R help - Aug 2014 - 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

	[[alternative HTML version deleted]]

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

	[[alternative HTML version deleted]]

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