Thanks a lot ! At the end I found that the problem was in the data input. Once I normilized the data input to use the chord distance as measure of dissimilarity
gaps_flor_norm<-decostand(gaps_flor, "norm"), then I run the nMDS several times comparing them through procrustes plot(procrustes(gap_flor_NMDS1, gap_flor_NMDS2)) Can not say more, Thanks a lot for your response and all your work, Cheers, Rodrigo Vargas G. ----------------------------------------- Silviculture Institute Freiburg University +49 0761 203 8621 Tennenbacher str 4 Freiburg ibr 2011/9/28 Jari Oksanen [via R] <ml-node+s789695n3850347...@n4.nabble.com> > rodrock <rodrigo.vargasgaete <at> gmail.com> writes: > > > > I am using the envfit function over an ordination of floristic data. > > > > The problem is that every time that I run it changes the results. > Sometimes > > dramatically, selecting variables that the first time were not > significant. > > I do not get what could be the problem or if is normal given the > > permutations are different. > > > > # the NMDS ordination > > > > gap_flor_NMDS_chord <- metaMDS(gaps_flor, distance = "euclid", k = 2, > trymax > > = 20, autotransform =TRUE, > > noshare = 0.1, wascores = TRUE, expand = TRUE, trace = 1, > > plot = FALSE, old.wa = FALSE, zerodist = "add") > > > > > # the Envfit calculation > > exp_flor1 <- envfit(gap_flor_NMDS_chord, explain1, permu = 999, na.rm=T) > > > > > Rodrigo, > > Do you re-run your NMDS when the envfit results change? The results of NMDS > may > change between two runs. You should first check that the NMDS results are > nearly > identical. This you can do with procrustes() function in vegan: > > plot(procrustes(gap_flor_NMDS1, gap_flor_NMDS2)) > > where the arguments gap_flor_NMDS1 and gap_flor_NMDS2 are two NMDS results > that > gave you different envfit results. Use of plot() above helps you to avoid > looking at tiny differences in a numeric results: if you cannot see a > difference > in the procrustes plot, there is no difference you need to worry about. > Only > worry about envfit differences if the NMDS results are practically > identical. > > I'm surprised if metaMDS didn't issue any warning on the combination of > arguments you used in metaMDS: having no.share > 0 and distance = "euclid" > sounds dubious, and I have tried to catch those cases and issue an > informative > warning. You could also try higher trymax to get more consistent NMDS > results. > > Cheers, Jari Oksanen > > ______________________________________________ > [hidden email] <http://user/SendEmail.jtp?type=node&node=3850347&i=0>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. > > > ------------------------------ > If you reply to this email, your message will be added to the discussion > below: > > http://r.789695.n4.nabble.com/Envfit-inconsistant-result-tp3836585p3850347.html > To unsubscribe from Envfit, inconsistant result?, click > here<http://r.789695.n4.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_code&node=3836585&code=cm9kcmlnby52YXJnYXNnYWV0ZUBnbWFpbC5jb218MzgzNjU4NXw5MTY2NDczMDU=>. > > ----- Rodrigo Vargas G. ----------------------------------------- Silviculture Institute Freiburg University -- View this message in context: http://r.789695.n4.nabble.com/Envfit-inconsistant-result-tp3836585p3859115.html Sent from the R help mailing list archive at Nabble.com. [[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.
