[R] distance matrix from metaMDS
clfiore at gmail.com
Fri Aug 29 16:45:50 CEST 2014
Yes I looked at this and I tried metaMDSdist but got an error and for some
reason I didn't try metaMDSredist which seems to be the right thing. So the
main thing I was confused about was what to call dist() on -i.e., getting
the correct ordinal distance, and then if I assume that the NMDS scores are
the coordinates, which I believe they are, then how do I call dist() on one
column? But, I just found the answer in a translation from matlab to R -
you have to use drop=FALSE (and hopefully I am calling dist() on the right
euc.dist.axis1=dist(NMDS2[,1, drop=FALSE], method="euclidean")
Maybe this is obvious to other folks but just in case there is anyone like
me out there I figured I'd write back. Thanks for the info I have never
written to this list before because I always found what I needed online. I
appreciate your help and patience.
On Thu, Aug 28, 2014 at 10:19 PM, David L Carlson <dcarlson at tamu.edu> wrote:
> 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,
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> PLEASE do read the posting guide
> and provide commented, minimal, self-contained, reproducible code.
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