[R] multiple comparisons/tukey kramer

[Tyler Smith]

Hi,

I'm trying to make sense of the options for multiple comparisons
options in R. I've found the following options:

pairwise.t.test, which provides standard t-tests, with options for
choosing an appropriate correction for multiple comparisons

TukeyHSD, which provides the usual Tukey test

glht(package multcomp), which provides a variety of options

>From the help list, it appears that glht is the preferred approach.
However, I don't understand what the options are. ?glht refers to a
very technical paper on the numerical computations involved, and I
couldn't find a description corresponding to the McDermott or AVE
options. I did notice that the Tukey option provides the same result
as TukeyHSD for balanced data. Is this the same as Tukey-Kramer?

As I understand it, there is no universal consensus as to which test
is best. TukeyHSD appears to be appropriate for balanced designs. I
have an unbalanced design to analyze. I can use glht, but can someone
tell me what each option is actually calculating? A reference to a
paper that describes the procedures would be great, but I'm afraid I
the one offered in ?glht[1] is beyond me.

Thanks,

Tyler

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