[R] paired t-test vs pairwise t-test

Duncan Murdoch murdoch at stats.uwo.ca
Thu Aug 19 21:22:12 CEST 2004

On Thu, 19 Aug 2004 13:42:21 -0300 (ADT), Rolf Turner
<rolf at math.unb.ca> wrote :

>You wrote:
>> What's the difference between t.test(x, y) and pairwise.t.test()? Is
>> it just that the former takes two vectors, whereas the latter takes a
>> vector and a factor?
>	No.  The pairwise.t.test() function (according to the help
>	file) does a multiplicity of t-tests, on more than two
>	samples, adjusting the p-value to compensate for the
>	multiplicity by various methods.
>	IMHO the name of this function is bad, because to me it
>	suggests doing ***paired*** t-tests, which would trip up the
>	naive user, who probably wouldn't notice or would ignore the
>	"t tests with pooled SD" message in the output.  As one of
>	the Ripley fortunes says ``It really is hard to anticipate
>	just how silly users can be.''  But why go out of the way to
>	give them a chance to be silly?

And Jack wrote:

>But the documentation, which I valiantly tried to make sense of BEFORE 
>asking my stupid question, is not clear enough for this particular idiot. 
>Might I suggest that the documentation be altered? It could use an example 
>(as in, real-life applied statistical problem) of when pairwise.t.test() 
>ought to be used, and why t.test(paired=TRUE) would be inappropriate in that 
>context; it could also use a reference to some published paper, website or 
>some such that explains the rationale and correct procedure for using this 

I think it's unlikely that we would rename the function; it's been
around a while with its current name so that's a bad idea.  On the
other hand, clearer documentation is always a plus:  why not submit

Duncan Murdoch

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