Hello,

Please forgive my ignorance if this is really basic.

I am Using NMDS and envfit in the package vegan to determine the
environmental variables contributing to the differences between two
distinct groups of sites and to determine if the two groups of sites are in
fact distinct.

Envfit provides r2 values that, if I understand it correctly, quantify the
degree to which the environmental variables influence the distribution of
the sites (points) in the ordination space. They don't however reflect the
degree to which the variables affect the separation of the distinct site
groups.  An environmental variable may have a high r2 value but be
perpendicular to the axis of greatest group separation.

Is my understanding of the r2 values provided by envfit correct? Is there a
way to quantify the contribution of environmental variables to site group
separation in NMDS? Or should I separately use something like randomForest?


Thank you for your help.

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