Simulation Analysis of Forest Ecosystems (3 credits)
FOR 6156
Lectures and Discussion: Three times per week for one period each.
Instructor: Wendell Cropper wcropper@ufl.edu
School of Forest Resources and Conservation
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. Wellesley, Mass. (pdf)
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.
Caswell, H. 1988. Theory and models in ecology: A different perspective. Ecological Modelling 43:33-44.
Introduction to Python programming.
complete Python tutorial.
turn in first problem set program.
Introduction to Matrix Algebra and Matrix Models
Tree Population modeling
Forest succession modeling
Landscape Transition (Markov) modeling
Pinard, M. 1993. Biotropica 25(1):2-14
Anderson, P.J. and F.E. Putz 2002. For. Ecol. Manage. 170:271-283.
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
Lytle, D.A. and D.M. Merritt 2004. Ecology 85:2493-2503.
Holm et al. 2008. Biotropica 40:550-558.
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.
Hastings, A. 1993. Annu. Rev. Ecol. Syst. 24:1-33
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
Wyckoff, P.H. and J.S. Clark. 2002. Journal of Ecology 90:604-615.
Liu, J. and Ashton. 1995. Forest Ecology and Management 73:157-175.
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. Can. J. For. Res. 37:2080-2089
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. Can. J. Soil Sci. 86:665-673.
Allison and Martiny. 2008. PNAS 105:11512-11519.
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
Lek and Guegan. 1999. Ecol. Modelling 120:65-73.
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 oral presentation. A written report describing objectives, significance, model structure, and results and discussion is due on the last day of class. (50%)
Participation is required; discussions of topics, homework, assigned papers and projects are an essential part of this course.
Grading Scale:
93% - 100% A
90% - 92.9% A-
86% - 89.9% B+
83% - 85.9% B
80% - 82.9% B-
76% - 79.9% C+
73% - 75.9% C
70% - 72.9% C-
60% - 69% D
Below 60% E
UF grading policies:
http://www.registrar.ufl.edu/catalog/policies/regulationgrades.html
Minus grades: http://www.isis.ufl.edu/minusgrades.html
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. You must receive an A on the project to receive an A for the course.
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.