how to calculate "axis variance" in metaMDS, pakage vegan?
gian, you may try consecutive MDS-analyses with increasing number of dimensions (the parameter k in the isoMDS() or metaMDS() function). then plot stress against the number of dimensions and judge similar to a scree-plot in PCA. this should tell you how many dimensions to use for the MDS and as such also an appropriate associate stress-value. cheers, gabriel
Gian Maria Niccol? Benucci wrote:
Okey, really many thanks... So having low Stress value is foundamental, as it is as lower as higher the model fit the data, is that right? How can I know if my Stress is correct? I mean, if it is enough low to asses that the model fit good the samples data shifts into the graph... Is there a treshold or something? I would appreciate any pdf or kind of reviews on ordination models for community ecology data... :) Thank you really much! Cheers, Gian 2009/12/1 Gian Maria Niccol? Benucci <gian.benucci at gmail.com>
Hi Hi there,
I am trying to use funcion metaMDS (vegan pakage) for Community Ecology
data, but I find no way to calculate the "expressed variance" of the first 2
axis? is there a way to do that?
Thanks a lot in advance,
Gian
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Dr. Gabriel Singer Department of Freshwater Ecology - University of Vienna and Wassercluster Lunz Biologische Station GmbH +43-(0)664-1266747 gabriel.singer at univie.ac.at