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.
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
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.
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) \(\frac{e^\frac{-x^2}{2}}{\sqrt{2\pi }}\).
On a Mac, install using the instructions here. For other file systems, download here.
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) \(\frac{e^\frac{-x^2}{2}}{\sqrt{2\pi }}\).
| Mathematica | Maxima | |
|---|---|---|
| Notebook | Notebook | Embeded below |
| Hints and solutions | Hints and solutions | |
| Homework | ||
| Homework answers | Homework answers | |
| Guide | Guide |
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.
An Introduction to Mathematical Modeling in Ecology and Evolution (Otto and Day 2007).
Niki Love and Gil Henriques did a great job of translating the code into wxMaxima, with limited help from me. Thanks, Niki and Gil!!
@online{p.otto2020,
author = {Sarah P. Otto},
title = {Mathematical {Modeling} in {Ecology} and {Evolution}},
date = {2020-01-14},
url = {https://bios2.github.io/posts/2020-01-14-mathematical-modeling-in-ecology-and-evolution},
langid = {en}
}