Here's an example how to conveniently summarize data with the cast function (package reshape). By the way you see how this could be done "in-conveniently" by hand. You also see how a for-loop works and how a matrix is constructed and filled. In addition this serves as an illustrative example how flexible "indexing" in R works, as seen in the below loop! (download data) (this example is adapted from https://stat.ethz.ch/pipermail/r-sig-ecology/2011-May/002174.html)
