Mathematical Modeling in Ecology and Evolution

Technical EN

This workshop will introduce participants to the logic behind modeling in biology, focusing on developing equations, finding equilibria, analyzing stability, and running simulations.Techniques will be illustrated with the software tools, Mathematica and Maxima. This workshop was held in two parts: January 14 and January 16, 2020.

Dr Sarah P. Otto (University of British Columbia)
2020-01-14

In this workshop, I introduce various modelling techniques, using mostly ecological and evolutionary examples, with a focus on how computer software programs can help biologists analyze such models.

Content

Part 1: Classic one-variable models in ecology and evolution
Part 2: Equilibria and their stability
Part 3: Beyond equilibria
Part 4: Example of building a model from scratch
Part 5: Extending to models with more than one variable
Part 6: Another example of building a model from scratch

Software

In my research, I primarily use Mathematica, which is a powerful software package to organize and conduct analytical modelling, but it is not free (at UBC, we have some licenses available). I will also show some example code and provide translation of most of what I present in a free software package called Maxima.

Mathematica installation

There is a free trial version that you can use for 15 days, if you don’t have a copy (click here to access), or you can buy a student version online. If you want to make sure that all is working, copy the code below, put your cursor over each of the following lines and press enter (on some computers, “enter” is a separate button, on others, press “shift” and “return” at the same time):

D[x^3,x]
ListPlot[Table[x, {x,1,10}],Joined->True]
RSolve[{x[t+1]\[Equal]A x[t],x[0]\[Equal]x0},x[t],t]
PDF[NormalDistribution[0,1],x]

You should see (a) \(3x^2\), (b) a plot of a line, (c) \({{x[t]->A^t x0}}\), and (d) \(\frac{e^\frac{-x^2}{2}}{\sqrt{2\pi }}\).

Maxima installation:

On a Mac, install using the instructions here. For other file systems, download here.

Maxima testing

When you first open Maxima, it will give you a choice of GUIs, chose wxMaxima. Once wxMaxima is launched type this command and hit return to see if it answers 4:

2+2;

If it doesn’t, then scan the installation document for the error that you run into.

If it does return 4, then type in and enter these commands:

diff(x^3, x);

wxplot2d (3*x, [x, 0, 2*%pi]);

load("solve_rec")$
solve_rec(x[t+1] = A*x[t], x[t], x[0]=x0);

load("distrib")$
pdf_normal(x,0,1);

You should see (a) \(3x^2\), (b) a plot of a line, (c) \({{x[t]->A^t x0}}\), and (d) \(\frac{e^\frac{-x^2}{2}}{\sqrt{2\pi }}\).

Material

Mathematica Maxima PDF
Notebook Notebook Embeded below
Hints and solutions Hints and solutions
Homework
Homework answers Homework answers
Guide Guide

Follow along PDF

This PDF was generated from the Mathematica notebook linked above. It doesn’t include dynamic plots, but it’s a good alternative if you want to print out or have a quick reference at hand.



Stability analysis of a recursion equation in a discrete-time model.

Other resources

Thanks

Niki Love and Gil Henriques did a great job of translating the code into wxMaxima, with limited help from me. Thanks, Niki and Gil!!

Otto, Sarah P, and Troy Day. 2007. A Biologist’s Guide to Mathematical Modeling in Ecology and Evolution. Vol. 13. Princeton University Press.

References

Corrections

If you see mistakes or want to suggest changes, please create an issue on the source repository.

Reuse

Text and figures are licensed under Creative Commons Attribution CC BY 4.0. Source code is available at https://github.com/bios2/bios2.github.io, unless otherwise noted. The figures that have been reused from other sources don't fall under this license and can be recognized by a note in their caption: "Figure from ...".

Citation

For attribution, please cite this work as

Otto (2020, Jan. 14). BIOS2 Education resources: Mathematical Modeling in Ecology and Evolution. Retrieved from https://bios2.github.io/posts/2020-01-14-mathematical-modeling-in-ecology-and-evolution/

BibTeX citation

@misc{otto2020mathematical,
  author = {Otto, Dr Sarah P.},
  title = {BIOS2 Education resources: Mathematical Modeling in Ecology and Evolution},
  url = {https://bios2.github.io/posts/2020-01-14-mathematical-modeling-in-ecology-and-evolution/},
  year = {2020}
}