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Revision 18 as of 2014-01-16 10:28:46

location: FAQ / Rss

Sums of Squares used by R in lm, aov and lmer

R calculates sequential or Type I SS by default when using lm, lmer and aov as opposed to the type III SS (default in SPSS) which partials out effects of other terms in the model. A hierarchical approach is suggested which gives the same results for both sums of squares and only looks at the highest order terms in a model.

Type III SS may be obtained using terms of form 

fit <- anova(lm(y~x+z)) 
anova(fit, ssType=3)

and 

model.2 <- lme(y~a + b, random=~1|group)
anova(model.2,type="marginal")

for lm, aov and lme. The Anova() procedure can be used to obtain type 3 sums of squares for lmer in R. The Anova () procedure is available by downloading the car extension package from here and can be inserted into the R library folder located in C:\Program Files\R\R2.x. You can also use the summary() procedure, for obtaining type III SS for lmer from version 2.7.2 of R.