Sums of Squares in lm, aov and lmer in R
R calculates sequential or Type I SS by default when using lm, lmer and aov as opposed to the usual type III SS which partial out effects of other terms in the model. A hierarchical approach is suggested which gives the same results for both sums of squares. See [http://tolstoy.newcastle.edu.au/R/help/05/04/2981.html here].
Type III SS may be obtained using [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)
for lm and the Anova() procedure for lmer.