On Wed, 2011-05-11 at 07:07 -0400, Michael Denslow wrote:
> 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))
Indeed, this is an essential step because we probably shouldn't
interpret the "axes" of nMDS as separate components a la PCA/CA...
> fit
> plot(ord, choices=c(1,3))
> plot(fit, choices=c(1,3))
...as such, a 3-d plot might be better (for some definition of
"better"). See ?ordirgl
G
> >>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]]
> >
> > ______________________________________________
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> > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
> >
>
>
>
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Dr. Gavin Simpson [t] +44 (0)20 7679 0522
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