Ecological Models and Data in R

Ecological Models and Data in R

This is the web site for a book published by Princeton University Press (ISBN 0691125228). It is available from Princeton University Press and Amazon.com.
book cover: Ecological Models and Data in R There's a wiki for the book at http://emdbolker.wikidot.com/: this has errata (not too many yet) and added notes for each chapter. If you have suggestions for improvements in the R code, or you think you've found an error, please check the wiki and/or contact me (e-mail to bolker "at" ufl.edu).

The book is based on a class I have taught several times at the University of Florida, covering the nitty-gritty of constructing and fitting simple (statistical) ecological models to real data sets. Here is the material for the labs I usually teach in that class.

Exercises:

(The PDF and HTML files are self-explanatory; XML may render math better in some browsers. The R files are raw R code (open them in a text editor), and the Rnw files are "Sweave files", a mixture of LaTeX and R code. You probably only want the Rnw files if you're planning on modifying the labs for your own use.)

Data and scripts for labs:

Other data and scripts:

Most of the data for the book are available in the emdbook package on CRAN. If you would like the goby data (in the emdbookx package), please contact me (bolker at ufl.edu). R scripts for each chapter: 1 2 3 4 5 6 7 8 9 10 11  (these are R scripts, with extension ".R": open them with a text editor such as (Windows) Wordpad, Tinn-R, (MacOS) TextWrangler, BBEdit, or the R script editor). These have some gory details, but should reproduce exactly the code chunks and figures in the text.  (You may also want chapskel.R, a "chapter skeleton" file with miscellaneous setup code.)

Most of the R code for doing things in the book is now in the two packages bbmle (also available in a development version) and emdbook, both available from R archive (CRAN) or via install.packages from inside R.

Other miscellaneous R code: pdf html xml Rnw R
Warning: everything below here may be somewhat out of date ...
If you want to see the existing notes for the course, start here. 

Old PDFs

Individual chapters

Last update: 27 December 2006

Formats: PDF, Rnw (Sweave -- original "source code"), R (R code only)


last modified 6 July 2008