[R-sig-eco] Help with mixed-effects model in lme

[ONKELINX, Thierry]

Dear Jonathan,

I would move the block factor from the ramdom effects to the fixed
effects. You have only two levels of that, which can give rather
unprecise estimates of the variance of the random effects. Moving block
to the fixed effects will cost you only one degree of freedom. So that
would not be a big problem.

lme(species.richness ~ water*fuel*seed*year + block, random = ~1 |plot) 

HTH,

Thierry


------------------------------------------------------------------------
----
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
Belgium
tel. + 32 54/436 185
Thierry.Onkelinx at inbo.be
www.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
data.
~ John Tukey

-----Oorspronkelijk bericht-----
Van: r-sig-ecology-bounces at r-project.org
[mailto:r-sig-ecology-bounces at r-project.org] Namens Jonathan Myers
Verzonden: donderdag 17 september 2009 22:52
Aan: r-sig-ecology at r-project.org
Onderwerp: [R-sig-eco] Help with mixed-effects model in lme

Dear List Members,

I am using a mixed-effects model in lme and would like to know whether I
am using the proper structure for the random-effects component of the
model. My experiment consists of three categorical treatments (fire,
water, seed) arranged in a split-plot design. The fire treatment (2
levels) and water treatment (3 levels) were assigned to plots, and the
seed treatment (2
levels) was assigned to two subplots within each plot. There are 60
total plots (120 total subplots), divided equally among two large blocks
(30 plots per block). I measured species richness in each subplot in
three separate years. My goal is to test for main effects of the three
treatments, a main effect of year, and all interactions. My current
model consists of four factorial fixed effects (fire, water, seed, year)
and 1 random effect (block), with plots nested within blocks (to account
for the split-plot structure of the experiment):

model = lme(species.richness ~ water*fuel*seed*year, random = ~1 |
block/plot)

The ANOVA output includes two denominator degrees of freedom (denDF): 53
denDF for plot factors (fire, water, fire x water interaction) and 270
denDF for split-plot factors (everything else).

I would greatly appreciate feedback as to whether the random-effects
component of the model looks appropriate, and if not, how it should be
modified.

Thanks very much!

Cheers,

Jonathan


~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Jonathan A. Myers
Department of Biological Sciences
Division of Systematics, Ecology, and Evolution Louisiana State
University Baton Rouge, LA 70803 USA

E-mail: jmyer19 at lsu.edu
Telephone: 225-578-7567
Fax: 225-578-2597

Website: http://www.biology.lsu.edu/labpages/harmslab/jmyers/index.html
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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