R/cm.ci.R

In TKoscik/tk.r.misc: TKoscik's Miscellaneous R Functions

cm.ci <-
function(data.frame, conf.level = 0.95, difference = TRUE) {
    #cousineau-morey within-subject CIs
    k = ncol(data.frame)
    if (difference == TRUE) {
        diff.factor = 2^0.5/2
    } else {
        diff.factor = 1
    }
    n <- nrow(data.frame)
    df.stack <- stack(data.frame)
    index <- rep(1:n, k)
    p.means <- tapply(df.stack$values, index, mean)
    norm.df <- data.frame - p.means + (sum(data.frame)/(n * k))
    t.mat <- matrix(, k, 1)
    mean.mat <- matrix(, k, 1)
    for (i in 1:k) t.mat[i, ] <- t.test(norm.df[i])$statistic[1]
    for (i in 1:k) mean.mat[i, ] <- mean(norm.df[ ,i])
    c.factor <- (k/(k - 1))^0.5
    moe.mat <- mean.mat/t.mat * qt(1 - (1 - conf.level)/2, n - 1) * c.factor *
        diff.factor
    ci.mat <- matrix(, k, 2)
    dimnames(ci.mat) <- list(names(data.frame), c("lower", "upper"))
    for (i in 1:k) {
        ci.mat[i, 1] <- mean.mat[i] - moe.mat[i]
        ci.mat[i, 2] <- mean.mat[i] + moe.mat[i]
    }
    ci.mat
}