Geog 5400 Environmental Modeling

Miguel F. Acevedo, University of North Texas

Syllabus, Fall 2005

• Announcements (Anuncios): Make sure you know what is going on. Check this link periodically.
• Class Calendar (Calendario de clases): Class topics by week

General Information

• Meetings: Monday 6-7:20 pm lecture 7:30-8:50 pm lab demo, EESAT 163 (Video-Conference class room)
• Instructor: Miguel Acevedo, Office hours EESAT 310H, Mondays 4-5:30 pm, Phone: 565-2381 Email acevedo@unt.edu
• Texbook: Acevedo M.F. 2004. Simulation of Ecological and Environmental Models. Second Edition. XanEdu press.
• Download and check the Errata with some revisions of book
• Addendum to Chapter 3 on use of R commander
  
• Download completely revised chapters: Revised version of chapters 5 and 6
• Teaching Assistant: Heinrich Goetz, Office hours: To be announced, E-mail: hegoetz@unt.edu 
  
• Grade: 70% graded homework assignments. 30% two take-home exams.
• The first exam will be a midterm. The second will be at the time of the final but will not be comprehensive.
  
• Weekly reading and homework assignments due by class time 6 pm the following week.
  
• Assignments and exams cover the lectures and the lab exercises for hands-on practice with simulation models
• Policy on Cheating and Plagiarism. See below.
• Recommended Background Mathematics: pre-calculus; Computers: fundamentals of Windows; Science: fundamentals of Physics, Chemistry and Biology
• Software: DOS, MS Windows,WINSEEM, R ,Excel, PDF reader

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Calendar

• Week 1 - August 29
  
• Lecture: Introduction (Chapter 1), basic math concepts (Chapter 2).
• Lab 1: Introduction to the lab (lab0-CSAM.pdf), Windows (win2000.pdf) and using the R data analysis system (Chapter 3). Downloading lab files (Lab files) 
• Those taking the class remotely (and UAEM participants) your main concerns in the  lab0-CSAM.pdf document are sections 0.4 and 0.5.
• Homework Assignment #1 due Sept 12  Exercises 1-1, 1-4, 2-2, 2-5, 2-8, 2-9, 3-4, 3-7, 3-8, 3-5A.
  
• Note Exercise 3-5A is in the Addendum to Chapter 3 on use of R commander
• Make sure you check the Errata with some revisions of the book.
• Week 2 - September 5 (Labor Day, no class)
• This week please review as much as you can on mathematical and computer concepts and read ahead on Chapters 4, 5 and 6 for next week.
• Make sure you use Revised version of chapters 5 and 6
• Week 3 -September 12
  
• Lecture: Linear models: exponential dynamics, population growth, chemical decay (Chapter 4). Model simulation Numerical integration, finite differences. Parameter estimation. (Chapter 5).
• Lab 2: Simulation, C programs, input files, output files. Parameter estimation (Chapter 6)
  
• Homework Assignment #2: due Sept 19 Exercises 4-1, 4-3, 4-4, 4-6, 4-7,5-2, 5-3, 6-4, 6-8, 6-10
• Week 4 -  September 19
  
• Lecture: Model evaluation and sensitivity analysis (Chapter 7)
• Lab 3: model evaluation, multiple runs and sensitivity analysis; (Chapter 8)
•  Homework Assignment #3 due September 26 Exercises 7-2, 7-3, 7-4, 8-2, 8-5
  
• Week 5 - September 26
  
• Lecture: Non-linear models: logistic dynamics, Michaelis-Menten-Monod. (Chapter 9).
  
• Lab 4:  WINSEEM interface (chapter 10), non-linear models (chapter 11)
  
•  Homework Assignment #4 due October 4 Exercises 9-1, 9-5, 10-3, 11-1, 11-3
  
• Week 6 - October 3 Revised
  
• Lecture: Stability, environmental variability, populations under environmental stress, natural and human-induced disturbances. (Chapter 12),
  
• Lab 5: forcings, more on sensitivity analysis (Chapter 14, sections 14-1 and 14-2)
  
• Homework Assignment #5 due October 10 Exercises 12-1, 12-3, 14-5, 14-6
  
• Week 7 - October 10 Revised
  
• Lecture: More on sensitivity analysis: full factorial designs, Latin Hypercubes, Monte Carlo method. Response surfaces and scenarios (Chapter 13). Review of matrices and linear algebra  (Chapter 15) Age and size structure in populations. Projection matrix (Chapter 17, sections 17-1, 17-2 and 17-3)
  
• Lab 5: Sensitivity, response surface and scenarios (Chapter 14, section 14-3)  Lab 6a: Matrices (Chapter 16),  Lab 6b Projection matrices, (Chapter 18, sections 18-1 and 18-2)
  
• Homework Assignment #6 due October 17 Exercises 13-1, 13-5, 14-10  and Exercises 15-10, 16-2, 17-3, 17-4, 18-1, 18-2
  
• Week 8 - October 17 Revised
  
• Lecture:   Time delays, Life cycles and networks (Chapter 17, sections 17-4, 17-5). Community Dynamics (Chapter 20)
  
• Lab 7: Structured Populations (Chapter 18, sections 18-3,18-4) Structured populations. (Chapter 19)
• Midterm exam: will cover Chapters 1-20 due Oct 24 6 pm. Open book. There will be questions from both the theory and the computer exercises. Most questions will be from the exercises in the book.
• Week 9 - October  24
  
• Lecture: Ecosystems, nutrient cycles and primary productivity. Compartment models (Chapter 21). Biophysical processes: photosynthesis, diffusion and rate limited processes, respiration. (Chapter 22)
• Lab 8: Nutrient cycle models and primary productivity (Chapter 23)
• Homework Assignment #7 due October 31 Exercises 21-4, 21-13, 22-5, 22-9, 23-4, 23-8
  
• Week 10 - October 31
  
• Lecture: Productivity (continued), Eutrophication. Eutrophication models (Chapter 22), Terrestrial ecosystems: Soil, plant and water interactions. Weather generators. (Chapter 25)
  
• Lab 9: Productivity, eutrophication (Chapter 24), Weather generators. (Chapter 26)
  
• Homework Assignment #8 due November 7 Exercises 22-11, 22-12, 22-13, 24-2, 24-3, 25-1, 26-1
  
• Week 11 - November 7
  
• Lecture: Terrestrial ecosystems (continued): Soil, plant and water interactions. Soil water dynamics. Evapotranspiration. (Chapter 25), Vegetation dynamics. Terrestrial ecosystems. Successional dynamics (Chapter 27)
  
• Lab 10: Terrestrial ecosystems (continued) Evapotranspiration. Soil water dynamics. (Chapter 26), Successional dynamics. Landscape dynamics. Grassland and forest dynamics. (Chapter 28)
  
• Homework Assignment #9 due November 14 Exercises 25-4,  26-2, 26-3, 26-4,  27-1, 28-1,  28-3
  
• Week 12 - November 14
  
• Lecture: Vegetation dynamics (continued). Terrestrial ecosystems. Successional dynamics. Spatial analysis and linkages to GIS. (Chapter 27), Non-point source pollution models. Hydrological models. Pesticide run-off models. Land use, habitat changes, spatial analysis and linkages to GIS (Chapter 29)
• Lab 11: Successional dynamics (continued)  Landscape dynamics. Grassland and forest dynamics. (Chapter 28), Runoff. Hydrological models. Soil erosion. (Chapter 30)
  
• Homework Assignment #10 due November 21 Exercises 28-6, 29-1, 30-2 (other exercises to be annunced)
  
• Week 13 - November 21
  
• Lecture: Water quality models. Hydrodynamics and transport/fate models. BOD and oxygen dynamics. Rivers, lakes and estuaries. (Chapter 31). Groundwater (Chapter 33)
  
• Lab 12:. Water quality, Transport and Fate (Chapter 32)
  
• Homework Assignment #11 due November  28 Exercises 32-1, 32-2 (other exercises to be announced)
  
• Week 14 - November 28
  
• Lecture: Air quality models. Plume rise (near-field models) and Far-field models. Air transport. Dispersion. Deposition. (Chapter 34)
• Lab 13: Air quality Near and far field models. (Chapter 35)
• Homework Assignment #12 due December 5 Exercises 35-3, 35-4 (other exercises in Ch 34 to be announced)
  
• Week 15 - December 5
  
• Lecture: Ecotoxicological models. Bio-availability. Bio-Concentration, uptake and depuration kinetics. Fate models. (Chapter 36)
• Lab 14: Ecotoxicology; compartment models. (Chapter 37)
• Final Exam will cover Chapters 21-37 due Dec 12.  Open book. Take Home. There will be questions from both the theory and the computer exercises. Most questions will be from the exercises in the book
  
• Week 16 - December 12 Finals week
• Final Exam due 6 pm. No exam will be accepted after this deadline.
  

• UNT students: If you want to take this class remotely for credit this Fall04, you would enroll regularly in Geog 5400 but will not need to attend class on campus Monday evening.
• You will study the book and conduct the computer exercises on your own.
• The final grade will be calculated using the same system as those taking the class in the conventional manner.
  
• The homework assignments will be submitted by 6pm every monday preferably in hard-copy or alternatively in electronic form (if you will not be coming to campus at all). Homework assignments and deadlines for submitting them as well as the required format will be provided in the announcements (link above). You will be required to progress at the same rate as the calendar given below.
  
• To access the lab files you would need a web browser and Internet access (user id and password will be provided later). To write assignments you will need  MS word. It would be even better if in addition you get Adobe Acrobat and convert to pdf.
  
• You will be able to run on your own machine all of my own software (C programs, WINSEEM), the GNU free software (R system), and software that you most likely already have (e.g., excel)
• If you want to enroll in another Monday evening class you will have to get help from Tami or Eva in the Geog. Dept to override the time conflict.
• Please notify me by E-mail after you enroll in the class and decide to follow this distance learning option and let me know whether you are enrolled in another Monday evening class. At that time I will provide the userid and passwd.

ADA

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Bibliography available in the library

Materials in reserve at the Science and Technology Library  (http://www.library.unt.edu/ search on course reserves)

• Ford, A. 1999. Modeling the Environment. Island Press. 401 pp. [GE45.D37 F67 1999]
• Hemond H.F. and E.J. Fechner. 1994. Chemical fate and transport in the environment.  Academic Press. 338 pp. [TD193 .H46 1994]
• James A. (Ed.) 1984. An introduction to Water Quality Modeling. Wiley. First Edition (there is a second edition of 1993).  [TD367 I58 1984]
• Lyons T.J. and W.D. Scott. 1990. Principles of air pollution meteorology. CRC Press. [QC 882 P744 1990]
• Swartzman G.L. and S. Kaluzny. 1987. Ecological Simulation Primer. MacMillan. [QH541 15M3 S89]

• Acevedo M.F. and T.W. Waller. 2000. Modelling and Control of a simple trophic aquatic system. Ecological Modelling 131:269-284.
  
• Acevedo M.F., M. Ablan, K.L. Dickson, W.T. Waller, F.L. Mayer and M. Morton. 1997. Estimating pesticide exposure in tidal streams of Leadenwah Creek, South Carolina. Journal of Toxicology and Environmental Health 52:295-316.
• Acevedo M.F., W.T. Waller, D.P. Smith,D.W. Page and P.B. McIntyre. 1995. Modeling cladoceran population responses to stress with particular reference to sexual reproduction. Nonlinear World 2:97-129.
• Acevedo M.F., D.P. Smith and M. Ablan. 1997. Vegetation Dynamics in North-Central Texas: A Prospectus for Landscape Scale Modeling. In: D.Lyons and P. Hudak (Eds.) Geographic Perspectives on the Texas Region. Association of American Geographers, Washington DC pp:115-124.
• Acevedo, M.F. D.L. Urban and H.H. Shugart. 1996. Models of forest dynamics based on roles of tree species. Ecological Modelling. 87:267-284.
• Acevedo, M.F. D.L. Urban and M. Ablan. 1995. Transition and gap models of forest dynamics. Ecological Applications. 5(4):1040-1055.
• Arnold J.G., J.R. Williams, R.H. Griggs and N.B. Sammons. SWRRBWQ: A basin scale model for assessing management impacts on water quality. USDA-ARS.
• Ginot V. and J.C. Herve. 1994. Estimating the parameters of dissolved oxygen dynamics in shallow ponds. Ecological Modelling 73:169-187.
• Hallam T.G. 1986a. Population Dynamics in a Homogeneous Environment. In: Hallam T.G. and S.A. Levin (eds) Mathematical Ecology. Springer-Verlag. pp:61-94.
• Hallam T.G. 1986b. Community Dynamics in a Homogeneous Environment. In: Hallam T.G. and S.A. Levin (eds) Mathematical Ecology. Springer-Verlag. pp: 242-285.
• Jorgensen S. 1988. Fundamentals of Ecological Modelling, Chapter 7. Elsevier. pp:193-319.
• Kirk J.T.O. 1983. Light and Photosynthesis in aquatic systems. pp:219-246 Cambridge University Press.
• Maidment D. 1993. GIS and Hydrological Modeling. In: Goodchild M.F., B.O. Parks and L.T. Steyaert (Eds.) Environmental Modeling and GIS. Oxford University Press. pp: 147-167.
• Meyer S.P., T.H. Salem and J.W. Labadie. 1993. Geographic Information Systems in Urban Storm-Water Management. Journal of Water Resources Planning and Management 119: 206-228.
• Moore I. D., A. K. Turner, J.P. Wilson, S.K. Jenson and L. E. Band. 1993. GIS and land-surface-subsurface process modeling. In: Goodchild M.F., B.O. Parks and L.T. Steyaert (Eds.) Environmental Modeling and GIS. Oxford University Press. pp: 198-230.
• Nisbet R.M. and W.S.C. Gurney. 1986. The formulation of age-structured models. In: Hallam T.G. and S.A. Levin (eds) Mathematical Ecology. Springer-Verlag. pp: 95-115.
• Nix S.J. 1991. Applying urban runoff models. Water Environment & Technology. June 1991 pp 47-49.
• Novotny V. 1986. A review of hydrologic and water quality models used for simulation of agricultural pollution. In: Giorgini A., F. Zingales, A. Marani, and J. Delleur (eds) Agricultural Nonpoint source pollution: Model Selection and Application. Elsevier. pp:9-35.
• O'Connor D.J., J.P. Connolly and E.J. Garland. 1989. Mathematical Models - Fate, Transport, and Food Chain. In: S.A. Levin, M.A. Harwell, J.R. Kelly and K.D. Kimball (Eds.). Ecotoxicology: Problems and Approaches. Springer-Verlag.pp 221-242.
• Thomann R.V. 1989. Deterministic and statistical models of chemical fate in aquatic systems. In: S.A. Levin, M.A. Harwell, J.R. Kelly and K.D. Kimball (Eds.). Ecotoxicology: Problems and Approaches. Springer-Verlag.pp 245-277.
• Williams J.R. and A.D. Nicks and J.G. Arnold. 1985. Simulator for Water Resources in Rural Basins. Journal of Hydraulic Engineering. 111:970-986.
• Williams J.R., C.A. Jones and P.T. Dyke. 1990. The EPIC model. In: Sharpley, A.N. and J.R. Williams (Eds) EPIC-Erosion/Productivity Impact Calculator: 1 Model Documentation. USDA Technical Bulletin No: 1768 235 pp.

Statement on Cheating and Plagiarism

• use of any unauthorized assistance in taking quizzes, tests, or examinations
• dependence upon the aid of sources beyond those authorized by the instructor in writing papers, preparing reports, solving problems, or carrying out other assignments
• the acquisition, without permission, of tests or other academic material belonging to a faculty or staff member of the university
• dual submission of a paper or project, or resubmission of a paper or project to a different class without express permission from the instructor(s); or
• any other act designed to give a student an unfair advantage.

• the knowing or negligent use by paraphrase or direct quotation of the published or unpublished work of another person without full and clear acknowledgment; and
• the knowing or negligent unacknowledged use of materials prepared by another person or agency engaged in the selling of term papers or other academic materials.