Syllabus - WLF 625 - Analysis of Vertebrate Populations

WLF 625 - Vertebrate Population Analysis Syllabus - Spring 2007
Week	Lecture Topic	Lab Topic	Readings
15 Jan.		Software Check	Text - Chapters 2-4, Chapters 5 and 6 (optional) Anderson/White Notes (You may need additional fonts to read these notes) Stats Review Random Sampling See also Glossary
22 Jan.	Statistical Review, Binomial and Likelihood Theory, Maximum Likelihood Estimation	Dispersion and Precision Additional Variances Notes Sampling and Iterative Solutions Penny.sas	White et al. (1982), Chapter 2. Program MARK: An Introduction Chapter 1 Doherty/White Notes Binomial/Multinomial Coefficients Binomial Sampling Binomial Likelihood Function Maximum Likelihood Estimation MLE not in Closed Form Expected Value -lab Confidence Interval - lab
29 Jan.	Multinomial Distributions, Band Recovery Models + Addition, Model Selection	Brook Trout Analysis Welcome to MARK Parameter Index Matrix Band Recovery Models Lab Instructions Solution	Text - Chapter 16 Doherty/White Notes Multinomial Distribtuion Goodness-of-fit Band Recovery Models PIM - lab Brook Trout Lab - lab Program MARK: - lab Chapter 2 Chapter 3 Chapter 4 Chapter 5
5 Feb.	Model Selection cont., Cormack-Jolly-Seber Models	European Dipper Analysis Solution	Anderson et al. 2000 - discussion Text, Pages 417-453 Doherty/White Notes AIC related material CJS Models See also Pollock et al. 1990, Lebreton et al. 1992
12 Feb.	Linear Models/Comparing Groups	Simple Design Matrix Solution	Doherty/White Notes Design Matrix/Covariates PIM to Design Matrix More on Design Matrix/Model Selection Program Mark - lab Chapter 6 Chapter 7
19 Feb.	Covariates, Quasi-likelihood/Extra Binomial Variation	Advanced Design Matrix Solution GOF with U-CARE and median c-hat See Also Sage Grouse Data and documentation Exercise 1 Exercise 2	Doherty/White Notes Overdispersion Program MARK Chapter 8 Chapter 10 M. Anderson et al. 2001
26 Feb.	Robust Design/Temporary Emigration	Small Mammal - Closed Models Solution Small Mammals - Robust Design Solution	Text - Chapters 14 and 19 Doherty/White Notes Capture Likelihoods Individual Heterogeneity Robust Design CAPTURE and MARK - Lab Program MARK Chapter 16 See Also Otis et al. 1978 Kendall Article
5 Mar.	Midterm 2005 Midterm 2003 Model Summary
12 Mar.	Spring Recess
19 Mar.	Multistate Models, Discuss midterm	Multistate Analysis Solution	Text - Pages 454-468 Doherty/White Notes Multistrata Program MARK Chapter 9 Nichols and Kendall 1995 Lindberg and Sedinger 1998
26 Mar.	Model Averaging, Confidence Intervals, Known Fate Models	Mule Deer Analysis	Anderson and White Notes Known fate analysis Confidence Intervals Program MARK Chapter 17
2 Apr	Nest Survival	Analysis of Existing Data or part of Dinsmore's input and weather data	Text - Chapter 15 Program MARK Chapter 18 Dinsmore et al. 2002
9 Apr	Pradel's Models - Transients / Reverse, Combined Models	Discussion	Text 468-472, Chapter 18 Program MARK Chapter 13 Doherty/White Notes Burnham's Joint Model Nichols and Hines 2002a - reverse Nichols and Hines 2002b - reverse Pradel et al. 1997 - transient Loery et al. 1997 - transient Cilimburg et al. 2002 - transient Lindberg et al. 2002 - combined
16 Apr	Monte Carlo Simulations	Simulations	Program MARK Appendix A
23 Apr	Components of Variance/Shrinkage Estimators	Discussion (Efron et al. 1977 and other papers)	Doherty/White Notes Random Effects Burnham and White 2002 Franklin et al. 2002
30 May	Sensitivity Analysis/Matrix Modeling	Final Exam 2003 Take Home Question 2003	Text Chapter 20 Nichols et al. 2000 Bouliner et al. 2001 - community dynamics MacKenzie et al. 2002 - site occupancy
7 May	Final Exams

Electronic Copies of Primary Literature

Brownie, C., D. R. Anderson, K. P. Burnham, and D. S. Robson. 1985. Statistical inference from band recovery data -- a handbook, 2nd ed. U. S. Fish and Wildl. Serv. Res. Publ. 156, Washington, D. C. 305pp.

Burnham, K. P., D. R. Anderson, G. C. White, C. Brownie, and K. H. Pollock. 1987. Design and analysis methods for fish survival experiments based on release-recapture. Am. Fish. Soc. Monogr. 5:1-437.

Lebreton, J.-D., K.P. Burnham, J. Clobert, and D.R. Anderson. 1992. Modeling survival and testing biological hypotheses using marked animals: case studies and recent advances. Ecol. Monogr. 62:67-118.

Otis, D. L., K. P. Burnham, G. C. White, and D. R. Anderson. 1978. Statistical inference from capture data on closed animal populations. Wildl. Monogr. 62:1-135.

Pollock, K.H., J.D. Nichols, C. Brownie, and J.E. Hines. 1990. Statistical inference for capture-recapture experiments. Wildl. Monogr. 107:1-97.

White, G. C., D. R. Anderson, K. P. Burnham, and D. L. Otis. 1982. Capture-recapture and removal methods for sampling closed populations. Los Alamos Nat. Lab. Report LA-8787-NERP, Los Alamos, NM. 235pp.