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

[Dunbar, Michael]

Dear Jonathan

A couple of things.

If your have treatments applied to sub-plots then it makes sense to have subplot in the random component, i.e. random = ~1|plot/subplot.

The other issue you have is ALL interactions. With four factors, this is an awful lot of interactions which together will eat a lot of degrees of freedom which would be better in your residual. In the most extreme case, unless you have replicate samples within each year and sub-plot, you may not even be able to estimate the four way interaction correctly. Are you sure that if you see a one of the three way interactions or the four way interaction that you can explain what it means ecologically? 

cheers
Mike


-----Original Message-----
From: r-sig-ecology-bounces at r-project.org [mailto:r-sig-ecology-bounces at r-project.org] On Behalf Of Jonathan Myers
Sent: 17 September 2009 21:52
To: r-sig-ecology at r-project.org
Subject: [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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