[R] glm with nesting

[Jeffrey Stratford]

I just had a manuscript returned with the biggest problem being the
analysis.  Instead of using principal components in a regression I've
been asked to analyze a few variables separately. So that's what I'm
doing.

I pulled a feather from young birds and we quantified certain aspects of
the color of those feathers.  Since I often have more than one sample
from a nest, I thought I should use a nested design. 

Here's the code I've been using and I'd appreciate if someone could look
it over and see if it was correct. 

bb.glm1 <- glm(rtot ~ box/(julian +purbank), data=bbmale,
family="gaussian", na.action=na.omit)

where rtot = total reflectance, box = nest box (i.e., birdhouse), 
julian = day of the year and purbank = the proportion of urban cover in
a 1 km buffer around the nest box.  I'm not interested in the box effect
and I've seperated males and female chicks.   

 I've asked about nestedness before and I was given code that included
"|" to indicate nestedness but this indicates a grouping does it not?  I
suspect that there is something wrong.  In the summary I get 

Coefficients:
              Estimate Std. Error t value Pr(>|t|)    
(Intercept)  2.880e-01  3.224e-03  89.322   <2e-16 ***
box         -3.219e-05  6.792e-05  -0.474    0.636    
box:julian   7.093e-08  3.971e-07   0.179    0.859    
box:purbank -1.735e-05  1.502e-04  -0.115    0.908   

The other question I have is how do I test a null hypothesis - no
explanatory variables?  [rtot ~ NULL?]

Many 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