Individual-Based Ecological Modeling at Humboldt State University

Research on the use of individual-based models (IBMs) for applied and theoretical ecology is affiliated with the Mathematical Modeling Program, HSU Mathematics Department. This research is a collaboration of mathematicians, ecologists and biologists, environmental engineers, and software professionals. See below for our research goals.

Visit this new site to learn more about Humboldt State's Mathematical Modeling graduate program!

What's New

• New review of foraging theory that can reproduce trait-mediated indirect interactions and non-consumptive effects emerge. TMIIs and NCEs are exciting areas of ecological research because they illustrate the effects of individual adaptive behavior on population and community dynamics. But how can we model the individual foraging decisions from which these complex trophic dynamics emerge? These decisions must trade off food intake vs. predation risk, when the alternatives available and the intake and risk associated with them are subject to feedbacks from how the individuals behavior. Trait-mediated trophic interactions: is foraging theory keeping up? is our new review of this subject in the journal Trends in Ecology and Evolution. It shows how the foraging theory we use in our trout models can reproduce a wide range of observed TMIIs and NCEs. See the Publications and Products page.
  
  
• Updated review of agent-based modeling software platforms. Our collaborator Steve Lytinen (professor of computer science, DePaul University) just updated our often-cited 2006 review of software platforms for agent-based modeling. This update compares the new Version 5.0 of NetLogo with the new ReLogo platform from the Repast project. See the Publications and Products page.
  
  
• Version 5 of inSTREAM, our individual-based stream trout model, is released. inSTREAM, one of our primary products, is an individual-based model of stream trout populations and communities. It is designed to address a variety of applied and research questions about how habitat and individual adaptive behavior interact to produce population and community dynamics. Version 5.0 is a major software update. Key new features include a graphical user interface, easy installation in Windows, and a generic habitat simulation approach that allows use of any two-dimensional (or pseudo-two-dimensional) hydraulic model to represent multiple stream reaches.
  
  
• New individual- and agent-based modeling textbook. The new book Agent-based and Individual-based Modeling: A Practical Introduction by Steve Railsback and Volker Grimm is the first textbook devoted to individual-based (or "agent-based") modeling in science. The text is designed for courses in which instructors as well as students are new to this kind of modeling. The book is not specific to ecology, but general to all scientific fields. It teaches basic concepts of modeling, the design of individual-based models, how to program models in the NetLogo platform, and analysis of models to solve scientific problems and develop theory. Much more information is at the book's web site.
  
  
• Short courses on teaching individual- and agent-based modeling. In June of 2011 and 2012, we conducted one-week short course intended to help instructors, including those new to individual-based modeling, develop and teach courses at the university level. Additional information is at the course web site. If you are interested in future courses, please contact Steve Railsback.
  
  
• Summer short courses in individual- and agent-based modeling. Our friends at the Institute of Forest Growth and Forest Computer Sciences of Technical University Dresden, Germany, conduct one- or two-week intensive summer courses in individual- and agent-based simulation modeling. The courses are taught in English at a lovely small town in the "Switzerland of Saxony" park area near Dresden. See the course web site for information.
  
  
• Recent Masters theses in the Mathematical Modeling Graduate Program that use individual-based models. Elizabeth Arnold built an IBM of how wild dogs (Lycaon pictus) disperse among game reserves in South Africa. The model imported GIS data on landscape features (roads, towns, etc.) and simulated their effect on dog movement and survival. Kyle Falbo built a model of pelagic ocean dispersal of juvenile Hawksbill sea turtle (Eretmochelys imbricata) that hatch on the Big Island of Hawaii. Kyle's model uses satellite data to examine the effects of both ocean currents and turtle behavior on their location in their first 3 years. In collaboration with Argonne National Laboratory, Tyler Belarde is using a model of the juvenile Colorado pikeminnow (Pytchocheilus lucius) in backwaters on the Green River, Utah, to simulate the interacting effects of flow alteration (daily power-generation cycles) and exotic species (an introduced fish that competes with and preys on pikeminnow) on survival and growth of the endangered pikeminnow. Math Modeling MS theses are available here.
  
  
• New model of ecosystem services by birds in coffee plantations. Prof. Matt Johnson of Humboldt State's Wildlife Department studies how migratory songbirds from North America consume and control coffee borer beetles on Jamaican coffee plantations. The beetles are the only major coffee pest worldwide, and Matt's research is the first to document natural control by birds. But the beetles are extremely small and cannot by themselves support the bird population; insects in forest and shade-grown coffee habitat make up most of the bird diet. How coffee production—and bird survival—should vary with the relative amounts of forest, shade- or sun-grown coffee is not at all clear. For example, more forest might support more birds, but provide less incentive for birds to eat coffee beetles. To address such questions we built a simulator that includes habitat patches, birds, coffee borer beetles, and insect food. The first publication about this model also provides a clear example of "pattern-oriented modeling" to design IBMs and test their theory for individual behavior. See the Publications and Products page.
  
  
• inSTREAM used in McCloud River Project instream flow studies. Our individual-based trout model was used as one of several instream flow assessment methods in the regulatory process to update the operating license of the McCloud River hydroelectric project. Public documents on the regulatory process are here. This was the first completely non-research application of inSTREAM. The model predicted that higher instream flows in summer could increase the relative abundance of brown vs. rainbow trout, but high winter flows could have the opposite effect.
  
  
• inSTREAM training opportunities. We occasionally provide training in our inSTREAM individual-based trout model. Classes are usually but not always here in Arcata. Contact Steve Railsback if you are interested.
  
  

Research Goals:

• Developing a conceptual and theoretical basis for individual-based ecology. Differential calculus provides the conceptual basis for classical ecological models, but IBMs lack such a basis. We find the new science of Complex Adaptive Systems to be a fruitful source of concepts for thinking about and designing IBMs.
• Applying fish IBMs to river management issues. We developed several generations of stream salmonid IBM to address such management questions as: How do the magnitude and timing of instream flow releases affect populations? What are the cumulative effects of changes in flow and temperature on fish populations? What effects do habitat alterations (e.g., loss of pools, increased turbidity), competition, predation, and habitat connectivity have on population dynamics?
• Using IBMs to test and develop ecological theory. We use IBMs as 'virtual ecosystems' for testing ecological theory and linking behavioral ecology to population ecology.
• Developing software and software engineering approaches for IBMs. Software engineering is much more important for IBMs than for other ecological models. We develop software engineering guidance, flexible and re-usable code for stream fish models, and a library of Swarm-based code for IBMs.
• Integrating individual-based approaches in ecological and modeling education. We integrate IBMs in ecological modeling courses at HSU, and gladly offer software and guidance to instructors at other institutions.

WebMASTER:  steven.railsback@humboldt.edu
Last Updated:  24 Sept 2012