Don't the functions metaMDSdist() and metaMDSredist() that are documented on the metaMDS manual page give you the distance matrix? If you want to compute the distances based on a single axis, you could use vegdist().
David C
-----Original Message-----
From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org] On Behalf Of Cara Fiore
Sent: Thursday, August 28, 2014 7:02 PM
To: r-help at r-project.org
Subject: [R] distance matrix from metaMDS
Dear R users,
I would like to access the distance matrix generated by metaMDS as well as use the dist function to calculate the euclidean distance for each axis in the NMDS. I am having trouble finding a way to access these variables and any help is greatly appreciated.
For the distance matrix I know I could just calculate the bray-curtis distance but it would be nice to know how to get it from the NMDS function.
For the euclidean distance, the only thing I can find within metaMDS is the score function but there must be some way for me to call on/access the ordination distance for one axis right?
The reason for this is I would like to do something like the stressplot function but for each axis.
Thank you,
Cara
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