Agent Based Models and RNetLogo

July 24, 2014
By

(This article was first published on Revolutions, and kindly contributed to R-bloggers)

by Joseph Rickert

If I had to pick just one application to be the “killer app” for the digital computer I would probably choose Agent Based Modeling (ABM). Imagine creating a world populated with hundreds, or even thousands of agents, interacting with each other and with the environment according to their own simple rules. What kinds of patterns and behaviors would emerge if you just let the simulation run? Could you guess a set of rules that would mimic some part of the real world? This dream is probably much older than the digital computer, but according to Jan Thiele’s brief account of the history of ABMs that begins his recent paper, R Marries NetLogo: Introduction to the RNetLogo Package in the Journal of Statistical Software, academic work with ABMs didn’t really take off until the late 1990s.

Now, people are using ABMs for serious studies in economics, sociology, ecology, socio-psychology, anthropology, marketing and many other fields. No less of a complexity scientist than Doyne Farmer (of Dynamic Systems and Prediction Company fame) has argued in Nature for using ABMs to model the complexity of the US economy, and has published on using ABMs to drive investment models. in the following clip of a  2006 interview, Doyne talks about building ABMs to explain the role of subprime mortgages on the Housing Crisis. (Note that when asked about how one would calibrate such a model Doyne explains the need to collect massive amounts of data on individuals.)

 

Fortunately, the tools for building ABMs seem to be keeping pace with the ambition of the modelers. There are now dozens of platforms for building ABMs, and it is somewhat surprising that NetLogo, a tool with some whimsical terminology (e.g. agents are called turtles) that was designed for teaching children, has apparently become a defacto standard. NetLogo is Java based, has an intuitive GUI, ships with dozens of useful sample models, is easy to program, and is available under the GPL 2 license.

As you might expect, R is a perfect complement for NetLogo. Doing serious simulation work requires a considerable amount of statistics for calibrating models, designing experiments, performing sensitivity analyses, reducing data, exploring the results of simulation runs and much more. The recent JASS paper Facilitating Parameter Estimation and Sensitivity Analysis of Agent-Based Models: a Cookbook Using NetLogo and R by Thiele and his collaborators describe the R / NetLogo relationship in great detail and points to a decade’s worth of reading. But the real fun is that Thiele’s RNetLogo package lets you jump in and start analyzing NetLogo models in a matter of minutes.

Here is part of an extended example from Thiele's JSS paper that shows R interacting with the Fire model that ships with NetLogo. Using some very simple logic, Fire models the progress of a forest fire. 

Snippet of NetLogo Code that drives the Fire model

to go
  if not any? turtles  ;; either fires or embers
    [ stop ]
  ask fires
    [ ask neighbors4 with [pcolor = green]
        [ ignite ]
      set breed embers ]
  fade-embers
  tick
end
 
;; creates the fire turtles
to ignite  ;; patch procedure
  sprout-fires 1
    [ set color red ]
  set pcolor black
  set burned-trees burned-trees + 1
end

The general idea is that turtles represent the frontier of the fire run through a grid of randomly placed trees. Not shown in the above snippet is the logic that shows that the entire model is controlled by a single parameter representing the density of the trees. 

This next bit of R code shows how to launch the Fire model from R, set the density parameter, and run the model.

# Launch RNetLogo and control an initial run of the
# NetLogo Fire Model
library(RNetLogo)
nlDir <- "C:/Program Files (x86)/NetLogo 5.0.5"
setwd(nlDir)
 
nl.path <- getwd()
NLStart(nl.path)
 
model.path <- file.path("models", "Sample Models", "Earth Science","Fire.nlogo")
NLLoadModel(file.path(nl.path, model.path))
 
NLCommand("set density 70")    # set density value
NLCommand("setup")             # call the setup routine 
NLCommand("go")                # launch the model from R

Here we see the Fire model running  in the NetLogo GUI after it was launched from RStudio.

R_NetLogo_Screen

This next bit of code tracks the progression of the fire as a function of time (model "ticks"), returns results to R and plots them. The plot shows the non-linear behavior of the system. 

# Investigate percentage of forest burned as simulation proceeds and plot
library(ggplot2)
NLCommand("set density 60")
NLCommand("setup")
burned <- NLDoReportWhile("any? turtles", "go",
                c("ticks", "(burned-trees / initial-trees) * 100"),
                as.data.frame = TRUE, df.col.names = c("tick", "percent.burned"))
# Plot with ggplot2
p <- ggplot(burned,aes(x=tick,y=percent.burned))
p + geom_line() + ggtitle("Non-linear forest fire progression with density = 60")

Fire_Progression_den_60

As with many dynamical systems, the Fire model displays a phase transition. Setting the density lower than 55 will not result in the complete destruction of the forest, while setting density above 75 will very likely result in complete destruction. The following plot shows this behavior.

  Phase_transition_pctb_vs_d

RNetLogo makes it very easy to programatically run multiple simulations and capture the results for analysis in R. The following two lines of code runs the Fire model twenty times for each value of density between 55 and 65, the region surrounding the pahse transition.

d <- seq(55, 65, 1)                  # vector of densities to examine
res <- rep.sim(d, 20)                # Run the simulation

The plot below shows the variability of the percent of trees burned as a function of density in the transition region.

  Boxplots_transition_region

My code to generate plots is available in the file:  Download NelLogo_blog while all of the code from Thiele's JSS paper is available from the journal website.

Finally, here are a few more interesting links related to ABMs.

 

To leave a comment for the author, please follow the link and comment on his blog: Revolutions.

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