[R] glm with nesting

[Jeffrey Stratford]

Harold and list,

I've changed a few things since the last time so I'm really starting
from scratch.  

I start with

bbmale <- read.csv("c:\\eabl\\2004\\feathers\\male_feathers2.csv",
header=TRUE)
box <-factor(box)
chick <- factor(chick)

Here's a sample of the data

box,chick,julian,cltchsz,mrtot,cuv,cblue,purbank,purban2,purban1,pgrassk,pgrass2,pgrass1,grassdist,grasspatchk
1,2,141,2,21.72290152,0.305723811,0.327178868,0.003813435,0.02684564,0.06896552,0.3282487,0.6845638,0.7586207,0,3.73
4,1,164,4,18.87699007,0.281863299,0.310935559,0.06072162,0.2080537,0.06896552,0.01936052,0,0,323.1099,0.2284615
4,2,164,4,19.64359348,0.294117388,0.316049817,0.06072162,0.2080537,0.06896552,0.01936052,0,0,323.1099,0.2284615
7,1,118,4,13.48699876,0.303649408,0.31765218,0.3807568,0.4362416,0.6896552,0.06864183,0.03355705,0,94.86833,0.468
12,1,180,4,21.42196378,0.289731361,0.317562294,0.09238011,0.1342282,0,0.2430127,0.8322148,1,0,1.199032
12,2,180,4,18.79487905,0.286052077,0.316367349,0.09238011,0.1342282,0,0.2430127,0.8322148,1,0,1.199032
12,3,180,4,12.83127682,0.260197475,0.292636914,0.09238011,0.1342282,0,0.2430127,0.8322148,1,0,1.199032
15,1,138,4,20.07161467,0.287632782,0.318671887,0.07046477,0.03355705,0.03448276,0.2755622,0.6577181,0.8275862,0,1.503818
15,2,138,4,17.61146256,0.305581768,0.315848051,0.07046477,0.03355705,0.03448276,0.2755622,0.6577181,0.8275862,0,1.503818
15,3,138,4,20.36397134,0.271795667,0.30539683,0.07046477,0.03355705,0.03448276,0.2755622,0.6577181,0.8275862,0,1.503818
15,4,138,4,20.81940158,0.269468041,0.304160648,0.07046477,0.03355705,0.03448276,0.2755622,0.6577181,0.8275862,0,1.503818

As you can see I have multiple boxes (> 70).  Sometimes I have multiple
chicks per box each having their own response  to mrtot, cuv, and cblue
but the same landscape variables for that box.  Chick number is randomly
assigned and is not an effect I'm interested in.  I'm really not
interested in the box effect either.  I would like to know if landscape
affects the color of chicks (which may be tied into chick
health/physiology).  We also know that chicks get bluer as the season
progresses and that clutch size (cltchsz) has an effect so I'm including
that as covariates.  

Hopefully, this clears things up a bit. 

I do have the MASS and MEMS (Pineiro's) texts in hand. 

Many thanks,

Jeff