Re: [R] ANOVA model

From: Douglas Bates <>
Date: Fri 22 Apr 2005 - 02:28:10 EST

Street N.R. wrote:
> Hi,
> Could someone tell me if this is the correct model syntax for the
> following dataset:
> lme(height~treatment+genotype+treatment*genotype,drought,random=~genotyp
> e)
> The dataset has two factors: one fixed - treatment, and one random -
> genotype. I need to test the effect of both factors to identify their
> significance. There are multiple (but not equal) replicates at each
> level of genotype (the replicates are independent biological samples).
> What I need are the p values for genotype, treatment and their
> interaction. It is the specification of the random factor that I am
> unsure of.
> Also, does anyone know if biologists 'expect' to see type I or type III
> SS results presented in a standard (i.e. non statistical) journal
> article?

I'm not sure exactly what you want but the syntax you have given won't work. If you say that you want a fixed effect for treatment plus random effects for genotype and for the treatment:genotype interaction then I would write the model as

lme(height ~ treatment, drought, random = list(genotype = ~ treatment - 1))

or, from the lme4 package,

lmer(height ~ treatment + (treatment - 1 | genotype), drought)

How many levels of treatment do you have? If you have k levels you will end up estimating (k * (k + 1))/2 variance-covariance parameters for the random effects. This is not difficult for a small value of k but larger k would produce a problem.

I'm not even going to start discussing Type I and Type III sums of squares again. There has been an active thread on that topic for the last several days. Please refer to the archives. mailing list PLEASE do read the posting guide! Received on Fri Apr 22 02:33:58 2005

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