Introduction to Ecological Modeling: Concepts, Methods and Applications

FISH/QSCI 454: Introduction to Ecological Modeling
M/W/F 10:30-11:20 W 12:30 - 12:20 Instructor: Tim Essington 318B Fisheries essing@u.washington.edu TA: Anne Beaudreau annebeau@u.washington.edu 360 Fisheries
Syllabus Optional Textbook information			Electronic Reserves Assignment Information
*SCHEDULE*
		Lecture	Lab	Skills

Week 1: Jan 7 - Jan 11	Why do we model? What is a model? Process of model development (ppt1; ppt 2) Week 1 Lecture Notes		Process of Model Building (key) Optional Readings (link to e-reserves): Walters 1986. A process of model building. Chapter 3 of "Adaptive management of renewable resources". Hall, C.A.S and J.W. Day. 1977. Systems and models: terms and basic principles. in C.A.S. Hall and J.W. Day, (Eds.), Ecosystem Modeling in Theory and Practice Wiley, NY. Jackson, L.J. , A.S. Trebitz, and K.L. Cottingham. 2000. An introduction to the practice of ecological modeling. Bioscience 50:694-70	Mastering Microsoft Excel Logistic example
Week 2: Jan 14 - Jan 18	Population Models Week 2 Lecture Notes Logistic Model Notes on matrix analyses		Single-Species Population Models (key) Program Files (zipped) How'd you do that? Poptools Excel Add-in Optional Readings (link to e-reserves): Crouse et al. 1987. A stage-based population model for loggerhead sea turtles and implications for conservation. Ecololgy 68: 1412-1423 Gotelli, N.J. 1995. Age-structured population growth. In A primer of ecology. Sinauer Associates. Sunderland, MA. pages 56-85.	Modeling differential equations in spreadsheets Optional Reading: Chapter from Numerical Recipes in C Logistic Population Model
Week 3: Jan 21 - Jan 25	Multi-species models and stability analysis Lecture Notes		Competion and Predation Models (key) More Notes on Stability Analysis Competition Model Nicholson Bailey Model Nicholson Bailey w/ Density Dependence
Week 4: Jan 28 - Feb 1	Stochastic Population Models & Metapopulation Models (ppt) Optional Reading: Gotelli, N. 2001. A Primer of Ecology, 3rd ed. Sunderland, MA: Sinauer Associates, Inc. pp. 126-153. [Chapter 6: Predation]		Population Viability Analysis (key) PVA.xls file DD_Model.xls	Basics of Visual Basic Programming
Week 5: Feb 4- Feb 8	Ecosystem Models Lecture Notes		Compartment Models (key) Optional Readings (link to e-reserves): DeAngelis, D.W. 1992. General concepts of nutrient flux and stability. in Dynamics of nutrient cycling and food webs. Pages 17-37 Carpenter, S. R., Kraft, C. E., Wright, R., Xi, H., Soranno, P. A. and Hodgson, J. R. 1992. Resilience And Resistance Of A Lake Phosphorus Cycle Before And After Food Web Manipulation. Am. Nat. 140: 781-798	TBA
Week 6: Feb 22 - Feb 15	Tactical Models (ppt) and Sensitivity analysis. (ppt)		Sensitivity Analysis Seal sensitivity analysis (key)	Developing Monte Carlo Simulation Demo Excel File
Week 7: Feb 18 - Feb 22	Simulation Studies and Policy Evaluation (ppt) "Open Loop" Policy Analysis		Simulation Studies Operational Model (key; output from 100 runs) Policy Simulation	Advanced sensitivity analysis
Week 8: Feb 25 - Feb 27	Probability and Likelihood PDF Demos Lecture Notes		Probability and Likelihood (key; spreadsheet) link to "Introduction to Probability"	Numerical Optimization Grid Search Newton Method
Week 9: March 3 - March 5	Parameter Estimation and Model Selection Bayes Theorem and Applications Bayesian Squirrel		Parameter Estimation (key) Likelihood Comparison (includes setup instructions)	Assignment 4 help
Week 10: March 10 - Mar 14	Life history Optimization Lecture Notes		Optimal prey selection (key) Prey selection model	Evolutionary Invasion Analysis and optimization methods