Hey there.
R is my main (only) programming language, so I use it religiously.
The library I use is called quantstrat, and it's written by a quant who's an algo-trading partner at DV Trading (a Chicago/Toronto firm).
Long story short, there's a metric ton of depth to it, and it's highly general, with lots of levers to pull.
Look for the R/Finance 2013 quantstrat pdf to get started.