, "has tied values. Might want to used medpb"))
        }
        x[[j]] <- val[xx]
        xbar[j] <- median(x[[j]])
        w[j] <- msmedse(x[[j]])^2
    }
    if (sum(con^2 != 0)) 
        CC <- ncol(con)
    if (sum(con^2) == 0) {
        CC <- (J^2 - J)/2
        psihat <- matrix(0, CC, 5)
        dimnames(psihat) <- list(NULL, c("Group", "Group", "psihat", 
            "ci.lower", "ci.upper"))
        test <- matrix(NA, CC, 6)
        dimnames(test) <- list(NULL, c("Group", "Group", "test", 
            "crit", "se", "p.value"))
        jcom <- 0
        for (j in 1:J) {
            for (k in 1:J) {
                if (j < k) {
                  jcom <- jcom + 1
                  test[jcom, 3] <- abs(xbar[j] - xbar[k])/sqrt(w[j] + 
                    w[k])
                  test[jcom, 6] <- 2 * (1 - pt(test[jcom, 3], 
                    999))
                  sejk <- sqrt(w[j] + w[k])
                  test[jcom, 5] <- sejk
                  psihat[jcom, 1] <- j
                  psihat[jcom, 2] <- k
                  test[jcom, 1] <- j
                  test[jcom, 2] <- k
                  psihat[jcom, 3] <- (xbar[j] - xbar[k])
                  crit <- NA
                  if (CC == 1) 
                    crit <- qnorm(1 - alpha/2)
                  if (CC > 1) {
                    if (alpha == 0.05) 
                      crit <- smmcrit(500, CC)
                    if (alpha == 0.01) 
                      crit <- smmcrit01(500, CC)
                    if (is.na(crit)) 
                      warning("Can only be used with alpha=.05 or .01")
                  }
                  test[jcom, 4] <- crit
                  psihat[jcom, 4] <- psihat[jcom, 3] - crit * 
                    test[jcom, 5]
                  psihat[jcom, 5] <- psihat[jcom, 3] + crit * 
                    test[jcom, 5]
                }
            }
        }
    }
    if (sum(con^2) > 0) {
        if (nrow(con) != length(x)) 
            warning("The number of groups does not match the number of contrast coefficients.")
        psihat <- matrix(0, ncol(con), 4)
        dimnames(psihat) <- list(NULL, c("con.num", "psihat", 
            "ci.lower", "ci.upper"))
        test <- matrix(0, ncol(con), 5)
        dimnames(test) <- list(NULL, c("con.num", "test", "crit", 
            "se", "p.value"))
        for (d in 1:ncol(con)) {
            psihat[d, 1] <- d
            psihat[d, 2] <- sum(con[, d] * xbar)
            sejk <- sqrt(sum(con[, d]^2 * w))
            test[d, 1] <- d
            test[d, 2] <- sum(con[, d] * xbar)/sejk
            test[d, 5] <- 2 * (1 - pt(abs(test[d, 2]), 999))
            crit <- NA
            if (CC == 1) 
                crit <- qnorm(1 - alpha/2)
            if (alpha == 0.05) 
                crit <- smmcrit(500, ncol(con))
            if (alpha == 0.01) 
                crit <- smmcrit01(500, ncol(con))
            test[d, 3] <- crit
            test[d, 4] <- sejk
            psihat[d, 3] <- psihat[d, 2] - crit * sejk
            psihat[d, 4] <- psihat[d, 2] + crit * sejk
        }
    }
    list(test = test, psihat = psihat)
  }

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