[R] glm with nesting

From: Jeffrey Stratford <stratja_at_auburn.edu>
Date: Thu 05 Oct 2006 - 10:46:36 GMT

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


              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,


Jeffrey A. Stratford, Ph.D.
Postdoctoral Associate
331 Funchess Hall
Department of Biological Sciences
Auburn University
Auburn, AL 36849
FAX 334-844-9234


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