# Teaching Resources

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

To enter a new resource, enter a title (be sure that it’s different from any of the titles in the table below) and click the button to provide further information:

If you would like to edit a page that you previously created, then first click on the linked title in the table below for your resource, and second click the edit button at the bottom right-hand corner of the page.

## Select an entry from the table below to get a link to the corresponding resource:

Resource selected: Interactive Computer Labs

**File posted to this wiki:** file:labs/labs.zip

**Link to material posted outside this wiki:** http://www.des.ucdavis.edu/faculty/baskett/downloads/labs.zip

Description: 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.

Type: Lab(s)

Topic: Dynamical modeling

Level: Undergraduate course

Contact: mlbaskett(at)ucdavis.edu

Date entered: 08 Jun 2015 07:00

## 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 |

metastability | Lab(s) | Dynamical modeling | Any | N/A | |||

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 |

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/