[R] Nested ANOVA in R

[Majid Iravani]

Dear R users,

I installed an experiment as following setup:

- Four plant species
- Seed addition as main factor with two levels: control and seed addition.
- Four replicates (sites)
- 8 plots in each site arranged as two rows (each rows 4 plots) one meter 
far from each other
- Four sub-plots in each plot (therefore 32 sub-plots in each site)
- In the four plots in each site (first row of plots) seeds of each of four 
plant species were sowed onto one sub-plot by random (therefore 4 sub-plots 
sown by a plant species in four different plots in each site).
In the other four plots (second row of plots) one sub-plot selected by 
random as control for each of four plant species (therefore 4 sub-plots in 
four different plots in each site as control for a plant species).

Now, my first question is about the name of this design. I thought this is 
a 3-factor split-plot arrangement.

My second question is about data analysis for this experiment in R. I would 
like to test the effect of seed addition and sites on the seedling 
emergence of each plant species separately using a three- way ANOVA (??). 
Because of the hierarchical experimental design, the experiment must be 
analyzed by nested ANOVA but I do not know how I must arrange dataset and 
then how to write ANOVA model in R.

I would greatly appreciate if somebody gives me some comments on these cases

Thank you very much in advance,

Majid
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  Majid Iravani
  PhD Student
  Swiss Federal Research Institute WSL
  Research Group of Vegetation Ecology
  Zürcherstrasse 111  CH-8903 Birmensdorf  Switzerland
  Phone: +41-1-739-2693
  Fax: +41-1-739-2215
  Email: Majid.iravani at wsl.ch
http://www.wsl.ch/staff/majid.iravani/