I've got an ecological data set that I've worked up to the point of having
a relative abundance matrix I created with the decostand() command in Vegan.


Here is the distance matrix data:

S1<-c(0.4451517, 0.37919827,   0.10590466, 0.06974540)
S2<-c(0.5064846, 0.32464164,  0.09679181, 0.07208191)
S3<-c(0.4481876, 0.26556447, 0.10486995, 0.18137797)
S4<-c(0.5090950, 0.11474913, 0.17636805, 0.19978778)
S5<-c(0.5996147, 0.05875069,  0.24532196, 0.09631260)
S6<-c(0.7122068, 0.04365640, 0.14552133, 0.09861543)
S7<-c(0.6490743, 0.06382979,  0.14396242, 0.14313346)
S8<-c(0.5958636, 0.10774176,  0.16908888, 0.12730576)

DF<-rbind(S1,S2,S3,S4,S5,S6,S7,S8)


At first I was having issues with metaMDS producing two distinctly
different NMDS plots at seemingly random intervals as I re-ran my analysis
over multiple runs. I figured out it was because I was not using
set.seedfor my metaMDS call. But now I am concerned that the seemingly
small change
of setting set.seed() has such a large impact on my analysis.

As can be seen in the below oridplots, it looks to me like there is a
change in relative distances between some of the latter  'sites'.



set.seed(1)
mds10<- metaMDS(DF, dist='bray')

ordiplot(mds10,display='sites',type='text')


vs.

set.seed(999)
mds10<- metaMDS(DF, dist='bray')

ordiplot(mds10,display='sites',type='text')


The difference between the two plots is large enough that it would change
my interpretation of my analysis, so as this is my first foray into NMDS I
am a bit concerned. Can someone tell me if this is just part of how NMDS or
Vegan works (different local minimums)? Or does this imply a certain
ambiguity about my data set? Or am I completely misreading the plots.


If I add vector arrows for the 'species' influence like so:

envfit10<-envfit(mds10, DF,perm=999)
plot(mds10, display='sites',type='t')
plot(envfit10)


I can see that the two plots have different 'species' vectors, but it looks
like the relative distance between S5 and some of the other sites changes
between the two plots.

Is one ordiplot more 'correct' than the other? If not, what am I to make of
the difference between plots?

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