sintmcp:

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

Usage

sintmcp(x, con = 0, alpha = 0.05)

Arguments

x
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, con = 0, alpha = 0.05) 
{
    flagcon = F
    if (!is.matrix(x)) 
        x <- matl(x)
    if (!is.matrix(x)) 
        stop("Data must be stored in a matrix or in list mode.")
    con <- as.matrix(con)
    J <- ncol(x)
    x <- elimna(x)
    nval <- nrow(x)
    if (sum(con^2 != 0)) 
        CC <- ncol(con)
    if (sum(con^2) == 0) 
        CC <- (J^2 - J)/2
    ncon <- CC
    if (alpha == 0.05) {
        dvec <- c(0.05, 0.025, 0.0169, 0.0127, 0.0102, 0.00851, 
            0.0073, 0.00639, 0.00568, 0.00511)
        if (ncon > 10) {
            avec <- 0.05/c(11:ncon)
            dvec <- c(dvec, avec)
        }
    }
    if (alpha == 0.01) {
        dvec <- c(0.01, 0.005, 0.00334, 0.00251, 0.00201, 0.00167, 
            0.00143, 0.00126, 0.00112, 0.00101)
        if (ncon > 10) {
            avec <- 0.01/c(11:ncon)
            dvec <- c(dvec, avec)
        }
    }
    if (alpha != 0.05 && alpha != 0.01) 
        dvec <- alpha/c(1:ncon)
    if (sum(con^2) == 0) {
        flagcon <- T
        psihat <- matrix(0, CC, 7)
        dimnames(psihat) <- list(NULL, c("Group", "Group", "psihat", 
            "ci.lower", "ci.upper", "p.value", "p.crit"))
        temp1 <- 0
        jcom <- 0
        for (j in 1:J) {
            for (k in 1:J) {
                if (j < k) {
                  jcom <- jcom + 1
                  dv <- x[, j] - x[, k]
                  temp = sintv2(dv, pr = FALSE)
                  temp1[jcom] <- temp$p.value
                  psihat[jcom, 1] <- j
                  psihat[jcom, 2] <- k
                  psihat[jcom, 3] <- median(dv)
                  psihat[jcom, 4] <- temp$ci.low
                  psihat[jcom, 5] <- temp$ci.up
                  psihat[jcom, 6] <- temp$p.value
                }
            }
        }
        temp2 <- order(0 - temp1)
        zvec <- dvec[1:ncon]
        sigvec <- (psihat[temp2, 6] >= zvec)
        dd = 0
        if (sum(sigvec) < ncon) {
            dd <- ncon - sum(sigvec)
            ddd <- sum(sigvec) + 1
        }
        psihat[temp2, 7] <- zvec
    }
    if (sum(con^2) > 0) {
        if (nrow(con) != ncol(x)) 
            warning("The number of groups does not match the number\n of contrast coefficients.")
        ncon <- ncol(con)
        psihat <- matrix(0, ncol(con), 6)
        dimnames(psihat) <- list(NULL, c("con.num", "psihat", 
            "ci.lower", "ci.upper", "p.value", "p.crit"))
        temp1 <- NA
        for (d in 1:ncol(con)) {
            psihat[d, 1] <- d
            for (j in 1:J) {
                if (j == 1) 
                  dval <- con[j, d] * x[, j]
                if (j > 1) 
                  dval <- dval + con[j, d] * x[, j]
            }
            temp = sintv2(dval, pr = FALSE)
            temp1[d] = temp$p.value
            psihat[d, 5] = temp$p.value
            psihat[d, 2] <- median(dval)
            psihat[d, 3] <- temp$ci.low
            psihat[d, 4] <- temp$ci.up
        }
        temp2 <- order(0 - temp1)
        zvec <- dvec[1:ncon]
        sigvec <- (psihat[temp2, 5] >= zvec)
        psihat[temp2, 6] <- zvec
        dd = 0
        if (sum(sigvec) < ncon) {
            dd <- ncon - sum(sigvec)
            ddd <- sum(sigvec) + 1
        }
    }
    list(output = psihat, con = con, num.sig = dd)
  }

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