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 thing)
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. Cara On Thu, Aug 28, 2014 at 10:19 PM, David L Carlson <dcarl...@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-boun...@r-project.org [mailto:r-help-boun...@r-project.org] > On Behalf Of Cara Fiore > Sent: Thursday, August 28, 2014 7:02 PM > To: r-help@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]] > > ______________________________________________ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.