Lecture Notes
R Tips
Randomization and the number of trials
Problem Sets
Project
Handouts
Data
Goodies
Contact
Introduction
Welcome to Data Analysis in the Geosciences.
The first class will be on Thursday, 14 August. Class starts at 9:35 AM in Geology–Geography 142, but please arrive a few minutes early, so that we can start on time. Bring paper to take notes on, or you may use a tablet. No laptops, please. We will have a full class on day one.
This website will be used extensively in this course. Lecture notes will be posted here, with the most recent lecture appearing in this space. Previous lectures will be accessible through the list at the left, as will all problem sets and handouts. I will distribute hard-copies of two handouts on the first day: the syllabus and the R tutorial.
If you need to contact me, the best way is to click on my name under Contact at the left. Please leave the subject line as 8370. Throughout the course, begin the subject line of any email to me with 8370; this ensures that your email won't get lost in the deluge.
In the first few class periods, we will be learning the statistical software R. There will be no lectures notes for this, as we will follow the handout, A Short R Tutorial. I recommend that everyone install R on their own computers. R is available for OS X, Linux, and Windows platforms, and can be downloaded at no cost from the R Project for Statistical Computing. Some students prefer RStudio Desktop as their working environment for R, and it is available for free from Posit.
Some R References
The number of R-related books is astonishing, but here are a few I find especially useful. Springer is publishing several titles on R, including Borcard et al. (below) on numerical ecology, as well as volumes on phylogenetics, time series, spatial data analysis, multivariate data visualization, and bayesian computation.
Adler, J., 2009. R in a Nutshell. O'Reilly Media, 640 p. ISBN: 978–0-596–80170–0
Bolker, B.M., 2008. Ecological Models and Data in R. Princeton University Press, Princeton, 396 p. ISBN 978–0-691–12522–0
Borcard, D., F. Gillet, and P. Legendre, 2011. Numerical Ecology with R. Springer, New York, 306 p. ISBN 978–1-4419–7975–9
Crawley, M.J., 2005. Statistics: An Introduction Using R. John Wiley & Sons, West Sussex, 327 p. ISBN 0–470–02298–1. This is our textbook.
Crawley, M.J., 2013. The R Book. John Wiley & Sons, West Sussex, 1051 p. ISBN 978–0470–97392–9. A lap breaker, but a fantastic, comprehensive volume. If I could own only one R book, this would be it.
Dalgaard, P., 2002. Introductory Statistics with R. Springer, New York, 267 p. ISBN 0–387–95475–9
Maindonald, J., and J. Braun, 2003. Data Analysis and Graphics Using R: An Example-Based Approach. Cambridge University Press, Cambridge, 362 p. ISBN 0–521–81336–0
Matloff, N., 2011. The Art of R Programming. No Starch Press, 373 p. ISBN 978–1-59327–384–2. If you have programmed before, you will appreciate this approach.
Murrell, P., 2006. R Graphics. Chapman & Hall / CRC, Boca Raton, 301 p. ISBN 1–58488–486-X. A great source when you want to get serious with the graphics capabilities of R.
The R Core Development Team, 2004. The R Reference Manual Base Package, Volumes 1 and 2. Network Theory Limited, Bristol. ISBN 0–9546120–0-0. Note that this is just a hard-copy version of the help files that come with R. You might find it easier to browse and the proceeds help cover the development costs of R. Think of it as a donation to a good cause.
Teetor, P., 2011. R Cookbook. O'Reilly Media, 436 p. ISBN 978–0-596–80915–7.
Venables, W.N., D.M. Smith, and the R Development Core Team, 2009. An Introduction to R. ISBN 3–900051–12–7. This is available as a free pdf download, and is a solid reference. It’s often the first place I look.
Verzani, J., 2005. Using R for Introductory Statistics. Chapman & Hall / CRC, Boca Raton, 414 p. ISBN 1–58488–4509
Setting up your computer
You will often need to set extensions on file names, sometimes to non-standard ones, so that R is easier to use. Modern operating systems hide these by default because they don’t want your crazy Uncle Leo mucking around with them, so you will need to tell the operating system to display them.
For Windows, go to File Explorer, then the View menu. Select Show, then File name extensions.
For macOS, go to the Finder menu, and select Settings… In the window that opens, select the Advanced tab and check the box that says ’Show all filename extensions“.
