Thank you Michael; this was helpful! Katie
-----Original Message----- From: Michael Denslow [mailto:michael.dens...@gmail.com] Sent: Wednesday, May 11, 2011 06:07 AM To: Songer, Katherine B - DNR Cc: r-help@r-project.org Subject: Re: [R] metaMDS and envfit: Help reading output Hi Katie, On Tue, May 10, 2011 at 4:51 PM, Songer, Katherine B - DNR <katherine.son...@wisconsin.gov> wrote: > Hello R experts, > > I've used metaMDS to run NMDS on some fish abundance data, and am also > working on correlating environmental data to the NMDS coordinates. I'm fairly > new to metaMDS and NMDS in general, so I have what are probably some very > basic questions. My fish abundance data consists of 66 sites for which up to > 20 species of fish were identified and counted. I ran metaMDS on this data in > 3 dimensions (after using a scree plot to check for stress levels in the > different dimensions). I then used envfit to correlate a predictor dataset of > environmental variables with the NMDS results, using the following code. > >>Fish<-as.data.frame(read.csv("Fish.csv",header=TRUE, sep = ",")) >>Fish.mds<-metaMDS(Fish,zerodist = "add",k=3,trymax=20) > >>Predictors<-as.data.frame(read.csv("Predictors.csv",header=TRUE, sep = >>",")) Fish.fit <- envfit(Fish.mds$points, Predictors, k=3, 1000, na.rm >>= TRUE) Have a look at the choices argument in envfit, etc. This is how you specify which axes you want to plot. ord <- metaMDS(varespec, k=3) fit <- envfit(ord, varechem, perm = 999, choices=c(1:3)) fit plot(ord, choices=c(1,3)) plot(fit, choices=c(1,3)) >>Fish.fit > > The output of Fish.fit was as follows (table truncated): > > Dim1 Dim2 r2 Pr(>r) > DrainArea -0.5923233 -0.8057004 0.7674 0.000999 *** > Flow -0.5283236 -0.8490431 0.7847 0.000999 *** > StrmWidth -0.6993457 -0.7147836 0.6759 0.000999 *** > Gradient 0.4541225 0.8909392 0.2085 0.010989 * > > I'd like to better understand how to read this table. I understand that Dim1 > and Dim2 refer to the dimensions of the vectors produced by envfit, and r2 is > the r-squared of those vectors. But how do I visualize these vectors in a 3-d > plot? To which of the 3 NMDS dimensions are these vectors being correlated? > Is there code to produce the x, y, and z coordinates of each of the sites in > Fish.mds? > > Thanks very much. > Katie > > > [[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. > -- Michael Denslow I.W. Carpenter Jr. Herbarium [BOON] Department of Biology Appalachian State University Boone, North Carolina U.S.A. -- AND -- Communications Manager Southeast Regional Network of Expertise and Collections sernec.org 36.214177, -81.681480 +/- 3103 meters ______________________________________________ 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.
