Community Analysis

These are old slides for my lectures on multivariate methods in ecology. The slides were completely re-written for the autumn term 2017 and the slides here were used in spring 2017 and earlier.

Lecture themes:

These are all pdf files: Beware! The 2016 overheads are two slides per page, older ones are with four slides per page.

2016 Lectures

Old Lectures

While stuff here is old, it may still be useful if you want to go deep into ordination.

  1. Not lectured: Site description: Diversity, evenness etc., species abundance models.
  2. Not lectured: Gradient analysis: Basic concepts, weighted averages in bioindication, response models, beta diversity.
  3. Ordination: Basic methods. PCA, CA, MDS etc., problems and solutions.
  4. Ordination and environment: Interpreting ordination diagrams, Constrained ordination (CCA). The division of two ordination chapters is somewhat arbitrary, but ordination was growing too big, and I chopped it here.
  5. Evaluation and comparision of ordination methods: Explains how ordination is related to the gradient thinking, and how ordination methods should be evaluated for their ability to find gradients.
  6. Classification: Cluster analysis (one of the least satisfactory parts, but first I should study classification more deeply).
  7. Data Import to R: An appendix.
  8. Everything + notes (1.8MB): I made a first quick pass over all notes, and added some comments. These comments are pretty boring and usually tell how to do things in R. The slides are reduced to fit two to the page, with comments near to them.

Tutorial for computer Lab

The tutorials used in practicals:

  1. Unconstrained ordination: Base text, Text with results, The R commands of tutorials
  2. Constrained ordination: Base text, Text with results, The R commands of tutorials
  3. Classification: Base text, Text with results, The R commands of tutorials

A longer and deeper tutorial is available for those who are keenly interested in multivariate methods:

  • Google coordinate files of some data sets in R packages: Bryce Canyon (labdsv package), Barro Colorado Island (vegan).


    This is only a very small selection of software that I know personally.

    Other information

    The Web is a cornucopia of ordination texts. Here are some pages that I have found very useful:

    Jari Oksanen
    Last modified: Sat Sep 15 07:14:41 EEST 2012