|
We will read several chapters from
these texts:
|
|
McCune,
B & Grace, JB
2002
Analysis
of Ecological Communities. MjM Software, Gleneden Beach,
Oregon, USA
|
Available on reserve and for purchase
online
|
|
Peck,
JE
2010
Multivariate
Analysis for Community Ecologists, MjM Software, Gleneden
Beach, Oregon, USA
|
Available on reserve and for purchase
online
|
|
Clarke,
KR, & Warwick RM
2001
Change
in marine communities: an approach to statistical analysis
and interpretation, 2nd edition. PRIMER-E, Plymouth.
|
These
PDFs are for class use only.
Please
do not distribute.
Week
1
- Course Introduction
and Foundations
Task
for this Week: Install and Check Out PC-Ord
Lecture
1: Tuesday January 24
Consult
Software Help
If
you are a Mac User, please check out: fusion
|
Lecture
2: Thursday
January 26
|
McCune
& Grace 2002 - Ch 2: Community
Matrices
|
(PDF-
0.3 Mb)
|
|
McCune
& Grace 2001 - Ch 3: Sampling
Communities
|
|
Week
2
- Dealing
with Partials
Task
for this Week: Review Partial Correlation & Regression
Lecture
3: Tuesday
- February 1
|
Wells
et al. (2008) Untangling the relationships among climate,
prey and top predators in an ocean ecosystem
|
(PDF-
0.4 Mb)
|
|
Sokal
et al. (2000) Cancer incidences in Europe related to mortalities,
and ethnohistoric, genetic, and geographic distances
|
|
Lecture
4: Thursday
- February 3
|
Schwing
et al. (2002) The Northern Oscillation Index (NOI): A new
climate index for the northeast Pacific
|
(PDF-
1.3 Mb)
|
|
McCune
& Grace 2002 - Ch 8: Documenting
Analysis Flow
|
|
Week
3
- Dealing
with Residuals
Task
for this Week: Manipulate and Transform Data
Lecture
5: Tuesday
- February 8
|
McCune
& Grace 2002 - Ch7: Data
Screening
|
|
|
Homework
1 Dataset: stocks
|
|
|
Homework
1 Dataset: upwell
|
|
Lecture
6: Thursday
- February 10
|
McCune
& Grace 2002 - Ch9: Data
Transformations
|
(PDF
- 0.5 Mb)
|
|
Clarke
& Warwick 2001 - Ch 9:
Data Transformations
|
(PDF
- 5.6 Mb)
|
|
McCune
& Grace 2002 -Ch 6: Distance
Measures
|
|
|
Clarke & Warwick 2001 - Ch 2:
Similarity Measures
|
|
Week
4
- Grouping
Task
for this Week: Introduction to Grouping
Lecture
7: Tuesday
- February 15
James
& McCulloch (1990)
Review
of Multivariate Analyses
(Reference
Reading)
|
|
|
McCune
& Grace 2002 - Ch 5: Species
Distributions
|
|
|
McCune
& Grace 2002 - Ch 10:
Finding Groups
|
|
Lecture
8: Thursday
- February 17
|
McCune
& Grace 2002 - Ch 11:
Hierarchical Clustering
|
(PDF
- 0.3 Mb)
|
|
Clarke
& Warwick 2001 - Ch 3:
Hierarchical Clustering
|
|
|
Peck
2010 - Ch 23: Clustering
|
|
|
McCune
& Grace 2002 - Ch 12:
Two-Way Indicator Species
|
(PDF
- 0.2 Mb)
|
|
He et al. (1997) Cluster analysis of fishery
practices
|
|
|
Wolter (1987) Cluster Analysis of the
Southern Oscillation in Surface Circulation and Climate
|
|
|
Diehr
et al. (1982) Cluster analysis
headache types
|
|
|
Homework
2 Dataset: desserts & colors
|
|
Week
5
- Grouping
vs Ordination
Task
for this Week: Introduction to Ordination
Lecture
9: Tuesday
- February 22
McCune
& Grace 2002 - Ch 13:
Ordination
|
|
|
McCune
& Grace 2002 - Ch 14:
PCA
|
|
|
Clarke
& Warwick 2001 - Ch 4:
PCA
|
|
Lecture
10: Thursday
- February 24
|
Weicher
et al. (2004) Seabird distribution on the Humboldt Current
in northern Chile in relation to hydrography, productivity,
and fisheries
|
|
|
Ainley
et al. (2005) Physical and biological variables affecting
seabird distributions during the upwelling season northern
California Current
|
(PDF
- 0.6 Mb)
|
|
Peck
2010 - Ch 23: PCA
|
|
Week
6
- Extracting
Patterns from Data
Task
for this Week: Applications of PCA
Lecture
11: Tuesday
- March 1
|
Peck
2010 - Ch 13: Distance Measures
|
|
|
Peck
2010 - Ch 15: Weighting Variables
|
|
|
Nelson
et al. (2004)
|
|
|
Bonaiuto
et al. (2003)
|
|
|
Mantua
et al. (1997)
|
|
|
Homework
3 Dataset: Relativizations
|
|
|
Homework
3 Dataset: Upwell_PCA
|
|
Lecture
12: Thursday
- March 3
|
McCune
& Grace 2002 - Ch 16:
NMDS
|
|
|
Clarke
& Warwick 2001 - Ch 5:
NMDS
|
|
|
Peck
2010 - Ch 24: NMDS
|
|
Week
7
- Extracting
Patterns from Data
Task
for this Week: Applications of NMDS
Lecture
13: Tuesday
- March 8
|
Clarke
(1993)
|
|
|
Hyrenbach
et al. (2007)
|
|
|
Hebshi et al. (2008)
|
|
|
Yildirim
et al. (2010)
|
|
|
Aswani
(2005)
|
|
Lecture
14: Thursday
- March 10
|
McCune
& Grace 2002 - Ch 17:
Polar Ordination
|
|
|
Peck
2010 - Ch 20: Polar Ordination
|
|
Week
8
- Finishing
Ordination
Task
for this Week: Overview of Other Methods
Lecture
15: Tuesday
- March 15
|
McCune
& Grace 2002 - Ch 18:
Weighted Averaging
|
|
|
Peck
2010 - Ch 19: Weighted Averaging
|
|
|
McCune
& Grace 2002 - Ch 19:
Correspondence Analysis
|
|
|
McCune
& Grace 2002 - Ch 20:
Detrended Correspondence
|
|
|
Homework
4 Dataset: IndianOcean_seabirds
|
|
Lecture
16: Thursday
- March 17
|
McCune
& Grace 2002 - Ch 22:
Ordination Reliability
|
|
|
McCune
& Grace 2002 - Ch 21:
Canonical Correspondence
|
|
|
Peck
2010 - Ch 21: Canonical
Correspondence
|
|
Week 9 - Spring Break
(March 21 - 25)
Week
10
- Comparing
Groups
Task
for this Week: Overview of Group Comparisons
Lecture
17: Tuesday
- March 29
James
& McCulloch (1990)
Review
of Multivariate Analyses
(Reference
Reading)
|
|
|
McCune
& Grace 2002 - Ch 23:
Comparing Groups
|
|
|
McCune
& Grace 2002 - Ch 24:
MRPP
|
|
|
Peck
2010 - Ch 26: MRPP
|
|
Lecture
18: Thursday
- March 31
|
Peck
2010 - Ch 27: PerMANOVA
|
|
|
Peck
2010 - Ch 28: sum f
|
|
|
McCune
& Grace 2002 - Ch 25:
Indicator Species
|
|
|
Peck
2010 - Ch 29: Indicator
Species
|
|
Week
11
- Examples
of Applied Analyses I
Task
for this Week: Applied Examples 1
Tuesday
- April 5 -
KDH at workshop
Students
work on Data Screening
Lecture
19: Thursday
- April 7 -Case
1: Ocean Climate
(Guest
Lecture - David Field)
|
Field
et al. 2006. CalCOFI Reports
|
|
|
Field
et al. 2006. Science
|
|
Week
12
- Examples
of Applied Analyses II
Task
for this Week: Applied Examples 2
Lecture
20: Tuesday
- April 12 -
Case
2: Morphometrics
|
Spear
& Ainley (1998)
|
|
|
Guicking
et al. (2004)
|
|
Thursday
- April 14
- Exam Review
|
Jeopardy
Questions + Answers
|
|
Week
13
- Start
Course Synthesis
Task
for this Week: Synthesis
1
Tuesday
- April 19
- EXAM
|
Answers to Knowledge Celebration
|
|
Thursday
- April 21
- Group Discussion
|
Individual
Project - Guidelines: Content and Format
|
|
Week
14
- Complete
Course Synthesis
Task
for this Week: Synthesis 2
Lecture
21: Tuesday
- April 26 -
Conclusions
|
Peck
2010 - Ch 17: Selecting
the Tools
|
|
James
& McCulloch (1990)
Review
of Multivariate Analyses
|
|
Clarke
et al. (2006)
Exploring
interactions by second-stage community analyses
|
|
Clarke
et al. (2008)
Testing of null hypotheses in exploratory community
analyses: similarity profiles and biota-environment
linkage
|
|
Thursday
- April 28
-
Analysis Exercise
|
Take
Home Practical Exercise - Guidelines
|
|
|
Take
Home Practical Exercise - Dataset
|
|
Week
15
- Student
Presentations
Task
for this Week: Synthesis 3
Tuesday
- May 3
- Presentations 1-6
(PPTs
posted by May 2, 9 pm)
|
Jessica
Lake (Reviewer: Tim Thomas)
|
|
|
Coulson
Lantz (Reviewer: Jessie Lopez)
|
|
|
Jessie
Lopez (Reviewer: Daniel Luck)
|
|
|
Daniel
Luck (Reviewer: Shannon Lyday)
|
|
|
Shanon
Lyday (Reviewer: Coulson Lantz)
|
|
|
Tim
Thomas (Reviewer: Jessica Lake)
|
|
Thursday
- May
5 - Presentations
7-12
(PPTs
posted by May 4, 9 pm)
|
Devon
Francke (Reviewer: Amelia
Murphy)
|
|
|
Emma
Kabua (Reviewer: Rachel
Knapstein)
|
|
|
Rachel
Knapstein (Reviewer: Emma
Kabua)
|
|
|
Amelia
Murphy (Reviewer: Devon
Francke)
|
|
|
Jaimie
Nevins (Reviewer: Lennon Thomas)
|
|
|
Lennon
Thomas (Jaimis Nevins)
|
|
|
