2-way anova on unbalanced dataset

Question

Is aov appropriate for unbalanced datasets. According to help ...provides a wrapper to lm for fitting linear models to balanced or unbalanced experimental des

Answer 1

Function anova (or summary.aov) will give you the so called type I (or sequential) sum of squares. To get type III sum of squares, you can use the Anova function from library car with parameter type="III". The difference between these two approaches in unbalanced datasets (and also sample R code to produce both tables) is presented in detail here.