(to be read before lecture)

Lecture 2:

• Pages 6-25 in 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.
• Chapters 1 and 2 and the Glossary in 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.

• Chapter 1 of 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.
• Study a book on Sampling to augment the class material
• Find your linear algebra book and review material on multiplication of vectors and matrices

• Scan Chapter 9 of 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.
• Snoop around Appendix C of 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.
• Scan a book on applied probability to gain familiarity with the binomial and multinomial distributions
• Study Chapter 1 of 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.
• Find your calculus book and review derivatives for log and exponential functions
• Come to class with some questions!

• Continue scanning 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.
• Goodness-of-fit of Product Multinomial Models
• Be certain you understand the binomial and multinomial probability functions, likelihoods and log-likelihoods

• Program MARK: Survival Estimation from Populations of Marked Animals -- Gary C. White and Kenneth P. Burnham
• First Steps with Program MARK: Linear Models -- Evan Cooch
• Be aware of "Program MARK: First Steps" by Evan Cooch and Gary C. White.

• Section on design matrices and computing the mean of a set of parameters from Advanced Features of Program MARK -- Gary C. White, Kenneth P. Burnham, and David R. Anderson
• First Steps with Program MARK: Linear Models -- Evan Cooch
• Two good references on likelihood methods:
  Azzalini, A. 1996. Statistical inference based on the likelihood. Chapman and Hall.
  Royall, R. M. 1997. Statistical evidence: a likelihood paradigm. Chapman and Hall.

• 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.
• Models Versus Full Reality (in the "Additional Reading" section)
• Keep working to understand the concept of a design matrix
• Study the figures and model naming conventions of various models in lecture6; this will help understand what the (sub)model is achieving (a picture is worth a 1000 words-type of thing).
• Start to review old mid-term exams to understand the type of questions to expect
• Keep reading and re-reading materials; as your understanding of the subjects
  increases, you can better understand points that were unclear on first reading.

Lecture 9:

• 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.
• The Set of Candidate Models (in the "Additional Reading" section)
• Goodness-of-fit of Product Multinomial Models (in the "Additional Reading" section)
• Advanced Features of Program MARK -- Gary C. White, Kenneth P. Burnham, and David R. Anderson
• White, G. C.  2002.  Discussant: The Use of Auxiliary Variables in Capture-Recapture Modeling: An Overview.  Journal of Applied Statistics 29(1-4):103-106. 
• Anderson, D. R., K. P. Burnham, and G. C. White. 1994. AIC model selection in overdispersed capture-recapture data. Ecology 75:1780-1793.

• Jointly Analyzing Live and Dead Encounters using MARK -- Richard J. Barker and Gary C. White
• Szymczak, M.R. and Rexstad, E.A. 1991.   Harvest distribution and survival of a gadwall population.  Journal of Wildlife Management: 55:592-600.
• Pradel, R. 1996. Utilization of capture-mark-recapture for the study of recruitment and population growth rate.  Biometrics 52:703-709.
• Nichols, J. D., and J. E. Hines. 2002. Approaches for the direct estimation of lambda, and demographic contributions to lambda, using capture-recapture data. Journal of Applied Statistics 29(1-4):539-568.
• Hines, J. E., and J. D. Nichols. 2002. Investigations of potential bias in the estimation of lambda using Pradel's (1996) model for capture-recapture data. Journal of Applied Statistics 29(1-4):573-587.

• Scan Parts 1,2,4,6,7, and 9 (software) of  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.

• Data Dredging -- Two Examples (in the "Additional Reading" section)
• Review

• Midterm I

• Exploring Ecological Relationships in Survival and Estimating Rates of Population Change Using Program MARK -- Alan B. Franklin
• Pollock, K. H. 2002. The use of auxiliary variables in capture-recapture modelling: an overview. Journal of Applied Statistics 29(1-4):85-102.

•  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.

    Optional, concerning DNA mark-recapture

• Lukacs, P. M., and K. P. Burnham. 2005. Estimating population size from DNA-based closed capture-recapture data incorporating genotyping error. Journal of Wildlife Management 69:396-403.
• Lukacs, P. M., and K. P. Burnham. 2005. Review of capture-recapture methods applicable to noninvasive genetic sampling. Molecular Ecology 14:3909-3919.
   

• 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.
• White, G. C.  2002.  Discussant: The Use of Auxiliary Variables in Capture-Recapture Modeling: An Overview.  Journal of Applied Statistics 29(1-4):103-106.

    Optional, concerning a more detailed discussion of multimodel inference

• Burnham, K. P., and D. R. Anderson. 2004. Multimodel inference - understanding AIC and BIC in model selection. Sociological Methods & Research 33:261-304.
   

• The Robust Design for Capture-Recapture Studies: Analysis using Program MARK -- William L. Kendall
• Lebreton, J.-D., and R. Pradel.  2002.  Multistate recapture models: modelling incomplete individual histories.  Journal of Applied Statistics 29(1-4):353-369.

• Burnham, K. P. and G. C. White.  2002.  Evaluation of some random effects methodology applicable to bird ringing data.  Journal of Applied Statistics 29(1-4):245-264.
• Franklin, A. B., D. R. Anderson, and K. P. Burnham.  2002.  Estimation of long-term trends and variation in avian survival probabilities using random effects models.  Journal of Applied Statistics 29(1-4):267-287.

• Review