= 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 (for between subjects anova)

{{{
library(car)
fit <- Anova(lm(y~x+z),type=c("III"))
}}}
and for more complex designs with random effects, anova() can be used
{{{
library(nlme)
model.2 <- lme(y~a + b, random=~1|group)
anova(model.2,type="marginal")
}}}

The ''Anova()'' procedure can also 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\R3.x. You can also use the summary() procedure, for obtaining type III SS for ''lmer'' from version 2.7.2 of R. 

In addition to ''lm'' and ''lme'' (which requires the ''nlme'' extension package), ''aov'' may also be used to fit anovas in R.