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Biostatistics-II, Multivariate Methods

Ohio University

BIOS-870, Fall 2013

Schedule:  Weeks 1-7
Instructor: Brian C. McCarthy
Office:      207 Wilson Hall Admin.
Phone:      3-2979
Schedule:  Weeks 8-14
Instructor:  Donald B. Miles
Office:      131 Life Sciences Bldg.
Phone:      3-2317

Syllabus 2013 (McCarthy)

             Pre-class reading:  Zuur et al. (2010)

             Software: R home page

Lectures 1-3: Ecological resemblance, similarity & distance coefficients, ANOSIM   PDF

             Required reading: Wolda (1981), Faith et al. (1987), Koleff et al. (2003), Chao et al. (2006)

             Data sets: gower.csv, roach.csv veg.csv, pos.csv

             R scripts: Gower.r, S1.r anosim.r

             R documents: Package-Vegan, Help-Vegan

Lectures 4-6: Cluster Analysis and Data Visualization PDF

            Required reading:  James and McCulloch 1990.pdf

            Data sets: bryceveg.txt

            R scripts: SingleLink.R, Cluster.R, Star-Plots.R, KSmeans.R
            R documents: Package-labdsvPackage-cluster

            URLs (R): cluster analysis in R, R labs for vegetation ecology

            Assignment-1 (2012): Instructions, Data, Reprint

Self-Study: Matrix Algebra, eigenvalues & eigenvectors  PDF

Lecture 7: Introduction to Ordination, Principal Components Analysis (PCA)  PDF

          Required reading:  Peres-Neto et al. (2003)

          R scripts:  PCA.R

          URLs:  The Ordination Web PageQuick-R (PCA)
Lecture 8: Principal Coordinates Analysis (PCO), Nonmetric Multidimensional Scaling (NMDS) PDF

          Required reading: Gower (1966), Minchin (1987), Peres-Neto and Jackson (2001)

          R scripts: PCO.R, NMDS.R

          Assignment-2 (2012):  Instructions Reprint Data-1 Data-2 Data-3 Data-4

Lectures 9-10: Correspondence Analysis (CA & DCA) and Canonical Analysis (RDA, CCA, CCorA, DA) PDF

          Required reading:  Fasham (1977), ter Braak (1986), Palmer (1993), McCune (1997)

          R documents: Intro to Vegan, R-Reference Card        

          R scripts: RA.R, RDA.R

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