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 site to learn more about Humboldt State's
Mathematical Modeling graduate program!
- Effects of land use on bird populations and pest control services on coffee farms published in
Proceedings of the National Academy of Sciences. This new paper analyzes the coffee farm IBM developed
to understand Matt Johnson's field sites in Jamaica. In this system, the availability of different habitat types (forest, trees, shade- and sun-grown coffee) determines bird population densities, which determine how well birds control an insect
pest that infests coffee. We found that patches of trees, or a mix of shade-grown coffee, support bird populations well enough to provide economically important pest control; separate areas of intact forest and
coffee monoculture did not. See the Publications and Products page.
- 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.
- Facultative anadromy in salmonids: linking habitat, individual life history decisions, and population-level consequences in press at Canadian Journal of Fisheries and Aquatic Sciences. How useful are state-based dynamic models of whether an individual juvenile salmonid should migrate to the ocean or remain to mature in freshwater (e.g., Satterthwaite et al., 2010. State-dependent life history models in a changing (and regulated) environment: steelhead in the California Central Valley. Evolutionary Applications 3: 221-243) for making management decisions? How do habitat conditions that affect growth and survival therefore affect the number of smolts produced by a spawning stream? We addressed these and other questions using inSALMO-FA, our new individual-based model for 'facultative anadromous' species such as steelhead/rainbow trout, in which some but not all individuals migrate to the ocean. A pre-publication version is available at the Publications and Products page.
- Other new publications using our salmonid models.
Several new journal articles use our inSTREAM and inSALMO models to address topics such as whether the "food limitation" concept makes sense in trout populations, whether drift feeding is the only important feeding mode in stream trout, and the benefits of salmon habitat restoration projects. See the Publications and Products page.
- Updated review of agent-based modeling software platforms.
Our collaborator Steve Lytinen
(professor of computer science, DePaul University) 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, 2012, and 2013, 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
- 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 intensive summer courses in
individual- and agent-based simulation modeling. The courses are intended primarily for
graduate students, and taught in
English at a lovely country location 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 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.
- 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
- 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
Two-dimensional hydraulic simulation in
version 5.0 of inSTREAM.
Habitat cells are shaded by water depth (alternatively, by velocity);
pink dots indicate juvenile fish, and rectangles indicate adult trout.
Last Updated: 28 Apr 2014