[R-sig-eco] Unbalnced nested ANOVA

[Stephen Cole]

Hello R help

I have read over many of the help threads on the regular r help
archive and must admit i am still confused.

The data set i wish to analyze is a 2 level nested design with both
factors random.

Response variable: Density of barnacles

Explanatory one: Region ( 4 regions)
Explanatory two: Site nested within region (this is where the
unbalance is...... 3 regions have 6 sites each, 1 region has 3 sites)

The hypothesis I wish to test; Is there a difference among regions in
density, and are there differences among sites nested within region.

I know that i shouldn't (can't) use the aov function as i have read in
the help files that it can not deal with unbalanced designs.  So i
guess what i need to do is use the lm function, however i am unsure
what to do with the type II or III sums of squares.  I realize that
this decision is dictated by my hypothesis but what i dont know is
which type my hypothesis dictates.  there seems to be an issue with
interaction terms and order of factors in the model.  However neither
of these issues appliy to my data (at least i dont think so).

What i would really like by way of help is a guide to some sort of
reference i can use to A) learn about the issue, and B) cite as the
reason that i can analyze an unbalanced design as the work I am doing
will at some point be submitted for publication ( I hope).

Thanks for any help and advice in advance.

Stephen Cole
Graduate Student
Marine Ecology Lab
STFX