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Feature request: Extend CAP to include Canonical Analysis of Principal Coordinates based on Discriminant Analysis #361
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I'm not sure if this is an appropriate place to ask this, but @jarioksa can you justify why capscale has been shelved and dbrda is the main method? Do they achieve the same thing? Does dbrda have advantages over CAP? |
@ecologyjh |
The biodiversityR maintainer Roeland Kindt suggested that he would like to see several biodiversityR functions be incorporated in vegan. I agree. However, I've been busy with other issues. I am ready to incorporate any biodiversityR functionality (with possible enhancements). If any of you can construct a pull request, I'll be happy to merge that in vegan. However, please communicate with Roeland Kindt before your pull requests (I will ask him anyway, and if he says "no", that'll be it). |
Currently vegan includes Canonical Analysis of Principal Coordinates (CAP) via the function capscale but this conforms more to distance-based Redundancy Analysis (Legendre & Anderson, 1999) than to the original description for CAP (Anderson & Willis, 2003), which is a distance-based form of discriminant function analysis. This latter approach is useful for a number of different user groups aiming to classify samples to groups.
There is a function (CAPdiscrim) in the BiodiversityR package which utilises vegan. However, this function is not fully developed as it does not allow the classification of unknown samples.
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