[R] Expected pairwise.student.t and TukeyHSD behavior?

[Rolf Turner]

On 25/03/2010, at 4:03 PM, Walmes Zeviani wrote:

> 
> This is because pairwise.student.t and TukeyHSD use differents estimates for
> error term. TukeyHSD use the parameters covariance matrix and t use sample
> variance. In this case a treatment with only one value doesn't have sample
> variance but has a estimated standard error in a covariance matrix. The
> lines below will illustrate the point:
> 
> # toy data
> da <- data.frame(A=factor(rep(c("a","b","c"), c(1,5,7))))
> da$y <- rnorm(da$A)
> 
> # sample variance
> tapply(da$y, da$A, var)
> pairwise.t.test(da$y, da$A, p.adj="none") # problem!


The problem could be avoided if pairwise.t.test() were just a little
bit cleverer about how it calculated the pooled standard deviation.

I think that

	pooled.sd <- sqrt(sum(s^2 * degf,na.rm=TRUE)/total.degf)

would do the trick.

It's probably not worth the effort, but.

	cheers,

		Rolf Turner
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