Scott,

Thanks very much! That thread was especially helpful.

Katie

P Katie Songer
Water Resources Management Specialist
Wisconsin Department of Natural Resources
(*) phone:      (608)264-8947
(*) e-mail:     katherine.son...@wisconsin.gov



________________________________
From: Scott Chamberlain [mailto:scttchamberla...@gmail.com]
Sent: Tuesday, May 10, 2011 05:56 PM
To: Songer, Katherine B - DNR
Cc: r-help@r-project.org
Subject: Re: [R] metaMDS and envfit: Help reading output

Here is a thread I found on this 
issue:http://www.mail-archive.com/r-sig-ecology@r-project.org/msg00755.html   
It's not a simple correlation apparently, but I can't figure out how they get 
the output from envfit using lm(Y ~ scores1 + scores2).

You can plot the data like:
library(MASS); require(vegan)
data(varespec)
data(varechem)
ord <- metaMDS(varespec)
fit <- envfit(ord, varechem)
plot(ord)
plot(fit)
<http://www.mail-archive.com/r-sig-ecology@r-project.org/msg00755.html>

On Tuesday, May 10, 2011 at 3:51 PM, Songer, Katherine B - DNR 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)
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 understaand 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<mailto: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.

Reply via email to