Lecture 11: Canonical variates analysis - Bio723-class/Bio723-lecture GitHub Wiki

Learning goals checklist for this class session

• Understand the concept of Canonical Variates Analysis (CVA)
• Understand how CVA differs from PCA and when each method is preferred
• Learn how to carry out CVA in R

Slides

• Canonical Variates Analysis

In class activities

• Bio 723 Course Notes: Canonical Variates Analysis

• CVA as two step PCA in R -- there is an error in a couple of the figures in the Macleod article linked below. This R notebook shows how to carry out CVA as a two-step PCA and shows the corrected figures.

Assignment

Assignment Submission: Be sure to submit your assignment via Sakai, as an R Markdown file and the knit HTML document produced by your markdown file.

• Assignment 10, due 15 April 2020 by beginning of class.

  -- You can download a template R Markdown document for assignment at: homework-template.Rmd

Readings

• Macleod, N. Paleomath 101, Groups II. Paleontological Association Newsletter, Issue 64. MacLeod Groups II

  • Also see many other essays from MacLeod on multivariate techniques in the PalaeoMath Series of the Palaeontological Association newsletter.

• N. A. Campbell and William R. Atchley. 1981. The Geometry of Canonical Variate Analysis. Systematic Zoology, 30(3): 268-280. http://www.jstor.org/stable/2413249