[R] Nested ANOVA models in R

From: Daniel Bolnick <danbolnick_at_mail.utexas.edu>
Date: Tue, 05 Feb 2008 22:28:22 -0600


I'm trying to work through a Nested ANOVA for the following scenario: 20 males were used to fertilize eggs of 4 females per male, so that female is nested within male (80 females used total). Spine length was measured on 11 offspring per family, resulting in 880 measurements on 80 families.

I used the following two commands:

summary(aov(Spinelength ~ Male*Female))

summary(aov(Spinelength ~ Male/Female))

I get the same mean squares either way, which doesn't seem right to me. In the former case, the mean square for females should be calculated around the overall mean across all females, whereas the mean square in the latter case should be calculated using deviations from the set of 4 females nested within a given male, right?

Of course, it is more appropriate for me to treat each of these as random effects. I know Bates has objections to the SAS-style partitioning variances to obtain F statistics and p-values, and I have read relevant parts of Pinhero and Bates, but how can a specify a nested random effects model that yields p-values for both the males (tested against MS for females) and females nested within males?


Dan Bolnick
Section of Integrative Biology
University of Texas at Austin

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