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.
Last update:
 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
modeling projects.
 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 markrecapture

Information: (N.B. some files are pdf files, which require Acrobat
Reader)
 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
CaptureRecapture Analysis
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 Closedpopulation CaptureRecapture
Models, Chapter 2 in AMM
Chao and Huggins, Modern Closedpopulation CaptureRecapture
Models, Chapter 4 in AMM
 Part 1, open populations:
Pollock and AlpizarJara, Classical Openpopulation
CaptureRecapture Models, Chapter 3 in AMM
(optional) Nichols, Modern Openpopulation
CaptureRecapture Models, Chapter 5 in AMM
 Part 2, population models:
WNC, Chapter 7, Principles of model development and assessment (for
concepts)
Caswell et al., Structuredpopulation 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 8.48.6, but only skim 8.4.2.3.  8.4.4 and
omit 8.5.2
Caswell, Chapter 10, Life Table Response Experiments from Caswell,
Matrix Population Models, 2nd ed.
Dixon et al., Part of Sensitivity Analysis for Management, pp
496510 in Tuljurpurkar and Caswell.
(optional) The basics of matrix algebra
Homework: (N.B. Homework are in pdf format, which require Acrobat to
read
Data sets and programs
Links to commercial and publicdomain software (generally for
Windows)