[R] lme with nested factor and random effect

Mari Pesek marifrances at gmail.com
Thu Dec 15 19:48:17 CET 2011

Hello all,

I'm having difficulty with setting up a mixed model using lme in the
nlme package. To summarize my study, I am testing for effects of
ornamentation on foraging behavior of wolf spiders. I tested spiders
at two different ages (penultimate vs. mature) and of two different
phenotypes (one species tested lacks ornamentation throughout life
[non-ornamented males] while the other acquires ornamentation upon
maturation [i.e. brush-legged males]). I tested a sample of
brush-legged and non-ornamented males (as both penultimates and
matures) in 2009, and an additional sample of brush-legged males in
2010 (as both penultimates and matures again) because I had a very
small sample of brush-legged males in 2009.

I would like to set up my lme so the fixed effects are "age"
(penultimate vs mature), "phenotype" (non-ornamented vs brush-legged),
and "year" (2009 vs 2010) nested within "phenotype" to test for
differences between the two samples of brush-legged males.
Additionally I want to include "id" (a unique identification number
given to each spider tested) as a random factor to account for testing
each individual twice (once as a penultimate and once as a mature).

So far I have the following code: lme(behavior ~ age*phenotype,
random=~1|maturity/id, data)

But I don't know how to include the code to nest year within phenotype
while testing for all possible interactions. Any help would be greatly

Thank you!
Mari Pesek

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