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.
Email: stmary@zoo.ufl.edu or The Class
Lecture Schedule |
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Date |
Topic |
Readings |
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24 Aug |
NO CLASS |
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26 Aug |
Course organization, Introduction to optimization & DOM- Rogers Hall |
C&M: pp 3-7;
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31 Aug |
The simplest model – Rogers Hall |
M&C: 41-63; C&M: 7-18 |
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2 Sept |
Simple models continued– Rogers Hall |
as above |
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7 Sept |
Worksheet guided coding: Intro to R (Ben Bolker)- Computer Lab |
you might start on: C&M: 20-30; M& C chap 8; |
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9 Sept |
More coding in R (Mike McCoy)- Computer Lab |
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14 Sept |
Coding the simple models- Computer Lab |
C&M: 9-20
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16 Sept |
Coding the simple models (cont)- |
Same as above |
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21 Sept |
as above- Computer Lab |
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23 Sept |
Model examples: published; build our own-Rogers Hall |
C&M: 20-30; M& C chap 8; Thought problems 1 |
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28-30 Sept |
Model examples: published; build our own- Rogers Hall |
Altricial laying paper; Yerkes& Koops 1999 |
| 5 Oct | Tricks to deal with modeling complications- Rogers Hall | C&M chap 2&3 |
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7 Oct |
Programming one of our own model- Computer Lab |
reed
nesting & small bird foraging models for programming! |
| 12 Oct | Continue programming- Computer Lab | |
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14 Oct |
More modeling complications &/or programming-Rogers Hall |
C&M chap 10 & 11
for Thurs. |
| 19 Oct | Model presentations & Assessments- Rogers Hall | |
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21 Oct |
Model examples: published- Rogers Hall |
TBA |
| 26 Oct | Model presentations & Assessments- Rogers Hall | |
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28 Oct |
Model development and analysis- Computer Lab |
C&M as needed |
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2-4 Nov |
Model development and analysis- Computer Lab |
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9 Nov |
Model development and analysis- Computer Lab; NO CLASS NOV 11 |
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16-18 Nov |
Model development and analysis, Write Intro and Methods- Computer Lab |
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23 Nov |
Model analyses- Computer Lab; NO CLASS NOV 25 |
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30 Nov-2 Dec |
Finalize analyses, Write Results and Discussion- Computer Lab |
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7 Dec |
Review manuscript and plan submission- Rogers Hall |
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