[R-sig-eco] envfit function: is it possible to display correlation coefficient?

[Botta-Dukát Zoltán]

Dear Irene,

NMDS does not calculate coordinates along each axis separately (as do 
metric ordinations, e.g. cmdscale function), but it optimize the whole 
2-dimensional configuration of points. Any rotation does not change the 
configuration, but it changes coordinates along both axes. So 
coordinates along axes should not be interpreted, and correlation with 
first NMDS axis has no meaning.

Best regards,

Zoltan



2018. 05. 01. 15:50 keltezéssel, Irene Adamo írta:
>   Dear all,
> I have already looked at similar questions about this topic but I still
> have few doubts.
> when I run:
> data(varespec, varechem)
> library(MASS)
> ord <- metaMDS(varespec)
> (fit <- envfit(ord, varechem, perm = 999))
>
> I get this output:
> ***VECTORS
>
>              NMDS1    NMDS2     r2 Pr(>r)
> N        -0.05738 -0.99835 0.2536  0.041 *
> P         0.61980  0.78476 0.1938  0.105
> K         0.76650  0.64225 0.1810  0.098 .
> Ca        0.68524  0.72832 0.4119  0.001 ***
>
> are the numbers under NMDS1-2  the direction of the arrow or they show
> to which axis is the variable correlated? if I look at N can I conclude
> that N is negatively correlated to NMDS2, while K is positively correlated
> to NMDS1? is it possible to get the correlation coefficient of a variable
> with the axes? here we have r2 but I don’t understand if it refers to both
> of the axis or just one.
>
> thanks a lot for any help!
>
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>
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