Canonical Correspondence Analysis in R with Vegan library

Question

[Denis]

Hi there! I'm looking for a tutorial for performing Canonical Correspondence Analysis (CCA) and assesing its quality in R using Vegan library. Is there any useful materials to check? Exemple of CCA i found in Vegan documentation is not very detailed in my opinion.

Answer 1

[Jean-Karim Heriche]

Don't you have access to a web search engine? Just typing "R CCA tutorial" yields at least for me the following:

• vignette from the vegan package
• blog on the R functions site
• tutorial by one of the author of the vegan package

If these don't work for you, please be more specific about what your issues are.

[Denis]

Thanks for reply! I've checked all links you provided before posting the question of course. The 2-nd option from your list is suitable for me. But I confused, which commands related to CCA and which to Partial CCA?

[Jean-Karim Heriche]

Read the doc for the cca() function. Both CCA and partial CCA are done using this function. The difference is that for partial CCA you need a third matrix, i.e. as per the doc:

partial_cca <- cca(X, Y, Z)

or with a formula:

partial_cca <- cca(X ~ Y + Condition(Z))