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I would like to know if there is a way to extract something similar to the metaMDS "stress" value from a vegan cca object? I've tried the goodness.cca function and its relatives

(http://cc.oulu.fi/~jarioksa/softhelp/vegan/html/goodness.cca.html)

They tell me about the stats per sample, but I'm interested in the overall goodness of fit for reducing a multidimensional system to two dimensions (if something like that exists, as it uses different calculations). I would like to continue with vegan, if possible, though I found this link here:

(Goodness of fit in CCA in R)

Thanks a alot

RJ

crazysantaclaus
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  • I am confused as well when using `isomap`. Somehow I found out the attribute `GOF` is short for goodness of fit, though it has two values and I don't know how to use both. – GZ92 Apr 17 '18 at 22:04

1 Answers1

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It is called eigenvalue. Earlier people have complained that NMDS does not have something like eigenvalue, but only has stress. The total variation in the data is the sum of all eigenvalues so that proportion of the eigenvalue or the cumulative sum of eigenvalues from the total is proportion explained. All these can be extracted with eigenvals() and its summary() (see their help with ?eigenvals). The significance tests for axes are available with its anova.cca() function (look at its documentation for references).

The web page you referred to is about another method, canonical correlations. In vegan we have that in CCorA with permutation test. Just pick your method, and then find your tools.

Jari Oksanen
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  • Hey @Jari Oksanen, thanks for the explanation. With limited mathematical skills it was hard to understand what the Eigenvalues stands for (stress was better imaginable for me), but I think I got it now. So eventually I have all information together to show people my CCA is actually reliable ;-) – crazysantaclaus Feb 12 '18 at 16:17