[R] multiple comparisons/tukey kramer

[Tyler Smith]

Thank you for your response. I think you have misunderstood what I'm
asking, though.

On 2007-11-23, Emmanuel Charpentier <charpent at bacbuc.dyndns.org> wrote:
>
> - Tukey HSD will enable you to test the p(p-1)/2 pair differences one
> can create with p groups ;
> - Dunnett's procedure is made to compare (p-1) "treatments" to a common
> control ;
> - Scheffé's procedure is applicable to *any* ("reasonable") set of
> contrasts you can form ;
> - Newman-Keuls : aims to create separate subset of groups (but has
> serious conceptual and technical flaws ! Don't do that nunless you know
> what you're doing...).
> - etc ...
>
> You'll have to refer to the subject matter to make a choice.

Of course. I also have to know which function in R corresponds to which
test, which is my main question.

> Google ("multiple comparisons") will offer you some dubious and quite a
> few good references...

I have indeed found many dubious and a few good references to multiple
comparisons, both from google and r-site-search. Many posts in the
archive, including one made today in response to another question of
mine, point to glht as the appropriate function to use in R.

However, I don't know what exactly glht does, and the help file is
extremely terse. It offers the following options (in contrMat()):

     contrMat(n, type=c("Dunnett", "Tukey", "Sequen", "AVE", 
                        "Changepoint", "Williams", "Marcus", 
                        "McDermott"), base = 1)

The only reference to the source of these tests is:

     Frank Bretz, Alan Genz and Ludwig A. Hothorn (2001), On the
     numerical  availability of multiple comparison procedures.
     _Biometrical Journal_, *43*(5), 645-656.

This is a very technical paper, which as far as I can follow, is
primarily a discussion of the numerical methods involved in
calculating these contrasts, rather than the contrasts themselves. I
can't decide which one is appropriate without knowing what the
differences are. Dunnett seems pretty straightforward. Tukey, I think,
may refer to what is referred to as the Tukey-Kramer test in other
sources? Are any of them related to Scheffe? I have no idea. None of
them are related to Newman-Keuls, as several archive messages make
very clear that this is not a valid comparison to use, so R doesn't
implement it.

What I need is a reference to the tests implemented in glht, so I can
decide which one is appropriate for my data. Sequen, Changepoint et
al. may be common terms in some fields, but not in the references I'm
working from.

Thanks,

Tyler