This book is a work in progress.  It began as notes for students in SEFS 502, Analytical Techniques in Community Ecology, at the University of Washington.  These notes provide a background in multivariate analysis of a wide range of data.  My emphasis is on the practical application of these techniques.

Many students have used this course, and their associated project, as part of their thesis or dissertation.  A number of students have also published their work in the peer-reviewed literature.

Most of the functions used here are provided within R packages as indicated at the start of each chapter.  Other data files, scripts, and functions are available through a GitHub repository associated with this book (

The book is organized in five parts:

  • Foundational Concepts – an introduction to R, data adjustments, matrix algebra, and distance measures
  • Group Comparisons – ways to test for differences between pre-defined groups
  • Classification – ways to explore the data and group similar observations together
  • Ordinations (Data Visualization) – ways to reduce the dimensionality of multivariate data and/or to visualize patterns within it
  • Follow-Up Tests – tests to identify how individual response variables relate to one or more explanatory variables




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Applied Multivariate Statistics in R Copyright © 2024 by Jonathan D. Bakker is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License, except where otherwise noted.

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