MARS 6300

Web-Page

 
Last Updated April 27, 2018

Please report any problems here:

khyrenbach (at) hpu (dot) edu
 
Homework

Hw1- Partials

Data1.1 - stocks

Data1.2 - upwell

(due February 8)

Key 1

DataKey 1

DataKey 2

 

Hw2 - Clustering

Data2.1 (mosses)

Data2.2 (desserts-colors)

(due February 22)

Key 2

 

Hw3 - PCA

Data3.1 (relativizations)

Data3.2 (upwell_PCA)

(due March 1)

Key 3

 

Hw4 - NMDS

Data4.1 (IndianOceanSeabirds)

(due March 8)

Key 4

 

Hw5 - PO & WA

Data5.1 - Biogeo Data

Data5.2 - Biogeo Env

Data5.3 - Biogeo Samples

Data5.4 - Biogeo Weights

Dufrene_&_Legendre_1997

McGeoch_&_Chown_1998

(due March 22)

Key 5

 

Hw6 - MRPP & ISA

Data6.1 - Samples

Data6.2 - Groups

Anderson 2001

(due April 5)

Key 6

 
Project

(due March 13)

(due April 12)

Presentation

(due April 23)

(due May 1)

(due May 6)
Take Home

Instructions

Dataset

(due April 19)
Peer Review

Instructions

(due May 6)
     
 
Instructor
  

Dr. David Hyrenbach


CTSA #1

Oceanic Institute

Office Hours:

M; 11:00 - 13:00 (HLC, 2nd floor lanai)

T; 11:00 - 13:00 (HLC, 2nd floor lanai)

or by appointment at CTSA #1, OI
 

 

Reference Texts

 

We will read several chapters from these texts:

 

 

 

McCune, B. & Grace, J.B. (2002)

Analysis of Ecological Communities. MjM Software, Gleneden Beach, Oregon, USA

Available on reserve and for purchase online

 

 

Peck, J.E. (2010)

Multivariate Analysis for Community Ecologists, MjM Software, Gleneden Beach, Oregon, USA

Available on reserve and for purchase online

 

 

Course Readings and Lectures

 

 

These PDFs of scientific articles are for class use only.

Please do not distribute.

 
Note: Readings in italics are supplementary material

Date
Lecture Topic
Readings
Assignments
1 / 16

James & McCulloch (1990)

McCune & Grace (2002) - Ch 3: Sampling Communities

1 / 18
1 / 23

 

Schwing et al. (2002)

McCune & Grace (2002) - Ch 7: Data Screening

McCune & Grace (2002) - Ch 8: Documenting Analysis Flow

Hw1 (Due 02/08)
1 / 25

McCune & Grace (2002) - Ch 9: Data Transformations

Clarke & Warwick (2001) - Ch 9: Data Transformations

 

1 / 30

 

 

McCune & Grace (2002) - Ch 6: Distance Measures

Clarke & Warwick (2001) - Ch 2: Similarity Measures

 

2 / 1

McCune & Grace ( 2002) - Ch 5: Species Distributions

McCune & Grace (2002) - Ch 10: Finding Groups

McCune & Grace (2002) - Ch 12: Two-Way Indicator Species

 

2 / 6

McCune & Grace (2002) - Ch 11: Hierarchical Clustering

Clarke & Warwick (2001) - Ch 3: Hierarchical Clustering

Peck (2010) - Ch 25: Clustering

He et al. (1997)

Wolter (1987)

Diehr et al. (1982)

Hw2 (Due 02/22)

2 / 8

McCune & Grace 2002 - Ch 13: Ordination

McCune & Grace 2002 - Ch 14: PCA

Clarke & Warwick 2001 - Ch 4: PCA

Peck 2010 - Ch 23: PCA

 

2 / 13

PCA

Hw3 (Due 03/01)

2 / 15

Peck 2010 - Ch 13: Distance Measures

Peck 2010 - Ch 15: Weighting Variables

Ainley & Hyrenbach (2010)

Lopez et al. (2012)

 
2 / 20

McCune & Grace 2002 - Ch 16: NMDS

Clarke & Warwick 2001 - Ch 5: NMDS

Peck 2010 - Ch 24: NMDS

Hyrenbach et al. (2007)

Hebshi et al. (2008)

 

2 / 22

Hw4 (Due 03/08)
2 / 27

McCune & Grace 2002 - Ch 17: Polar Ordination

Peck 2010 - Ch 20: Polar Ordination

Bray & Curtis (1957)

Beals (1984)

 
3 / 1
Homework Review

 

 
3 / 6
NO CLASS
Spring Break
3 / 8
NO CLASS
Spring Break
3 / 13

McCune & Grace 2002 - Ch 18: Weighted Averaging

Peck 2010 - Ch 19: Weighted Averaging

Curtis & McIntosh (1951)

Borja et al. (2000)

 
3 / 15

McCune & Grace 2002 - Ch 19: Correspondence Analysis

McCune & Grace 2002 - Ch 20: Detrended Correspondence

McCune & Grace 2002 - Ch 21: Canonical Correspondence

Peck 2010 - Ch 21: Canonical Correspondence

Kenkel & Orloci (1986)

Hw5 (Due 03/22)

3 / 20

McCune & Grace 2002 - Ch 22: Ordination Reliability

Orloci & Pillar (1989)

Pillar (1999)

 
3 / 22

McCune & Grace 2002 - Ch 23: Comparing Groups

McCune & Grace 2002 - Ch 24: MRPP

Peck 2010 - Ch 26: MRPP

McCune & Grace 2002 - Ch 25: Indicator Species

Peck 2010 - Ch 29: Indicator Species

Hw6 (Due 04/05)
3 / 27

Peck 2010 - Ch 27: PerMANOVA

Peck 2010 - Ch 28: Sum f

Biondini et al. (1985)

Zimmerman et al. (1985)

 
3 / 29

Exam Review

4 / 3

In Class EXAM

4 / 5
4 / 10

McCune & Grace 2002 - Ch: Mantel Test

Peck 2010 - Ch: Mantel Test

Mantel (1967)

Dizon et al. (1994)

Rodrigues et al. (2002)

Borcard & Legendre (2012)
4 / 12
4 / 17

Peck 2010 - Ch 17:
Selecting the Tools

James & McCulloch (1990)

Clarke (1993)

4 / 19
NO CLASS

Take Home Exam

Due

(by email)
4 / 24

8 Project Presentations

(15 minutes per student)

9:00 - 11:00

Talk Sequence - Day 1

Filardo
Teague
Miyamoto
Golder
Fraser
Brown
Fossett
Weller

Project Write-up & Logbook Due

May 1

(by email)
4 / 26

10 Project Presentations

(15 minutes per student)

9:00 - 11:30

Talk Sequence - Day 2

Cabrera
Doughten
Bingo
Preble
Boyd
Kabraji
Duritsch
Johnson
Nimz
Lin

Project Write-up & Logbook Due

May 1

(by email)
4 / 27

Peer Review

Assignments

(Review the presentation posted next to your name)
Reviewer
File
Filardo
Weller
Teague
Fossett
Golder
Nimz
Preble
Lin
Cabrera
Fraser
Johnson

Kabraji
Duritsch
Doughten

Bingo
Miyamoto
Boyd

Project Peer Review & Re-analysis Due

May 6

(by email)

 

 

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