Paul J. Hurtado

Foundations of Quantitative Ecology Graduate Seminar (EEOB 8896.11)

Fall 2013 course website

Where: Aronoff Room 104     When: 12:45-2:45pm, Wednesday, Session 1 (21 Aug - 2 Oct, 2013)
Instructor: Paul Hurtado (hurtado.10)
Course website: http://www.pauljhurtado.com/teaching/FA13/
Registration details: EEOB 8896.11 - 100.   EEOB Graduate Seminar: Population Ecology.  Class Number 34241.  1 Credit.

Requirements: Students will use their own laptops during class. Contact the instructor if you have any questions.

Description: Mathematical and computational tools have become standard in biology, including ecology and evolutionary biology. This course will introduce graduate students in the biological sciences to computer programming basics (primarily using R) and useful concepts from statistics, probability, calculus, dynamical systems, linear algebra, and other areas of applied mathematics commonly encountered in the biological sciences. The aim of the course is to build students' familiarity with these concepts and tools as they are likely to encounter them in future courses, and their field of research. Special topics suggested by the class may also be covered.

This introductory course is intended to complement the EEOB course "Introduction to R for Biologists" taught by Simon Queenborough during the second 7 weeks of the fall semester. This is not a prerequisite for that course, but it will cover basic mathematical and statistical concepts, and build programming skills, relevant to that course.

Course Schedule

• Week 1 -- Course overview; Installing and using R (21 Aug)
  • Introduction to R using the Self-tutorials linked below.
  • Modify BBS Data Script: breeding-bird-survey-figs.R
• Week 2 -- Introduction to Probability (28 Aug)
  • Lecture Slides: Week2-Slides.pdf (Update below includes more on Liklihood functions).
  • Updated Slides: Week2.pdf [knitr source: Week2.Rnw]
• Week 3 -- Basic objects in R; Reading/writing files. (4 Sept)
  • Lecture Slides: Week3.pdf [knitr source: Week3.Rnw]
• Week 4 -- Functions, Iteration and Looping, Branching (if/else) (11 Sep)
  • Lecture Slides: Week4.pdf [knitr source: Week4.Rnw]
  • BBS data: BBS.zip -- BBS "data" are actually population estimates, based on BBS data, comprised by an Index of population size and confidence intervals for those estimates. They were obtained via the USGS BBS Summary and Analysis website, through the Regional Trend Analysis tool.
  • R code from class: week4_in-class-scratch.R -- Includes code, comments for plotting select BBS data (e.g. creating figures for just the genus Melospiza).
• Week 5 -- (Week 4 continued) Models and Simulation (18 Sep)
  • Lecture Slides: Week5.pdf [knitr source: Week5.Rnw]
• Week 6 -- Matrices, Eigenvectors and Eivenvalues, Model Simulation (25 Sep)
  • Lecture Slides: Week6.pdf [knitr source: Week6.Rnw]
• Week 7 -- ODE Simulation and Stochastic Simulation (2 Oct)
  • Lecture Slides: Week7.pdf [knitr source: Week7.Rnw] and R code from class week7-scratch.R.

R Resources

Please see my updated R Resources page.