On http://www.stats.ox.ac.uk/~snijders/mlbook.htm, you can find (in addition to other things) r scripts for the examples in Snijders & Bosker (2012). This covers various basic things you could do in multilevel analysis. For starting, see http://www.stats.ox.ac.uk/~snijders/ch45.r
Best regards,
Tom Snijders