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I run a CCA analysis using vegan with 7500 sites, 9 species and 5 constrains variable. The results are >

Call: cca(sitspe = Yp, sitenv = Xp)

            Inertia Proportion Rank
Total                              
Constrained  0.5051               6
Inertia is mean squared contingency coefficient 

Eigenvalues for constrained axes:
[1] 0.3317 0.1301 0.0328 0.0089 0.0014 0.0003

I don't understand why there is no unconstrained or total inertia?

Linus Juhlin
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Victor Tor
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1 Answers1

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Probably your constrained axes explained everything, and no constrained inertia was left. How many axes did you get with unconstrained ordination (CCA without constraints)?

Your data are really non-square: matrix dimensions are 7500 times 9. There are only nine species, and if these are dependent or otherwise redundant, you may be able to explain everything with your constraints.

Jari Oksanen
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