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? [[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.