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 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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