- 16 Nov: Posted my notes on using BUGS and rjags, exp.bug BUGS code to fit an exponential growth with process error model, grizz1.r R code illustrating rjags functions to fit the model in exp.bug, and grizzly.csv the data set.
- 11 Nov: Posted information on hierarchical modeling problem. We will discuss potential models in class on Thursday. That discussion will be more useful if you look at and think about the problem beforehand.
- 8 Nov: Posted data sets for HW 3: mghsize.csv for problem 3, mghfire.txt for problem 4.
- 5 Nov: HW 3 posted.
- 28 Oct: Posted my answers to HW 1, problems 1-3. data set posted.

- Syllabus
- References for parts 1 and 2, Estimation of Population Parameters
- References for part 3, Population Models

- If you want a review of introductory probability theory, look at Chapter 1 in Tuckwell, Elementary Applications of Probability Theory. Sections 1.1 - 1.4 are the most relevant to us.
- If you want a review of likelihood methods, look at Chapter 2: Using likelihood for estimation in Borchers, Buckland and Zucchini, Estimating Animal Abundance.
- Or, for a more concise treatment, look at WNC, chapter 4, especially sections 4.1 (distributions) and 4.2 (estimation) (these are not in the readings folder)

AMM is Amstrup, McDonald and Manly,

TC is Tuljapurkar, S. and Caswell, H. 1997. Structure-Population Models in Marine, Terrestrial and Freshwater Systems. Chapman and Hall.

- Part 1, closed populations:

WNC Chapter 1, but skim (i.e. don't worry about details) 1.5 and 1.6

Chao and Huggins, Classical Closed-population Capture-Recapture Models, Chapter 2 in AMM

Chao and Huggins, Modern Closed-population Capture-Recapture Models, Chapter 4 in AMM - Part 2, open populations:

Pollock and Alpizar-Jara, Classical Open-population Capture-Recapture Models, Chapter 3 in AMM

(optional) Nichols, Modern Open-population Capture-Recapture Models, Chapter 5 in AMM

- Part 3, population models:

Nichols, J. 2001. Using models in the conduct of science and management of natural resources. Chapter 2 in Shenk, T.M. and Franklin, A.B. (eds.) Modeling in Natural Resource Management. Island Press.

Caswell et al., Structured-population models: many methods, a few basic concepts, chapter 1 in TC

Caswell, Matrix methods for population analysis, chapter 2 in TC

**or**WNC, sections 8.4-8.6, but only skim 8.4.2.3. - 8.4.4 and omit 8.5.2 (in reading room, copy not provided)

Dixon et al., Part of Sensitivity Analysis for Management, pp 496-510 in Tuljurpurkar and Caswell.

Easterling, Ellner and Dixon, 2000, Ecology 81(3):694-708. Focus on pp 694 - 697 and skim the modeling details.

(optional) The basics of matrix algebra. Appendix A in Caswell, Matrix Population Models.

- Homework guidelines
- Homework 1 (Estimation of population parameters)

- Data sets
- R programs
- R for ecologists Tutorial in R for community ecologists, emphasizing data manipulation
- Introduction to R programming in ecology and epidemiology The first of a series of web tutorials; the rest are more specialized for plant pathologists. You can see the entire set at Ecology and epidemiology in the R programming environment

- CRAN: archive for R project, including downloadable binaries
- Program MARK: standalone program for Mark-Recapture and related methods. The RMark library links R and MARK.