Stat 534: Ecological Statistics, Fall 2015
These web pages will be used to distribute important and useful information
about the class. Important additions will be mentioned in class and
listed in the updates section.
- 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.
Optional readings (copies in readings folder):
Assigned Readings (copies in readings folder) :
- 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
AMM is Amstrup, McDonald and Manly, Handbook of
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
or WNC, sections 8.4-8.6, but only skim 220.127.116.11. - 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: (N.B. Homework are in pdf format, which require Acrobat to
Data sets and programs
Links to commercial and public-domain software (generally for