Simulation Analysis of
FOR
6156
Lectures and Discussion Three times per week for one period
each.
Instructor: Wendell Cropper wcropper@ufl.edu
214 Newins Ziegler Hall
Office Hours: After class or by appointment.
See me for help with programming, homework and projects. Email questions and
programs.
Course Description
This
course is designed to explore the conceptual basis, evaluation, implementation,
testing, and analysis of forest and tree simulation models.
Each
student will develop and present a modeling project based on their research or
other approved topics.
Course is Designed For: Graduate Students
Prerequisites: Undergraduate course(s) in
ecology, plant physiology. Ability
to use Algebra.
Course Resources:
Books
(recommended)
:
Modeling Biological
Systems. Principles and Applications.
J. W. Haefner. 1996. Chapman and Hall, NY.
473 pp.
Python programming books:
Learning Python. Mark Lutz, David Ascher. 1999.
O’Reilly and Associates, Inc. 366 pp. OR
How to Think Like a
Computer Scientist. Learning with Python. 2002.
A.Downey, et. Al.
Green Tea Press.
http://www.freenetpages.co.uk/hp/alan.gauld/
Python Programs: example programs provided
that illustrate each topic
Web Resources:
http://www.python.org/ (free download of Python
for windows,
mac, and Unix); Tutorials
http://en.wikibooks.org/wiki/NonProgrammer%27s_Tutorial_for_Python/Contents
http://sourceforge.net/projects/numpy
(free download of Numerical Python)
http://matplotlib.sourceforge.net/
(free download of MatPlotLib)
http://www.cse.csiro.au/poptools/index.htm (Excel plug in)
Lecture and Discussion Topics:
Introduction
to Modeling.
What is a model?
How are models made?
Testing and
Evaluation of models.
Haefner Chapt 1 - 3.
Jorgensen, S.E. 2008. Overview of the model types available for
development of ecological models. Ecol. Model. 215:3-9.
Introduction
to Python programming.
complete
Python tutorial.
turn in
first problem set program.
Introduction to
Matrix Algebra and Matrix Models
Tree Population modeling
Landscape Transition (Markov)
modeling
Pinard, M. 1993. Biotropica
25(1):2-14
Cropper, W.P., and
P.J. Anderson. 2004. Ecol. Modelling 177:119-127
Cropper, W.P. and
D. DiResta. 1999. Ecol. Modelling 118:1-15.
Cropper, W.P. and E.L. Loudermilk. 2006. Ecol. Model. 198:487-494.
Dalva, M., et al.
1999. Ecology 80(8):2635-2650
Acevedo, M.F. et al. 1995.
Ecological Applications 5(4):1040-1055
Horn, H.S. Succession.
Chapt. 10 in May, R.M. Theoretical
Ecology.
Haefner Chapter 13
Some
useful functions.
Haefner Chapter 4
Introduction
to Numerical Integration.
integration
error
Introduction to Stella and Berkeley
Madonna
simulation
packages.
Introduction to
Excel spreadsheet for simulation.
Anderson, R.M. et al. 1981. Nature
289:765-771
Ferguson et al. 2003. Nature
425:681-685
Madden, L.V. et al. 2002. BioScience
52:65-74
Earn, D.J.D. 2000. Science
287:667-670.
Harwell et al.
1981. Ecological Modelling 12:105-131
Haefner Chapter 6
Disease
Modeling.
Differential equation models
Cellular Automata
Agent-based Individually-Based
Models
Ferguson et al. 2006. Nature 442:452
Chaos.
Logistic Map (Difference Equation)
Lorenz Chaos (Differential
equations)
Matrix population models
(Density-Dependent)
Becks et al. 2005.
Nature 435:1226-1229
May 1974. Science 186:645-647.
Haefner Chapter 17
Gap Phase
Individual-Based Succession Models.
Examples: Jabowa, Linkages
Haefner p. 338
Post, W.M. and
J.Pastor. 1996. Climatic Change 34:253-261
Liu, J. and
Ashton.
Landscape
Modeling.
Higgins, S.I., et al. 2000.
Ecological Applications 10:1833-1848
Fitz, H.C. et al. 1996. Ecological
Modelling 88:263-295
Loudermilk,
and Cropper. 2007.
Haefner Chapter 15, 16, and 18
Modeling
Plant Competition.
Competition and coexistence - the
effects of resource transport and supply rates.
Huston M.A., DeAngelis D.L. 1994. Amer. Nat. 144 (6): 954-977.
Loreau, M. 1998. Proc. Natl. Acad. Sci. 95:5632-5636.
Haefner Chapter 14
Modeling
Soil Nitrogen Dynamics and Decomposition.
Nitrification
Denitrification
Mineralization
Uptake
Muller, C. Modelling Soil-Biosphere
Interactions.
CABI Publishing.
Chapt. 2
Gholz et al. 1985.
For. Sci. 31:463-478.
Kruys et al. 2002.
Ecol. Applications 12:773-781.
Comerford et al.
2006.
Biological
Inspired Modeling: Neural Nets and Genetic Algorithms
Cropper and
Anderson 2004. Ecol. Modelling 177:119-127
Cropper and
Comerford 2005. Ecol. Modelling 185:271-281
Haefner Chapters 19 and 20
Modeling
Tree Physiology.
assimilation
respiration
transpiration
estimation
of parameters
van den
Berg, M. et al. 2002. Ecol. Mod. 148:233-250.
Chen, J.M. et al. 1999. Ecol. Mod. 124:99-119.
Friend, A.D. 2001. Global Ecol.
Biog. 10:603-619.
Wang, Y.-P.
et al. 1998. Global Change Biology 4:797-807
Wang, YP and
Jarvis. 1990. Ag. For. Met.
51:257-280.
Cropper, W.P. and
Gholz. 1993. Ecol. Mod. 66:231-249
Cropper, W.P.
2000. For.
Course Requirements:
Although collaboration is an important
part of science,
learning modeling
techniques is best done individually.
No collaboration (except with the
instructor) is expected
for the weekly
problem sets or modeling project.
Problem sets (25%)
Presentation and leading discussion of
published
forest modeling
paper (25%)
Modeling project and presentation (50%)
Participation is required; discussions of topics, homework,
assigned papers and projects are an essential part of this course.
Grading Scale:
90% -
100% A
85% -
89.9% B+
80% -
84.9% B
75% -
79.9% C+
70% -
74.9% C
60% -
69% D
Below
60% E
Course Policies
Students are expected to attend class, engage in
discussion, and submit assignments on time. Problem sets may be revised after
initial grading without penalty. A new due date will be assigned for revised
problem sets. A 10% late penalty will be assessed for work turned in or
presented after the due date. Students must complete a written report of the
modeling project, as well as an in class presentation to receive credit for the
project.
Academic Honesty
As a
result of completing the registration form at the
every
student has signed the following statement: "I understand that the
work.
I agree to this commitment to academic honesty and understand that my
failure
to comply with this commitment may result in disciplinary action up
to
and including expulsion from the University."
UF Counseling Services
Resources
are available on campus for students having personal problems or
lacking
clear career and academic goals with interfere with their academic
performance. These resources include:
counseling);
Student Mental Health,
(personal counseling); Center for Sexual Assault /Abuse
Recovery and Education
(
sexual
assault and abuse);
(career development assistance and counseling).
Software Use
All
faculty, staff, and students of the University are required and expected
to
obey the laws and legal agreements governing software use. Failure to do
so
can lead to monetary damages and/or criminal penalties for the individual
violator.
Because such violations are also against University policies and rules,
disciplinary action will be taken as appropriate.
Accommodations for Students With Disabilities
Students
requesting classroom accommodation must first register with the Dean of
students Office. The Dean of Students Office will provide documentation to the
student who must then provide this documentation to the instructor when
requesting accommodation.