Hi Jari,
Thanks so much for the answer. I can see now I have confused the relationship between the vectors plotted from envfit and the ordination plot. I thought the length of the blue vector arrows was an indication of the influence a species had on the nMDS plot. So I assumed the fact that all 4 species had similar vector lengths, all 4 species had a similar impact on the plot. After reviewing your answer, I can see the above assumption is flawed. But if the magnitude of a species vector (blue arrow) does not equate to a species's importance, can you explain what kind of info I can take away from this kind of vector plot? Thanks again for your help, it is greatly appreciated. > From: [email protected] > To: [email protected] > CC: [email protected] > Subject: Re: [R-sig-eco] How does abundance effect output of vegan metaMDS > Date: Wed, 19 Feb 2014 07:01:52 +0000 > > Dear Vindoggy, > > I wondered how do you *know* that species three is influential. Your analysis > shows that it is linearly well explained by the ordination, but it does *not* > show that the species influences the ordination. > > We can study the influence of a species by seeing how much the result will > change if we remove the species: removal of an influential species will > change the result much. We can assess the change in ordination using the > residual sum of squares of Procrustes ordination where we compare results of > full data to results when we remove one species. The following continues from > your analysis where you had the ordination result 'mds': > > impo <- numeric(4) > for(i in 1:4) impo[i] <- procrustes(mds, metaMDS(DF[,-i]))$ss > > This gives us importance values: > > impo > # [1] 0.13510647 0.05256924 0.00666738 0.03128587 > > Third value is lowest. This means that removing of species 3 hardly > influences the results, and the species is not influential. By far the most > important species is number 1. > > Cheers, Jari Oksanen > > On 19/02/2014, at 06:10 AM, Vindoggy ! wrote: > > > > > > > I have a data set for benthic cover made up of 4 species, over 9 years. I > > have been using the vegan package to create nMDS plots for this data, but > > am a little confused by some of my results. > > > > > > Here is the data for 4 species (Sp 1-4) over the course of 9 years > > > > > > Sp1<-c(27.76 ,25.44, 34.72, 41.28, 44.00, 31.28, 32.00, 38.72, 40.40) > > Sp2<-c(36.72, 40.08, 36.96, 26.40, 34.40, 33.28, 31.28, 22.72, 14.00) > > Sp3<-c(0.16, 0.08, 0.32, 1.28, 1.76, 1.84, 2.24, 4.40, 1.76) > > Sp4<-c( 1.12, 2.24, 4.00 , 2.56, 4.40, 8.96, 12.24, 13.60, 23.36) > > > > DF<-data.frame(Sp1,Sp2,Sp3,Sp4) > > > > row.names(DF)<-c(2006:2014) > > > > > > > > At first I was advised to transform my data to relative abundance like so: > > > > > > > > DF<- decostand(DF, method='total') > > > > > > > > set.seed(999) > > mds<- metaMDS(DF, dist='bray',trymax=99) > > > > envfitHab<-envfit(mds, DF,perm=999) > > > > plot(mds,display='sites',type='t') > > > > plot(envfitHab) > > > > envfitHab > > > > > > > > > > > > > > > > > > > > But I found that Species 3 seemed to be having a greater impact on the plot > > (as I judged by looking at the blue vectors, p values, and scores data) > > than I would have gathered. Considering Sp3 has a relatively low abundance > > and does not change much over time, I would not expect it to influence the > > dissimilarity matrix much at all. And Sp1, which has a higher abundance and > > changes significantly over time, seems to have a much smaller impact and > > larger p value. > > > > I came to the conclusion that I should not be using relative abundance > > data, as I do care about total abundance. So I gave up on decostand and > > used raw abundance data instead. I was surprised to find that Sp3 played a > > similar if even larger role in impacting the plot. Which runs > > counterintuitive to my (admittedly limited) understanding of nMDS. > > > > So my question is why is a species with low abundance that does not vary > > much from year to year impacting my nMDS plot so much? > > > > > > > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > R-sig-ecology mailing list > > [email protected] > > https://stat.ethz.ch/mailman/listinfo/r-sig-ecology > [[alternative HTML version deleted]] _______________________________________________ R-sig-ecology mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
