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Ordination

Workshop         Friday, December  3, 2010.  14h-16h
Help Session    Friday, December 10, 2010.  14h-16h

We will introduce the major concepts behind ordination and practice analysing an example dataset with common methods, including PCA (Principal Component Analysis), PCoA (Principal Coordinate Analysis), and nMDS (non-metric Multi-Dimensional Scaling), using the 'vegan' package in R.  Participants will learn common transformations and metrics of similarity used in these analysis, and permutation-based hypothesis testing of whether groups defined a priori show expected patterns of similarity: Analysis of Similarity (ANOSIM).  
We expect participants will learn how to:
  • prepare data for ordination analysis
  • understand and justify major decision points throughout the analysis
    • transformation, similarity metric, ordination method
  • prepare and interpret ordination output (graphs, metrics)
Time permitting, we will quickly demonstrate other possible analyses, but the scope of this workshop will only include Unconstrained Ordination, for data sets that include samples (e.g. sites) and response variables (e.g. morphometric data, species abundances, etc.).  We will explain the use of Constrained Ordination for data sets with both response and explanatory variables, but we will not have time in this workshop to cover them in detail (maybe next semester ...).
 
We expect participants to be familiar with:
  • Basic R commands
  • How to import data in to R
  • basic plotting commands in R
Get the slides here.
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Ordinationtemplate.R
(4k)
Jonathan Whiteley,
Dec 2, 2010, 8:37 PM
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R-Ordination.R
(20k)
Jonathan Whiteley,
Dec 3, 2010, 6:24 PM
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WorldMapDistances.txt
(1k)
Jonathan Whiteley,
Dec 2, 2010, 8:33 PM
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