To do Type III sums of squares you'll need the car package. To split up your data by a grouping factor you'll need the doBy package.
install.packages("car")
install.packages("doBy")
library(car)
library(doBy)
Begin with a dataframe that has your factors, response, and grouping factor as columns (Y = response, A = factor A, B = factor B, Group = grouping factor)
If you have never read in data before into R, try something like this:
data<- read.table("/home/user/Desktop/data.txt")
I prefer to simply use text files that are delimited by space or tab.
Next name your columns:
names(data)<-c("Y","A","B","Group")
Now you need to split your data up according to your grouping factor.
data_split<-splitBy(~Group,data=data)
Lastly, run this loop:
i <-1 while(i <=length(data_split)){
print (Anova(lm(Y~A+B+A*B, data_split[[i]]),type="III")[4,4])
i<- i +1
}
R output can be accessed in row and column fashion [r,c]. I have this particular code give me only the p-value from the interaction of factors A and B. By changing [4,4] to other numbers you can access whatever part of the ANOVA table you want. Hope this helps.