= 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
[[http://tolstoy.newcastle.edu.au/R/help/05/08/9560.html|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 [[http://cran.r-project.org/|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.