[R] Type I or III SS with mixed model function lme

From: Bill Shipley <bill.shipley_at_usherbrooke.ca>
Date: Tue, 06 May 2008 14:12:45 -0400

Hello, I have come across a result that I cannot explain, and am hoping that someone else can provide an answer. A student fitted a mixed model using the lme function: out<- lme(fixed=Y~A+B+A:B, random=~1|Site). Y is a continuous variable while A and B are factors. The data set is balanced with the same number of observations in each combination of A and B. There are two hierarchical levels: Site and plots nested in site.  

He tried two different ways of getting theANOVA table: anova(out) and anova(out, type=”marginal”).  

Since the data were balanced, these two ways should (I think) give the same output since they correspond to Type I and III sums of squares in the SAS terminology. At least, this is the case with normal (i.e. not mixed) linear models. However, he finds very different results of these two types of ANOVA tables. Why?  

Bill Shipley

North American Editor, Annals of Botany

Département de biologie

Université de Sherbrooke

Sherbrooke (Québec) J1K 2R1

Canada

(819) 821-8000, poste 62079

(819) 821-8049 FAX
   <http://pages.usherbrooke.ca/jshipley/recherche/> http://pages.usherbrooke.ca/jshipley/recherche/  

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