Individual-Based Ecological Modeling at Cal Poly Humboldt

The Humboldt Mathematics Department has a long tradition of collaborating with faculty in Wildlife, Fisheries, and other departments to produce and use ecological models, and especially individual-based models (IBMs; also known as agent-based models). This tradition goes back to the pioneering work of Roland Lamberson and colleagues on a variety of bird and mammal models in the early 1990s. Steve Railsback and Bret Harvey joined the team in the late 1990s, focusing (but not exclusively) on inSTREAM and inSALMO, our river management models of salmonid fish. We collaborate closely with other individual-based modeling centers around the world (see Who We Are). In 2005, Volker Grimm and Steve Railsback published Individual-based Modeling and Ecology, the first monograph on IBMs. They also wrote the first textbook for agent/individual-based modeling, which is now in its second edition. Steve Railsback and Bret Harvey have now published Modeling Populations of Adaptive Individuals, a monograph on IBMs that include adaptive tradeoff decisions, in Princeton University Press's Monographs in Population Biology series. According to Google Scholar, our publications have been cited over 15,000 times.

Math Department faculty teach modeling classes and collaborate with faculty in Wildlife, Fisheries, and other departments, and co-supervise graduate students who include modeling in their research. More information is at the Mathematics Department web site, and example student projects are here.

Research Goals

Developing a conceptual and theoretical basis for individual-based ecology. Differential calculus provides the conceptual basis for classical ecological models, but IBMs have lacked such a basis. We help develop and promote standard concepts for thinking about and designing IBMs.

Applying IBMs to conservation and 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? We have also developed management models for river-breeding frogs and birds that provide pest control services on coffee farms.

Using IBMs to test and develop ecological theory. We use IBMs as 'virtual ecosystems' for testing ecological theory, especially theory for how organisms make adaptive decisions. Our focus is on "across-level" theory that links 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, and flexible and re-usable code for ecological models. We now collaborate with the developers of our preferred platform, NetLogo.

Integrating individual-based approaches in ecological and modeling education. We provide several kinds of support for users of our textbook.

User interface of our InSTREAM 7 trout model

What's new

New releases of InSTREAM, InSALMO, and tools

InSTREAM and InSALMO were updated 7 July 2023 with minor improvements to software and documentation, and additional tools for understanding results. See their distribution page.

InSTREAM applications in ecotoxicology

A new publication from the UK explores use of our InSTREAM model for evaluating population-level effects of contaminant chemicals: Hazlerigg, C. R. E., K. S. Mintram, C. R. Tyler, L. Weltje, and P. Thorbek. Harnessing modeling for assessing the population relevance of exposure to endocrine-active chemicals. Environmental Toxicology and Chemistry, DOI: 10.1002/etc.5640. The authors provide a completed EFSA (European Food Safety Agency) Good Modelling Practice Checklist for InSTREAM.

At the University of Windsor, Ontario, Kathleen Church and Christina Semeniuk are preparing a publication on their use InSTREAM to investigate interactions between trout personality traits (dominance, boldness) and concentrations of microplastics in the environment in affecting populations.

TARGETS-2D: New river management model for riparian tree establishment

We are announcing and distributing the first version of TARGETS-2D, a new model of how river management--flow regimes and channel restoration projects--affects when and where riparian trees take root and begin to develop. The model is fully 2-dimension and dynamic. It simulates processes including: fluctuation of groundwater and soil moisture levels with flow, seed dispersal and deposition, sprouting, development into seedlings, and seed/plant mortality due to desiccation, inundation, and scouring. We distribute a complete model description and user guide, the software (in NetLogo), and example input. The model was developed in collaboration with McBain Assoc. and funded by the Tuolumne River Conservancy and California Fish and Wildlife.

Chinese edition of Individual-based Modeling and Ecology

Our friend Yue Lin and his colleagues translated Individual-based Modeling and Ecology (Grimm and Railsback 2005) into Simplified Chinese and the book is now for sale in China.

New publication: Theory for how animals make tradeoff decisions through the circadian cycle

Our new article in Behavioral Ecology presents and tests theory for how animals decide whether and where to feed or hide, multiple times per day as changing light conditions affect both feeding rate and predation risk, in a population context with the individuals competing with each other for food and hiding places. The article presents four alternative ways to model this decision, using "State- and prediction-based theory" (see the 2020 Railsback and Harvey book, below), and then contrasts the alternative theories by their ability to reproduce a variety of observed patterns. This test is carried out in our new stream trout model (inSTREAM 7) that represents dawn, day, dusk, and night as explicit phases of the circadian cycle.

The article is: Railsback, S. F., B. C. Harvey, and D. Ayllón. in press. Contingent tradeoff decisions with feedbacks in cyclical environments: testing alternative theories. Behavioral Ecology. DOI: 10.1093/beheco/araa070

New book on modeling adaptive decisions in IBMs

The new book Modeling Populations of Adaptive Individuals, by Steven Railsback and Bret Harvey, is now for sale in Princeton University Press's Monographs in Population Biology series. The book explains the problem of modeling tradeoff decisions (e.g., where to forage as a tradeoff between food intake rate and predation risk) in individual-based models that are realistic enough that traditional optimization approaches are not feasible. It then illustrates and provides guidance on "state- and prediction-based theory", one way to model such decisions. The book's page at Princeton is here, and its supplemental materials are available via this link.

2nd edition of Railsback & Grimm textbook

Princeton University Press released the 2nd edition of Agent-based and Individual-based Modeling, A Practical Introduction, by Steve Railsback and Volker Grimm. See the book's web site for information and supporting materials.

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.