## Introduction to R

Here are some links to pages I have written to help you get started with R. These pages deal with data types in R, vectors and matrices in R, how to use existing R functions and write your own custom functions, how to use loops to do things for you, and how to plot.

Whenever you have questions about what R is capable of, internet searches can often be really helpful. It is how I figure out how to do things in R. So, for example, if you wanted to know how to add a legend to a plot, you could Google "r-project adding legends to plots" and would immediately get a lot of help. There are also a lot of Intro to R web resources that you can access.

**Please let me know if you are confused by anything!**These pages are meant to be helpful - if more information would make them more helpful, so much the better!Whenever you have questions about what R is capable of, internet searches can often be really helpful. It is how I figure out how to do things in R. So, for example, if you wanted to know how to add a legend to a plot, you could Google "r-project adding legends to plots" and would immediately get a lot of help. There are also a lot of Intro to R web resources that you can access.

## Calculating eigenvalues and eigenvectors in R

For transition matrices with more than 2-3 ages or stages, calculating eigenvalues and eigenvectors by hand is tedious. Computers make it easy. Click the link below to see how to calculate eigenvalues and right and left eigenvectors in R, using the example of right whale demography from class.

Eigenvalues and eigenvectors in R

Eigenvalues and eigenvectors in R

## Using R to simulate epidemic models

Follow the link below to a long page showing how to simulate epidemic models of increasing complexity, interpret common error messages, debug non-functional code, and make interesting plots of the results.

Simulating disease systems: examples

Simulating disease systems: examples

## Modeling project papers

Click here for a list of papers that can help you get started on the modelling project. These papers will tend to be older, presenting simpler mathematical models that are more easily extensible for the project. Remember, the focus of the project is not to break new research ground! Rather, it is to get hands-on experience translating a biological question into a mathematical model, carrying out the analysis of that model, and then translating the mathematical results back into biological understanding.

## R scripts for simulating models

## Supplementary Readings

Some books that you might find helpful at various points throughout the course are:

Caswell, H. 2001.

Edelstein-Keshet, L. 2005.

Ellner, S. P. and J. Guckenheimer. 2006.

Kot, M. 2001.

Murray, J. D. 2001.

At various points in the course I may also provide readings from the primary mathematical biology literature. Papers will be posted here at that time.

**Keeling, M. J. and P. Rohani. 2008.***Modelling Infectious Disease.*Princeton University Press, Princeton, NJ.- This book might be particularly useful for the project. I have a copy of this book and can photocopy chapters from it, but groups might consider buying a copy.

Caswell, H. 2001.

*Matrix Population Models.*Sinauer Associates, Sunderland, MA.Edelstein-Keshet, L. 2005.

*Mathematical Models in Biology*. Society for Industrial and Applied Mathematics, Philadelphia, PA.Ellner, S. P. and J. Guckenheimer. 2006.

*Dynamic Models in Biology.*Princeton University Press. Princeton, NJ.Kot, M. 2001.

*Elements of Mathematical Ecology*. Cambridge University Press, Cambridge, UK.Murray, J. D. 2001.

*Mathematical Biology, Part I: An Introduction*. Springer, New York, NY.At various points in the course I may also provide readings from the primary mathematical biology literature. Papers will be posted here at that time.