R/pw.unstd.R

In cribbie/equivalencetests: Equivalence Tests

#' Pairwise unstandardized
#'
#' Equivalence interval is in unstandardized metric. If at least one pairwise mean difference is found not statistically significant (in equivalence), then the whole test fails to reject the null hypothesis.
#' @param data a data.frame object
#' @param repeated a character vector containing the names of the repeated measures variables
#' @param ei equivalence interval, in unstandardized metric
#' @param alpha alpha/significance level
#' @references Mara, C. A., & Cribbie, R. A. (2012). Paired-samples tests of equivalence. \emph{Communications in Statistics-Simulation and Computation}, 41(10), 1928-1943.
#' @references Wellek, S. (2010). \emph{Testing statistical hypotheses of equivalence and noninferiority}. CRC Press.
#' @export pw.unstd
#' @examples 
#' dat <- simRepDat()
#' pw.unstd(data=dat, repeated=c('repA', 'repB', 'repC'), ei=0.25)
pw.unstd <- function(data, repeated, ei, alpha = 0.05) {
    if (class(data) != "data.frame") 
        stop("Data input is not a dataframe.")
    dat <- data[, repeated]
    n <- nrow(dat)
    k <- length(repeated)
    sigma <- cov(dat)
    means <- as.matrix(apply(dat, 2, mean))
    allcontrasts <- getContrast(k, type = "allPW")
    
    
    mean_diff_names <- pairwise_meanDiffs(means, 
        allcontrasts)
    sqrt_varcovar <- pairwise_sd(allcontrasts, sigma)  #sd of diffs 
    for (i in 1:length(mean_diff_names)) {
        leftside <- abs((mean_diff_names))
        rightside <- ei - (sqrt_varcovar/sqrt(n)) * 
            qt(df = n - 1, p = (1 - alpha))
    }
    
    # decision leftside<-unlist(leftside)
    find_nonequiv_res <- which((ifelse(leftside <= 
        rightside, check_equiv <- 1, check_equiv <- 0)) == 
        0)
    ifelse(length(find_nonequiv_res) > 0, decis <- "No evidence for equivalence", 
        decis <- "There is evidence for overall equivalence among the repeated measures")  #if at least one pairwise test is signif, omnibus is not signif. 
    res <- list(repeatedMeasures = k, means = t(means), 
        ei = paste(ei, "in unstandardized metric"), 
        Decision = decis)
    class(res) <- "pw.unstd"
    return(res)
}

#' @rdname pw.unstd
#' @param x object of class \code{pw.unstd}
#' @param ... additional arguments
#' @export
print.pw.unstd <- function(x, ...) {
    cat("------Pairwise unstandardized test for overall equivalence------\n\n")
    cat("There are", x[[1]], "repeated measures.", 
        "\n\n")
    cat("The", x[[1]], "means were ")
    cat(x[[2]])
    cat("\n\n")
    cat("The equivalence interval was ", x[[3]], 
        "in raw metric.", "\n\n")
    print(x[[4]])
}