mcmcpvalue and contrasts
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. Hank
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 http://www.cas.muohio.edu/~stevenmh/ http://www.cas.muohio.edu/ecology http://www.muohio.edu/botany/ "If the stars should appear one night in a thousand years, how would men believe and adore." -Ralph Waldo Emerson, writer and philosopher (1803-1882)