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extract t-values from pairwise.t.test

6 messages · Guido Parra Vergara, PIKAL Petr, Simon Blomberg +1 more

Guido Parra Vergara
# 
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.

Cheers
Guido



____________________________________

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
PIKAL Petr
# 
Hallo

My output lists more than p-values
Paired t-test

data:  rnorm(10) and rnorm(10) 
t = 1.7508, df = 9, p-value = 0.1139
alternative hypothesis: true difference in means is not equal to 0 
95 percent confidence interval:
 -0.1750263  1.3735176 
sample estimates:
mean of the differences 
              0.5992456
List of 9
 $ statistic  : Named num 1.75
  ..- attr(*, "names")= chr "t"
 $ parameter  : Named num 9
  ..- attr(*, "names")= chr "df"
 $ p.value    : num 0.114
 $ conf.int   : atomic [1:2] -0.175  1.374
  ..- attr(*, "conf.level")= num 0.95
 $ estimate   : Named num 0.599
  ..- attr(*, "names")= chr "mean of the differences"
 $ null.value : Named num 0
  ..- attr(*, "names")= chr "difference in means"
 $ alternative: chr "two.sided"
 $ method     : chr "Paired t-test"
 $ data.name  : chr "rnorm(10) and rnorm(10)"
 - attr(*, "class")= chr "htest"
t 
1.750790
The output is list and you can call any part of it by its name or by [] 
braces.

HTH
Petr
On 8 Aug 2005 at 16:26, Guido Parra Vergara wrote:

            

      
      
      
    

        

      
      
    

        
Petr Pikal
petr.pikal at precheza.cz

  
  


  


      

    

    

      
      

        


  

        

      Simon Blomberg
    

    

      
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I think the questioner was interested in pairwise.t.test. See 
?pairwise.t.test. From looking at the source, pairwise.t.test calls t.test 
if sd's are not pooled, or calculates its own t.val if sds are pooled. It 
looks very easy to hack to return the t values instead of the p values.

Simon.

        
At 04:46 PM 8/08/2005, Petr Pikal wrote:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Peter Dalgaard
    

    

      
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Guido Parra Vergara <guido.parravergara at jcu.edu.au> writes:

            

      
      
      
    

        
It's not a very complicated function. Why not just modify it to your
needs?

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Guido Parra Vergara
    

    

      
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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 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

  
  


  


      

    

    

      
      

        


  

        

      PIKAL Petr
    

    

      
      #
    

  


  

      
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:

        

            

      
      
      
    

        

      
      
    

        
Petr Pikal
petr.pikal at precheza.cz