[R] Split-split plot ANOVA

[Mike Saunders]

Jesus and the rest of the R-help community:

Thanks for your help.  I have been going over and over the examples in MASS 
and the Pinheiro and Bates example, but cannot get my model to run correctly 
with either aov or lme.  Could someone give me a hand with the correct model 
statement?

First a description of the design.  We are studying germination rates for 
various species under a variety of treaments.  This is a blocked split-split 
plot design.  The levels and treatments are:

Blocks:  1-6

Whole plot treatment:
   Overstory:  Yes or No

Split plot treatments:
   Caging (to protect against seed predators):  Yes or No
   Herbaceous competition (i.e., grass):  Yes or No

Split-split plot treatment:
   Tree species:  7 kinds

The response variable is Lag, which is a indication of when the seeds first 
germinated.  I will be doing this analysis for a couple other response 
variables as well in separate analyses.

I have had mixed results using the examples as a guide to build my 
statement; I am unsure how to specify the crossed factors at the split-plot 
level.

Lastly, I have unbalanced data since some treatment combinations never had 
any germination.  Since the data are highly nonnormal, I hope to do a 
permutations test on the F-values for each main effect and interaction in 
order to get my p-values.

Thanks for your help in advance,
Mike

Mike Saunders
Research Assistant
Forest Ecosystem Research Program
Department of Forest Ecosystem Sciences
University of Maine
Orono, ME  04469
207-581-2763 (O)
207-581-4257 (F)

----- Original Message ----- 

From: "Jesus Frias" <Jesus.Frias at dit.ie>
To: "Mike Saunders" <mike_saunders at umenfa.maine.edu>; "R Help" 
<r-help at stat.math.ethz.ch>
Sent: Tuesday, February 01, 2005 10:57 AM
Subject: RE: [R] Split-split plot ANOVA


Hi Mike,

*An example of the use of aov() for a split-plot is in MASS

library(MASS)
example(Oats)
The book also gives a detailed explanation

*pp 45-52 of the Pinheiro and Bates book gives you an example of the use of
lme() on a split-plot. If you have a non balanced design,  lme() from the
nlme library might be a better tool than aov().

Also, if you have the lme4 library installed you'll have a lot more
flexibility on the formulation of your random effects.

regards,

Jesus

--------------------------------------------------------------
Jesús María Frías Celayeta
School of Food Sci. and Env. Health.
Faculty of Tourism and Food
Dublin Institute of Technology
Cathal Brugha St., Dublin 1. Ireland
t +353 1 4024459 f +353 1 4024495
w www.dit.ie/DIT/tourismfood/science/staff/frias.html
--------------------------------------------------------------

> -----Original Message-----
> From: r-help-bounces at stat.math.ethz.ch
> [mailto:r-help-bounces at stat.math.ethz.ch]On Behalf Of Mike Saunders
> Sent: 01 February 2005 14:36
> To: R Help
> Subject: [R] Split-split plot ANOVA
>
>
> Does someone out there have an example of R-code for a
> split-split plot ANOVA using aov or another function?  The design
> is not balanced.  I never set up one in R before and it would be
> nice to see an example before I tackle a very complex design I
> have to model.
>
> Thanks,
> Mike
>
> Mike Saunders
> Research Assistant
> Forest Ecosystem Research Program
> Department of Forest Ecosystem Sciences
> University of Maine
> Orono, ME  04469
> 207-581-2763 (O)
> 207-581-4257 (F)
>
> [[alternative HTML version deleted]]
>
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