[R] lme: how to nest a random factor in a fixed factor?
Robert Buitenwerf
buitenwerfrobert at hotmail.com
Wed Aug 26 16:23:40 CEST 2009
Dear all,
I have an experimental setup in which a random variable is nested within a fixed variable; however I have troubles specifying the correct LMM with lme. I have searched the lists but haven't been
able to find an example like my setup, which I unfortunately need to get this stuff right. Pinheiro & Bates is great but I still can't figure out how to do it.
My experimental setup was as follows:
100 measurements per treatment plot
2 treatment plots per site
4 sites: 2 in one area and 2 in another area
Both treatment and area are fixed factors,while site is random. I am interested in the significance of the fixed effects,less in the magnitude of the random effect.
I have tried:
mod1 <- lme(response ~ area*treatment, data=data,random= ~1|site)
but now site is not nested in area…
mod2 <- lme(response ~ area*treatment, data=data,random= ~1|area/site)
but now area is both a fixed and a random variable, which doesn't seem to make sense, plus I run out of df for treatment
mod3 <- lme(response ~ area*treatment, data=data,random= ~1| plot)
but here plots are not grouped according to site
I hope someone would be willing to help me,
thank you in advance!
Robert Buitenwerf
Ecologist
South African Environmental Observation Network
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