[R] metaMDS and envfit: Help reading output

[Songer, Katherine B - DNR]

Thank you Michael; this was helpful!

Katie

-----Original Message-----
From: Michael Denslow [mailto:michael.denslow at gmail.com] 
Sent: Wednesday, May 11, 2011 06:07 AM
To: Songer, Katherine B - DNR
Cc: r-help at 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.Songer at 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
>
>
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>
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--
Michael Denslow

I.W. Carpenter Jr. Herbarium [BOON]
Department of Biology
Appalachian State University
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