Dear Matthew,
You specified year as a the grouping variable. In your case the tree id should
be the grouping variable. So the most simple random effect is ~1|id, which is a
random intercept for each tree. A more complex random effect would be ~
year|id, a random intercept and a random slope by year for each tree. You could
make it even more complex by using ~factor(year)|id as a random effect.
HTH,
Thierry
PS Have a look in the archives of R-sig-mixed, the list dedicated to mixed
models.
-----Oorspronkelijk bericht-----
Van: [EMAIL PROTECTED] namens Landis, R Matthew
Verzonden: wo 21-5-2008 19:54
Aan: 'r-sig-ecology@r-project.org'
Onderwerp: [R-sig-eco] nlme model specification
Greetings R-eco folks,
I'm trying to analyze a dataset on tree growth rates to see which factors are
important (and their relative importance too, if I can get that), and I'm
having some trouble figuring out how to specify the model, despite having
carefully read Pinheiro and Bates, the help files for nlme, Crawley's book on
Statistics with S, MASS, and other books besides.
The dataset consists of ~ 300 trees measured annually for 10 years. So, I have
9 pseudo-replicated intervals over which to assess growth (about 2700 rows in
the dataset). There are 5 different explanatory factors, which are a
combination of continuous variables and categorical factors. Some of these
vary with time. In the end, I would like to get both coefficient estimates and
partial R2 (or some other way of ranking them) for each factor. Unlike most
time-series examples in the books, I am not interested in how growth varies
with time, nor am I particular interested in interactions of explanatory
factors with time.
Based on this, I've convinced myself that I should specify the model as:
fit <- lme(fixed = growth ~ (x1 + x2 + x3+ x4 + x5)^2, random = ~1|year, method
= 'ML')
Year is clearly a random effect, and is the grouping variable for the analysis.
Each of the other coefficients is "inner" to this variable. I'm ignoring
individual tree as a grouping factor, since I don't want to estimate separate
coefficients for each tree. Does this sound like the correct way to do this?
Thanks for any help. Apologies if this is more of a statistics question and
less of an R question.
Matt Landis
****************************************************
R. Matthew Landis, Ph.D.
Dept. Biology
Middlebury College
Middlebury, VT 05753
tel.: 802.443.3484
**************************************************
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