[R-sig-ME] Random formula

ONKELINX, Thierry Thierry.ONKELINX at inbo.be
Mon Jun 15 17:00:23 CEST 2009

Dear Sebastiaan,

Models with nested random effects can be done with nlme. Have a loot at
section 4.2.3 of Pinheiro and Bates (2000) Mixed effects models in S and

You will need something like

lme(response ~ climate_factor*pruning, random = list(provenance = ~
pruning, tree = ~1))



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-sig-mixed-models-bounces at r-project.org
[mailto:r-sig-mixed-models-bounces at r-project.org] Namens De Smedt
Verzonden: maandag 15 juni 2009 16:23
Aan: r-sig-mixed-models at r-project.org
Onderwerp: [R-sig-ME] Random formula


I measured leaf characteristics. The leaves are grouped in trees which
are, on their turn, grouped in provenances.
I want to model those leaf characteristics in function of climate
variables (measured on provenance level) and pruning characteristics
(measured on tree level). I also want to see if the effect of pruning
differs between provenances (provenance-pruning interaction).
The problem is that there cannot be an interaction between pruning and
tree, because pruning is measured on tree level. 

in lme4, I think I can specify this model as follows:

response ~ climate_factor*pruning + (pruning|provenance) +

Or is there another way?

Is it possible to define this model in the nlme library (I need a
variance structure, which doesn't exist in lme4)?

Thanks a lot!

Sebastiaan De Smedt
Department of Bioscience Engineering
University of Antwerp
Tel.: +32 (0)3 265 35 17
Fax.: +32 (0)3 265 32 25

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