Dynamic Optimization Modeling
in
Behavioral and Evolutionary Ecology

Zoo 6308 section XXXX (3 credits)

Fall 2004


 


The Details:

* Instructor:  Colette M. St. Mary
                       610 Bartram Hall
                      392-1636 (phone is not a good way to reach me)

 Texts: Available at the Goerings Text Bookstore: 1717 NW 1st Ave
1)  C. W. Clark and M. Mangel, 2000. Dynamic state variable models in ecology: Methods and applications. Oxford University Press.

    Other resources: Ben Bolker’s link guide to the R programming language

 When and Where (Rogers 110 or McEdward Computer Teaching Facility, Carr 611 as indicated):
Tues. and Thurs. 12:45-2:45 (6th and 7th periods)

 Office Hours: By Appointment  

Dynamic optimization modeling (DOM) is a powerful and simple technique for formalizing behavioral and evolutionary hypotheses. This type of modeling is appropriate to address questions in the areas of life history evolution, ecology, behavioral ecology, and any other area in which the relative fitness of alternative choices, or strategies is compared. DOM requires only basic mathematical and programming skills, and the model structure easily allows field quantification of parameters and examination of predictions. Thus, this simulation modeling approach is useful and readily accessible to empiricists and theorists alike.

Format: This course will open with an introduction to dynamic optimization modeling, including the basics of the approach and the aspects of probability theory on which it depends. I will then highlight the application of DOM to questions in behavioral and evolutionary ecology, drawing from the literature. I will then introduce programming in Borland Delphi, one of various programming tools that can be used to implement these models. In the main portion of the course we will explore various complexities that can be built into the models and again draw on the literature to see these implemented. This exploration will involve programming some published models and constructing a model of our own devising. Students will then develop models on their own, based on their research interests, and present them to the class. Finally, the class will develop and analyze one of these models and write a manuscript for journal submission.


Course Communication and Announcements: 

Email: stmary@zoo.ufl.edu or The Class


Lecture Schedule

Date

Topic

Readings

24 Aug

NO CLASS

 

26 Aug

Course organization, Introduction to optimization & DOM- Rogers Hall

C&M: pp 3-7;

 

31 Aug

The simplest model – Rogers Hall

M&C: 41-63;

C&M: 7-18

2 Sept

Simple models continuedRogers Hall

as above

7 Sept 

Worksheet guided coding: Intro to R  (Ben Bolker)- Computer Lab

R files

you might start on: C&M: 20-30; M& C chap 8; 
we'll work with this reading 21 Sept.

9 Sept

More coding in R  (Mike McCoy)- Computer Lab

 

14 Sept

Coding the simple models- Computer Lab
(sample code provided; Toshi Okuyama)

C&M: 9-20

 

16 Sept

Coding the simple models (cont)

Same as above

21 Sept

as above- Computer Lab

 

23 Sept

Model examples: published; build our own-Rogers Hall

C&M: 20-30; M& C chap 8;

Thought problems 1

28-30 Sept

Model examples: published; build our own- Rogers Hall

Altricial laying paper;

Yerkes& Koops 1999

Thought problems 2 & 3

5 Oct Tricks to deal with modeling complications- Rogers Hall C&M chap 2&3

7 Oct

Programming one of our own model- Computer Lab

 reed nesting & small bird foraging models for programming!

12 Oct Continue programming- Computer Lab  

14 Oct

More modeling complications &/or programming-Rogers Hall

 C&M chap 10 & 11 for Thurs.

19 Oct Model presentations & Assessments- Rogers Hall  

21 Oct

Model examples: published- Rogers Hall

 TBA

26 Oct Model presentations & Assessments- Rogers Hall  

28 Oct

Model development and analysis- Computer Lab

 C&M as needed

2-4 Nov

Model development and analysis- Computer Lab

 

9 Nov

Model development and analysis- Computer Lab; NO CLASS NOV 11

 

16-18 Nov

Model development and analysis, Write Intro and Methods- Computer Lab

 

23 Nov

Model analyses- Computer Lab; NO CLASS NOV 25

 

30 Nov-2 Dec

Finalize analyses, Write Results and Discussion- Computer Lab

 

7 Dec

Review manuscript and plan submission- Rogers Hall