[R] regression with nestedness

Spencer Graves spencer.graves at pdf.com
Thu Jan 26 02:05:35 CET 2006

	  Have you considered "lme" in library(nlme)?  The companion book 
Pinheiro and Bates (2000) Mixed-Effects Models in S and S-Plus 
(Springer) is my favorite reference for this kind of thing.  From what I 
understand of your question, you should be able to find excellent 
answers in this book.  [You could also try "lmer" associated with the 
lme4 package.  However, many of the helper functions needed to do what 
you want are available for "lme" but not yet for "lmer";  "lmer" can do 
things that "lme" can not, but it doesn't sound like you need any of 
those extra features.  Even if you did, I would suggest you first ignore 
those issues and see what you can get from "lme".]

	  If this is not adequate and you would like more help from this list, 
please submit another post.  Before you do, however, PLEASE do read the 
posting guide! "www.R-project.org/posting-guide.html", especially the 
part about providing a brief but self-contained toy example illustrating 
what you tried to do and why it was not adequate.

Jeffrey Stratford wrote:

> Dear R-users,
> I set up an experiment where I put up bluebird boxes across an
> urbanization gradient.  I monitored these boxes and at some point I
> pulled a feather from a chick and a friend used spectral properties
> (rtot, a continuous var) to index chick health.  There is an effect of
> sex that I would like to include but how would I set up a regression and
> look at the effect of urbanization (purban, a continuous var)) on
> feather properties of chicks within boxes.  
> So the model should look something like rtot = sex + purban +
> (chick)clutch
> Also, when I plot purban against rtot using the plot function I get
> boxplots but I would like to ignore the clutch and just plot each point.
>  I've tried type = "p" but this has no effect.  
> Thanks,
> Jeff
> ****************************************
> Jeffrey A. Stratford, Ph.D.
> Postdoctoral Associate
> 331 Funchess Hall
> Department of Biological Sciences
> Auburn University
> Auburn, AL 36849
> 334-329-9198
> FAX 334-844-9234
> http://www.auburn.edu/~stratja
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