Teaching resources

Teaching Resources

This space is to share resources relevant to teaching theoretical ecology.

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List of resources

Title Type Topic Level Description Language Contact Date entered
Interactive Computer Labs Lab(s) Dynamical modeling Undergraduate course These computer labs use the manipulate package in RStudio and are designed to go with an undergraduate-level population dynamics course. They let students change parameter values in models with sliders (no programming by students necessary, they just need to run the code as is) to explore their effect on a variety of models (exponential, theta-logistic, Ricker, Leslie matrix, Lotka-Volterra competition, predator-prey with different Holling functional responses, SIR). This requires using the RStudio interface for R, and libraries needed are manipulate and, for later labs, deSolve. R mlbaskett(at)ucdavis.edu 08 Jun 2015 07:00
Populus software Lab(s) Dynamical modeling Undergraduate course The Populus software contains a set of simulations that we use to teach population biology and evolutionary ecology at the University of Minnesota. Simulation models may be chosen from a menu, and students can move among the parameter boxes of an input window, changing initial defaults to values of their own choosing. Most modules offer several graphical outputs of model dynamics, and their computational algorithms are detailed in an Acrobat-based help system packaged with the program. N/A populus@umn.edu 19 Jun 2015 04:00
Netlogo Lab(s) Other (specify in description) Any NetLogo is a multi-agent programmable modeling environment. It is used by tens of thousands of students, teachers and researchers worldwide. It also powers HubNet participatory simulations. It includes a Library with many models related to ecology/evolution. N/A Uri Wilensky 19 Jun 2015 04:00
BioQuest Lab(s) Dynamical modeling Any The BioQUEST Curriculum Consortium (BQCC) is a community of scientists, educators, and learners of all ages who are interested in supporting biology education that reflects realistic scientific practices. The site has links to numerous projects with models and modules appropriate for undergraduate ecology courses. N/A Kristin Jenkins 19 Jun 2015 04:00
Software Carpentry Tutorial Numerical methods/coding Self-guided learning Lessons for learning to code in R, Python, and Matlab, plus language-independent basics such as version control and best practices. Not specific to ecology/population biology, but useful for anyone learning to code. Other (specify in description) see link for contact 24 Jun 2015 07:00
Evolutionary games and replicator dynamics Tutorial Dynamical modeling Other (specify in description) These interactive notes are the basis of a series of lectures that I give to the “Mathematical Modeling of Biological Systems” Cluster of the UC Davis COSMOS program. The COSMOS program is a four week in residence program for high school students which introduces students to more advanced topics in mathematics and sciences. In these interactive lecture notes, I introduce evolutionary games, Nash equilibria, and replicator equations and their application to the evolution of aggression/cooperation and rock-paper-scissor dynamics. The notes were written in R studio using the shiny package. R Sebastian Schreiber (sschreiber@ucdavis.edu) 02 Aug 2016 07:00
Disease dynamics and networks Tutorial Dynamical modeling Any These interactive notes are the basis of a series of lectures that I give to the “Mathematical Modeling of Biological Systems” Cluster of the UC Davis COSMOS program. The COSMOS program is a four week in residence program for high school students which introduces students to more advanced topics in mathematics and sciences. In these interactive lecture notes, I introduce epidemiology, R0 and its application to managing the recent Ebola outbreak in West Africa, discrete-time SIR models and how they give rise to R0, networks and their degree distributions, SIR dynamics on networks, and R0 for these stochastic models. N/A sschreiber@ucdavis.edu 02 Aug 2016 07:00
math review Help sheet Dynamical modeling Undergraduate course Review of algebra, calculus, graphing, and linear algebra. Created to provide a math review for an undergraduate-level course in population dynamics. Please contact me if you would like the LaTeX file that this pdf comes from. N/A mlbaskett(at)ucdavis.edu 06 May 2015 07:00
List of useful R commands Help sheet Numerical methods/coding Any Rules of thumb for coding and a list of useful R commands for theoretical ecologists. Developed for a graduate-level course on numerical methods in population biology. Please contact me if you would like the original LaTeX file. R mlbaskett(at)ucdavis.edu 06 May 2015 07:00
FAT ESA Help sheet Data-model integration Undergraduate course
12 rue de la gironde
97418 a la plaine des cafres || Other (specify in description) || pierre || 09 Jul 2016 22:00||
Statistical rethinking Lecture notes Statistical modeling Graduate course Lecture notes and video recordings of Richard McElreath's "Statistical Rethinking" course, providing a unique introduction to hierarchical Bayesian modeling R mcelreath(at)ucdavis.edu 07 May 2015 07:00
Encyclopedia of Theoretical Ecology Other (specify in description) Other (specify in description) Self-guided learning This contains a collection of short summaries of a large set of topics in theoretical ecology by leading experts. These are designed to be self-contained summaries at the level of advanced undergraduate/beginning graduate students in ecology. Each entry is 4-10 pages and has connections to other topics and a short list of follow-on references. There is also a 30-page glossary that very briefly defines key terms. The book is available in many libraries. N/A Alan Hastings and Louis Gross 19 Jun 2015 04:00

Note also the list of Theory Books available at http://esa.org/theory/sample-page/theory-books/


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