[R-sig-ME] mcmcpvalue and contrasts

Hank Stevens HStevens at MUOhio.edu
Mon Mar 3 14:44:43 CET 2008

Hi Ken,
Have you seen the multicomp package? I found it pretty useful. Others  
have written packages that include their favorite ways of coding  
contrasts including packages Hmisc, gmodels, and contrast.
On Feb 29, 2008, at 5:25 PM, Ken Beath wrote:

> On 28/02/2008, at 4:42 AM, Hank Stevens wrote:
> <snip>
>> I have found, however, that it is often, yea, even more often, the
>> case that one factor, A, has a large independent effect, and that
>> another factor, B, moderates the effect of A to a small, albeit
>> detectable,  degree. In these cases, it makes biological sense to
>> discuss the "independent" effect of A. Whether one cloaks this in an
>> "average" effect of A, or states that the effect of A is "at least
>> b0, and as high as b0+b1, given some value of B."  I understand the
>> caution you express above -- I just did't want to see the baby go
>> along with the bath water.
> There is nothing wrong with calculating an average effect, just that
> it needs to be explicit that it is for a certain population. Most
> programs allow for calculating combinations of parameter estimates,
> but I can't see anything to do this directly in R, so maybe it's
> expected that the user works out the linear algebra. One thing that
> helps is to reparameterise the model, so rather than fitting an
> interaction, the estimates are for the effect of A for the levels of
> B, so that the calculations are for a weighted sum.
> Ken

Dr. Hank Stevens, Associate Professor
338 Pearson Hall
Botany Department
Miami University
Oxford, OH 45056

Office: (513) 529-4206
Lab: (513) 529-4262
FAX: (513) 529-4243

"If the stars should appear one night in a thousand years, how would men
believe and adore." -Ralph Waldo Emerson, writer and philosopher  

More information about the R-sig-mixed-models mailing list