Described in a new Methods in Ecology and Evolution paper here, a new R package RNetLogo allows you to use NetLogo from R.
NetLogo is software is a “multi-agent programmable modeling environment”. NetLogo can be used in individual- and agent-based modeling, and is used in the book Agent-based and Individual-based Modeling: A Practical Introduction by Railsback & Grimm.
I have not tried the package yet, but looks interesting. I am always a fan of running stand-alone programs from R if possible.