Taskview Individual-Based Models

This is a collection of agent-based (or individual-based) models in R. It includes packages, codes, and tutorials dealing with the simulation of any kidn of agents in a spatially explicit landscape as well as in a non-spatial way.

Contributions are welcome! Please submit an issue, or make a contribution.

Packages

• nlrx: The nlrx package provides tools to setup NetLogo simulations in R. It uses a similar structure as NetLogos Behavior Space but offers more flexibility and additional tools for running sensitivity analyses.
• SpaDES : Metapackage for implementing a variety of event-based models, with a focus on spatially explicit models. These include raster-based, event-based, and agent-based models.
• simecol: "a lightweight R package that employs an object oriented paradigm for the implementation of dynamic simulation models."
• NetLogoR: "Easily create agent-based models in R following the NetLogo framework (Wilensky, 1999)."
• BacArena: "An Agent-Based Modeling Framework for Cellular Communities."
• rtsetse: "R package for simulating tsetse fly populations to investigate control options."

Publications with code

spatially explicit

• "Using movement data to estimate contact rates in a simulated environmentally-transmitted disease system" (doi: https://doi.org/10.1101/261198)
• "Can stochastic geographical evolution re-create macroecological richness–environment correlations?" (doi: https://10.1111/j.1466-8238.2011.00661.x)

spatially implicit

• "Sexual selection can both increase and decrease extinction probability: reconciling demographic and evolutionary factors" (doi: https://10.1111/1365-2656.12601)

Tutorials

• "An introduction to Agent-Based Modelling in R" by Marco Smolla