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://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.
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. Modelling
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.
Haefner
Chapter 6
Disease
Modeling.
Differential equation models
Cellular Automata
Agent-based Individually-Based
Models
Chaos.
Logistic Map (Difference Equation)
Lorenz Chaos (Differential
equations)
Matrix population models (Density-Dependent)
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.
Haefner
Chapters 15 and 16
Higgins, S.I., et al. 2000.
Ecological Applications 10:1833-1848
Fitz, H.C. et al. 1996. Ecological Modelling 88:263-295
Loudermilk, E.L.
and W.P. Cropper. 2006. For. Ecol. Manage.
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.
American Naturalist 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. Can. J. Soil Sci.
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. Ecol. Man.
126:201-212.
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%)
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.
University of Florida Policies
Academic Honesty
As a
result of completing the registration form at the University of Florida,
every
student has signed the following statement: "I understand that the
University
of Florida expects its students to be honest in their academic
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:
University
Counseling Center, 301 Peabody Hall, 392-1575 (personal and career
counseling);
Student Mental Health, Student Health Care Center, 392-1171
(personal
counseling); Center for Sexual Assault /Abuse Recovery and Education
(CARE),
Student Health Care Center, 392-1161 ext. 4231 (counseling related to
sexual
assault and abuse); Career Resource Center, Reitz Union, 392-1601
(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.