NetLogo is a great tool for agent-based modeling of complex dynamic systems. It is commonly used in a number of disciplines including behavioral ecology and evolutionary biology, sociology and epidemiology.
There are a number of ways to export data from simulations run in Netlogo. One especially useful method is to use the RNetLogo R package. This packages allows you to interface directly
with NetLogo from R. Launching models, altering model settings and exporting data.
The following video and code is a tutorial of how to use the RNetLogo package.
Running Agent-Based Modeling in R with NetLogo