[R] extract t-values from pairwise.t.test

[Petr Pikal]

Hallo

I am not sure but this could be what you want. You has to change 
function compare.levels not only add t.val in ans. If you want t-
values AND p-values together in one table it probably is not so 
simple.

my.pairded.t.test <- function (x, g, p.adjust.method = 
p.adjust.methods, pool.sd = TRUE,
    ...)
{
    DNAME <- paste(deparse(substitute(x)), "and", 
deparse(substitute(g)))
    g <- factor(g)
    p.adjust.method <- match.arg(p.adjust.method)
    if (pool.sd) {
        METHOD <- "t tests with pooled SD"
        xbar <- tapply(x, g, mean, na.rm = TRUE)
        s <- tapply(x, g, sd, na.rm = TRUE)
        n <- tapply(!is.na(x), g, sum)
        degf <- n - 1
        total.degf <- sum(degf)
        pooled.sd <- sqrt(sum(s^2 * degf)/total.degf)
        compare.levels <- function(i, j) {
            dif <- xbar[i] - xbar[j]
            se.dif <- pooled.sd * sqrt(1/n[i] + 1/n[j])
            t.val <- dif/se.dif
            #  2 * pt(-abs(t.val), total.degf) 	this is commented out
            t.val    # this is added
        }
    }
    else {
        METHOD <- "t tests with non-pooled SD"
        compare.levels <- function(i, j) {
            xi <- x[as.integer(g) == i]
            xj <- x[as.integer(g) == j]
            t.test(xi, xj, ...)$statistic     	# this is changed in case 
					          	# pool.sd=F
        }
    }
    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
}

HTH
Petr




On 8 Aug 2005 at 18:28, Guido Parra Vergara wrote:

> Hi,
> 
> I am not familiar with changing R functions. I 
> can see in the code that t-values get calculated 
> as t. val, however when I modified the code to 
> include t.val under ans and then run the modified 
> function I get  Object "t.val" not found. How do 
> I properly modify the function to list t. val in the output?
> 
> Thanks
> Guido
> 
> 
> 
> At 05:20 PM 8/08/2005, Peter Dalgaard wrote:
> >Guido Parra Vergara <guido.parravergara at jcu.edu.au> writes:
> >
> > > Hi,
> > >
> > > how can I extract the t-values after running a pairwise.t.test?
> > > The output just list the p-values. Many thanks for your help.
> >
> >It's not a very complicated function. Why not just modify it to your
> >needs?
> >
> >--
> >    O__  ---- Peter Dalgaard             Řster Farimagsgade 5, Entr.B
> >   c/ /'_ --- Dept. of Biostatistics     PO Box 2099, 1014 Cph. K
> >  (*) \(*) -- University of Copenhagen   Denmark          Ph:  (+45)
> >  35327918
> >~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk)                  FAX: (+45)
> >35327907
> 
> ____________________________________
> 
> Guido J. Parra
> School of Tropical Environment Studies and Geography
> James Cook University
> Townsville
> Queensland 4811
> 
> Phone:  61 7 47815824
> Fax:            61 7 47814020
> Mobile: 0437630843
> e-mail:         guido.parravergara at jcu.edu.au
> 
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Petr Pikal
petr.pikal at precheza.cz