Stat 534: Ecological Statistics, Fall 2013
These web pages will be used to distribute important and useful information
about the class. Important additions will be mentioned in class.
- 11 Dec: Added reference lists for hierarchical modeling and species composition analysis.
- 11 Dec: Added R programs for species composition analysis.
- 3 Dec: Added "HW 4", i.e. a description of what I expect in your hierarchical
- 20 Nov: Added short descriptions of
two potential hierarchical modeling
projects from Chris Jennelle.
- 12 Nov: Added slides from a popular lecture I gave about Bayes
a few years ago "Why the buzz about Bayes?" Has the PSA example, a fungicide trial example, and
an early version of the Mourning Dove work including graphs I didn't use today.
- 10 Nov: Added My answers to HW 1 and
and my R code for HW 1.
- 7 Nov: Added Annotated references for population modeling
- 3 Nov: Added HW 3, due Friday 22 November, and associated data sets.
- 15 Oct: Added HW 2, due Friday, 1 November.
- 15 Oct: Added huggins.r code to simulate data sets with heterogeneity and define
the conditional lnL for the Huggins model.
- 19 Sept: Added annotated reference list for mark-recapture
Information: (N.B. some files are pdf files, which require Acrobat
- Optional 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.
Assigned Readings (copies in readings folder) :
Note: WNC is Williams, Nichols and Conroy,
Analysis and Management of Animal Populations
AMM is Amstrup, McDonald and Manly, Handbook of
The Statistics Reading Room has a copy of WNC.
- Part 1, closed populations:
WNC Chapter 1, but skim 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 1, 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 2, population models:
WNC, Chapter 7, Principles of model development and assessment (for
Caswell et al., Structured-population models: many methods, a few
basic concepts, chapter 1 in Tuljapurkar and Caswell
Caswell, Matrix methods for population analysis, chapter 2 in
Tuljurpurkar and Caswell
or WNC, sections 8.4-8.6, but only skim 18.104.22.168. - 8.4.4 and
Caswell, Chapter 10, Life Table Response Experiments from Caswell,
Matrix Population Models, 2nd ed.
Dixon et al., Part of Sensitivity Analysis for Management, pp
496-510 in Tuljurpurkar and Caswell.
(optional) The basics of matrix algebra
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