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

Liaw, Andy andy_liaw at merck.com
Thu Aug 19 21:42:49 CEST 2004

> From: Duncan Murdoch
> 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 
> >test.
> 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
> some?

I guess this is sort of related to the thread on whether R is good for
non-statisticians...  The help pages in R are sort of like *nix man pages.
They give the technical information about the topic, but not necessarily the
background.  E.g., the man page for `chmod' does not explain file
permissions in detail: the user is expected to learn that elsewhere.

Perhaps other stat packages do it differently?  Does SPSS manuals detail
what its t-test procedure does, including which t-test(s) it does and when
it's appropriate?  That might make it easier on users, but I still think the
users should learn the appropriate use of statistical procedures


> Duncan Murdoch
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