Recommended reading list

I’ll update this post with recommended readings as I come across them.


Model selection in ecology and evolution (2004) by Jerald B. Johnson and Kristian S. Omland. A great starting point for learning about model selection and mechanistic models.

Fitting population dynamic models to time-series data by gradient matching (2002) by Stephen P. Ellner, Yodit Seifu and Robert H. Smith. This quote from the abstract gives a good indication of what the paper is about: “Semimechanistic modeling makes it possible to test assumptions about the mechanisms behind population fluctuations without the results being confounded by possibly arbitrary choices of parametric forms for process-rate equations.” The idea of the paper is that functions and parameters that are well-supported by biological evidence are explicitly specified in the model; functions and parameters that are not well understood are fitted, hence the term ‘semimechanistic’.*

Why do populations cycle? A synthesis of statistical and mechanistic modeling approaches (1999) by Bruce Kendall, Cheryl Briggs, Bill Murdoch, Peter Turchin, Steve Ellner, Ed McCauley, Roger Nisbet and Simon Wood. This paper develops an approach, called probe matching, which can be used for parameter estimation and model fitting. Probe matching combines the best of both worlds – statistical models and mechanistic models – and this paper, along the way, highlights the advantages and rationale for using each.

Mathematics, ecology, ornithology (1980) by Simon Levin. A general discussion of mathematical modelling in ecology. I like that this article is concise and well articulated. [Read more].


Ignorance is bliss by Jeremy Fox. On deterministic versus stochastic model formulation.
Fusing theory and data a plea for help from Dan Bolnick by Dan Bolnick. Most of us agree that fusing theory and data is a worthy objective. How exactly to go about doing this is a topic that I wish received a bit more attention.
20 different stability concepts by Jeremy Fox. A compendium of ways to describe the properties of fixed points.
On the use and care of mathematical models by Simon Levin (1975) as quoted by Jeremy Fox.
Charles Elton on A.J. Lotka by Jeremy Fox at Dynamic Ecology.


*credit to J. Fox and E. Pederson for putting me onto this paper.

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About Amy Hurford

I am a theoretical biologist. I became aware of mathematical biology as an undergraduate when I conducted an internet search to learn about the topic. Now, twelve years later, I want to know, what is it that makes great models great? This blog is the chronology of my thoughts as I explore this topic.

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