Leonard Lab

Bob Farmer (CV)

PhD (defended August 2012)

farmerb 'at' dal.ca

Fax: (902) 494-3736

The main focus of my PhD was how bird communities can be measured using volunteers as surveyors. Using long-term datasets from the Christmas Bird Count, Breeding Bird Survey and Project Feederwatch (among others), I've also spent some time modeling the effects of land use change on bird community attributes, including the distribution of habitat generalists and specialists. By contributing to more effective data collection, population modeling and land-use planning, both of these projects have some important conservation implications.

I've also done some work studying long-term diet trends of Great Black-backed gulls (Larus marinus).

I'm a fan of the R-project for statistical computing, and I also like reptiles and the Great Lakes, two converging areas of focus of my MSc (Guelph).

Some of my lecture materials are posted below:

Course and Lecture Name

applied BE BIOL 3062: Applied Behavioural Ecology (2010)
  1. PDF
  2. Simulation website (from U of T; check it out for fun)
  3. Zombie simulations (examples of individual-based models; I presented Alan Gordon's 3D version)
so I says to Mabel BIOL 3062: On the Importance of Pretty Graphs (2011)
  1. Colour PDF
  2. Black-and-white PDF (for printing)
  3. Andrew Gelman's blog of statistics
  4. Edward Tufte's books about the graphical display of data (a few are also on NOVANET)
                                Data BIOL 5062: Graphing Data and Anscombe's Quartet
  1. PDF
  2. Wikipedia link demonstrating the quartet
  3. Blank R workspace file ("Save As" to a working folder, then self-extract (.exe))
  4. Raw Data (ans.txt; "Save As")
  5. Data Analysis Script (anscombe.R; "Save As")
  6. Shortcut Data Analysis Script (optional) (anscombe2.R; trickier, uses function by())
  7. How to make a dataframe (optional) (example for making the "ans.txt" datafile (makeAns.R))
Introduction to R BIOL 5062: An Introduction to R
  1. PDF
  2. R for Windows (download)
  3. R for Linux/Mac
  4. R mailing lists (for help!)
  5. Tinn-R, a text editor for R (for Windows). I've included an older version here, because, in my opinion, it runs better than the newer versions.
  6. Good Tinn-R settings (screenshots) 1, 2, 2a, 2b, 3.
  7. Tinn-R settings for Windows Vista (must use the most current version of Tinn-R on Vista) (screenshots) 1, 2, 3a, 3b, 3c, 4a, 4b, 5.
                                Regression BIOL 5062: Linear Regression
  1. Tutorial Slides (PDF)
  2. Script file for R
Mixed Models BIOL 5062: Mixed/Hierarchical Models
  1. PDF
  2. Electronic online version of Pinheiro and Bates (2000; browse to this item in NOVANET).
  3. Home page for Gelman and Hill (2007)
  4. Poisson link slide from talk (doesn't show up on PDF; is a great way to appreciate link functions in generalized linear models (here, a Poisson link does a log (ln) transform of y)).
Whoa BIOL 5062: Matrix Multiplication
  1. Example PDF