[R] pairwise.wilcox.test

[Dieter Menne]

LE PAPE Gilles <lepape.gilles <at> neuf.fr> writes:

> 
> Could somebody explain me why the pairwise.wilcox.test
> function ever gives the same result with either  "paired=FALSE" or 
> "paired=TRUE" ?

Because of what I would consider a .. let's call it feature to avoid 
flames...  in parameter passing in pairwise.wilcox.test. 


#----------------------------------------------
x = rnorm(100)
g = as.factor(rep(letters[1:4],25))

pairwise.wilcox.test <-
function (x, g, p.adjust.method = p.adjust.methods, paired = FALSE,...)
{
    p.adjust.method <- match.arg(p.adjust.method)
    DNAME <- paste(deparse(substitute(x)), "and", deparse(substitute(g)))
    g <- factor(g)
    METHOD <- if (paired)
        "Wilcoxon signed rank test"
    else "Wilcoxon rank sum test"
    compare.levels <- function(i, j) {
        xi <- x[as.integer(g) == i]
        xj <- x[as.integer(g) == j]
# was       wilcox.test(xi, xj, ...)$p.value
        wilcox.test(xi, xj, paired=paired,...)$p.value
    }
    PVAL <- pairwise.table(compare.levels, levels(g), p.adjust.method)
    ans <- list(method = METHOD, data.name = DNAME, p.value = PVAL,
        p.adjust.method = p.adjust.method)
    class(ans) <- "pairwise.htest"
    ans
}

wp = pairwise.wilcox.test(x,g,paired=FALSE,p.adjust.method="none")
wup = pairwise.wilcox.test(x,g,paired=TRUE,p.adjust.method="none")