[R] nested, unbalanced anova

[peter dalgaard]

On Jan 6, 2013, at 04:00 , Pfeiffer, Steven wrote:

> Hello,
> For an experiment, I selected plots of land within a forest either with
> honeysuckle or without honeysuckle.  Thus, my main factor is fixed, with 2
> levels: "honeysuckle present"(n=11) and "honeysuckle absent"(n=8).
> 
> Within each plot of land, I have a "trenched" subplot and an "untrenched"
> subplot.
> 
> Within each subplot of every plot, I measured soil moisture.  Now I need to
> do a nested Anova to compare the soil moisture values between treatments.
> I don't really want to discard some data to make the sample sizes
> balanced.
> 
> Does anyone know how to do a nested, unbalanced Anova in R?

As far as I can tell, this is still an orthogonal design, so just proceed as usual. You're not in real trouble unless you have plots with one of the subplots missing. The whole thing will boil down to an analysis of the within-plot differences.

Just avoid things like Type-III sums of squares (base R won't do them, but popular add-ons will) because they get it wrong when cell counts are unequal.

-- 
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: pd.mes at cbs.dk  Priv: PDalgd at gmail.com