[R] Anova problem with order of terms in model

Berton Gunter gunter.berton at gene.com
Tue Jan 17 22:13:34 CET 2006

I suggest you consult a local statistician or read up on linear
models,perhaps by reading the relevant section of V&R's MASS. Also search
the R-Help archives for "Type III SS." Further comments below.

-- Bert Gunter
Genentech Non-Clinical Statistics
South San Francisco, CA
"The business of the statistician is to catalyze the scientific learning
process."  - George E. P. Box

> -----Original Message-----
> From: r-help-bounces at stat.math.ethz.ch 
> [mailto:r-help-bounces at stat.math.ethz.ch] On Behalf Of Martin Julien
> Sent: Tuesday, January 17, 2006 12:34 PM
> To: r-help at stat.math.ethz.ch
> Subject: [R] Anova problem with order of terms in model
> Hi 
> I have a linear model and I want to tests whether the model terms are
> significant
> I used anova but F and P value depend on the order of the terms in the
> model.

Correct. Differennt hypotheses are being tested. R does **sequential** SS
(this preserves additivity/orthogonality of contrasts being tested). In a
non-orthogonal designs, these depend on order.  

> I have repeated the same analysis in another stat software 
> and F and P value
> did not differ with order of terms in the model.
> Can anyone can explain what happen or what am I doing wrong ?

And this "other software" is not doing a sequential SS, but rather what is
usually called Type III SS (google on "Type III SS" for more info).

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