BIEB 143. Computational Modeling in Ecology and Evolution. Spring 2020


Lin Chao, Scott Rifkin (professors). Adam Conn (IA)
General information and announcements
Welcome to the Spring 2020 web page for Computational Modeling in Ecology and Evolution. All course material and announcements will be posted or linked here.
- This is a course for students who want to improve their ability to use quantitative, mathematical, and statistical models in biology by learning to write and use computer code.
- Students will develop their own programs instead of using programs prepared by software engineers.
- A degree of familiarity with and desire to work with mathematical reasoning is required.
- Topics for modeling may include population genetics, epidemiology, ecological dynamics, evolutionary game theory, neural networks, and sexual selection.
- This is not a course for students who already know how to program. Only basic beginning code writing will be taught. All programming will be in the language R.

- We will use the free, open source computer language R in this course. You can download R here and you can also find more information about R as well as introductory tutorials here or by searching on the web. R is a programming language that is specifically geared towards statistical analyses, and it is the pre-eminent statistical software package in the world, especially in ecology and bioinformatics.

- You can run R by itself just like you would run any other program, but it has a tendency to make windows pop up all over your screen. We will use R Studio which is an R programming environment. Essentially, it is a nice program that keeps all the R windows together and makes it easy to switch from one to another.

First download and install R. Only then should you download and install RStudio

Syllabus
Week 1
Homework and quiz info

Turn in your homework using the template provided (even if not everything is working) by emailing to: ucsdbieb143 {at sign} gmail dot com
If relevant, include a write up indicating whether program worked or not and parts of program you do not understand. If it did not work, explain what you tried and where you think that bug could be. Put the title of the program as the subject line. Homework is due at midnight, Tuesday night/Wednesday morning unless stated otherwise Please use the templates to organize your homework code. That way Sarah can just run it all and then annotate your code. If any part doesn't work, as always, say what you tried to get it to work and where you think the bug might be. You can put this in comments in your code.


Please watch for emails about this class and homework from any of your instructors.

Creative Commons License
Unless superceded by preexisting copyrights or licenses, material developed for UCSD BIEB143 Spring 2020 by Lin Chao and Scott Rifkin is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 United States License.