[R] lme: how to nest a random factor in a fixed factor?

ONKELINX, Thierry Thierry.ONKELINX at inbo.be
Wed Aug 26 17:18:29 CEST 2009

Dear Robert,

Since you have only 4 sites, a random effect is not so good. You would
need at least 6 sites for a good estimate of the variance. You have
enough data to treat site as a fixed effects. It only costs 2 extra
degrees of freedom. Therefore I would model this like: 

lm(response ~ (area/site)*treatment, data = data)



ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature
and Forest
Cel biometrie, methodologie en kwaliteitszorg / Section biometrics,
methodology and quality assurance
Gaverstraat 4
9500 Geraardsbergen
tel. + 32 54/436 185
Thierry.Onkelinx at inbo.be

To call in the statistician after the experiment is done may be no more
than asking him to perform a post-mortem examination: he may be able to
say what the experiment died of.
~ Sir Ronald Aylmer Fisher

The plural of anecdote is not data.
~ Roger Brinner

The combination of some data and an aching desire for an answer does not
ensure that a reasonable answer can be extracted from a given body of
~ John Tukey

-----Oorspronkelijk bericht-----
Van: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org]
Namens Robert Buitenwerf
Verzonden: woensdag 26 augustus 2009 16:24
Aan: R Help
Onderwerp: [R] lme: how to nest a random factor in a fixed factor?

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

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


South African Environmental Observation Network
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