Dear Jari, Thank you very very much for your exhaustive explanation, now everything is more clear. Have a great day,
Gian On 21 February 2012 07:06, Jari Oksanen <jari.oksa...@oulu.fi> wrote: > > On 20/02/2012, at 22:01 PM, Gavin Simpson wrote: > > > On Mon, 2012-02-20 at 14:30 -0500, Sarah Goslee wrote: > >> References are given in the help for nmds. In particular, nmds() uses > >> Kruskal's formulation. > > > > And you can read the code. Look at nmds, at the top of the function body > > is an inline function sstress() which does the relevant computation, > > IIUC. > > > Unfortunately reading the code is not always quite easy in R, but you have > to decipher the logic of the whole function instead of single easy pieces. > The inline function sstress() gives the formula, but you have to read > further down to see what are the actual variables used in sstress(). If you > do so, you see that the ecodist::nmds stress is defined as: > > sum((dmat - dist)^2)/sum(dmat^2) > > where 'dmat' are the input dissimilarities and 'dist' are the distances > among points in the ordination configuration. > > This is *not* Kruskal's stress, at least not like he defined it in his > 1964 papers in Psychometrika. In vegan::monoMDS and in MASS::isoMDS Kruskal > stress (stress=1 in vegan::monoMDS) we define squared stress as: > > sum((dist-dhat)^2)/sum(dist^2) > > where 'dhat' are the fitted distances from the monotone regression, and > 'dist' the distances among points in ordination configuration (like above). > So the stresses do differ, and that is sufficient to explain the > differences. > > Cheers, Jari Oksanen > > > > >> Sarah > >> On Feb 20, 2012 1:48 PM, "Gian Maria Niccol Benucci" < > >> gian.benu...@gmail.com> wrote: > >> > >>> Dear Gavin and Sarah, > >>> > >>> I've found how metaMDS() calculate the stress [using monoMDS() of > vegan], > >>> but I do not find how nmds() of ecodist do it so. Could you please > link me > >>> the page or where I can find it, maybe it escapes me... > >>> Thank you very much for your aid, > >>> > >>> Gian > >>> > >>> > >>> 2012/2/20 Gavin Simpson <gavin.simp...@ucl.ac.uk> > >>> > >>>> On Mon, 2012-02-20 at 17:24 +0100, Gian Maria Niccol Benucci wrote: > >>>>> Dear Gavin, > >>>>> > >>>>> Thank you very much. I tried with your advice but the result is > almost > >>>>> unchanged... > >>>> > >>>>> Any further advice?? > >>>> > >>>> Yeah, what Sarah said. Read the documentation; the two functions use > >>>> different definitions of stress. > >>>> > >>>> You could always do a procrustes rotation on the two configurations to > >>>> see how well they compare. > >>>> > >>>> G > >>>> > >>>>> Gian > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> 2012/2/20 Gavin Simpson <gavin.simp...@ucl.ac.uk> > >>>>> > >>>>>> On Mon, 2012-02-20 at 16:28 +0100, Gian Maria Niccol Benucci wrote: > >>>>>>> Hi r-sig-ecology Members, > >>>>>>> > >>>>>>> I would please you to examine the differences I found in metaMDS() > >>>> and > >>>>>>> nmds() outputs and possibly draw some conclusions. As I wrote in > >>> past > >>>>>>> emails I have 24 samples of ectomycorrhizal fungi grouped into two > >>>>>>> different communities (12 natural and 12 cultivated). > >>>>>>> > >>>>>>> here is the code: > >>>>>>> > >>>>>>>> metaMDS(data_matrix2, distance="bray", k=2, autotransform=F) -> > >>>> metaMDS > >>>>>>>> metaMDS > >>>>>>> > >>>>>>> Call: > >>>>>>> metaMDS(comm = data_matrix2, distance = "bray", k = 2, > >>> autotransform > >>>> = F) > >>>>>>> > >>>>>>> global Multidimensional Scaling using monoMDS > >>>>>>> > >>>>>>> Data: data_matrix2 > >>>>>>> Distance: bray > >>>>>>> > >>>>>>> Dimensions: 2 > >>>>>>> *Stress: 0.04536661 * > >>>>>>> Stress type 1, weak ties > >>>>>>> No convergent solutions - best solution after 20 tries > >>>>>> > >>>>>> Perhaps you could try running metaMDS with random starts until it > >>> does > >>>>>> find convergent solutions?! Why expect metaMDS() to do better in 20 > >>>>>> tries than nmds() with 100 random tries? > >>>>>> > >>>>>> add `trymax = 100` and `halfchange = FALSE` to try to make the two > >>>>>> functions more comparable. > >>>>>> > >>>>>> HTH > >>>>>> > >>>>>> G > >>>>>> > >>>>>>> Scaling: centring, PC rotation, halfchange scaling > >>>>>>> Species: expanded scores based on data_matrix2 > >>>>>>> > >>>>>>>> nmds <- nmds(dist_bray, mindim = 2, maxdim = 2, nits = 100) > >>>>>>> Using random start configuration > >>>>>>> Using random start configuration > >>>>>>> ... > >>>>>>>> nmds_min > >>>>>>> X1 X2 > >>>>>>> 1 -0.66226262 0.16392824 > >>>>>>> 2 -0.68844987 -0.20891993 > >>>>>>> 3 -0.47717515 0.55323693 > >>>>>>> 4 -0.67213392 -0.09195847 > >>>>>>> 5 0.03305172 0.41844232 > >>>>>>> 6 0.31992006 0.53887910 > >>>>>>> 7 -0.61944875 0.34411146 > >>>>>>> 8 0.07013849 0.65723057 > >>>>>>> 9 0.53053436 0.37444633 > >>>>>>> 10 0.26704705 0.39849341 > >>>>>>> 11 -0.20981416 0.70391983 > >>>>>>> 12 -0.61620355 -0.43568743 > >>>>>>> 13 0.14219660 -0.69571194 > >>>>>>> 14 0.42365981 -0.43308767 > >>>>>>> 15 0.15840330 -0.12872863 > >>>>>>> 16 -0.00492407 -0.06889680 > >>>>>>> 17 -0.20513513 -0.58052156 > >>>>>>> 18 0.46546214 0.12019775 > >>>>>>> 19 0.36753709 -0.25048256 > >>>>>>> 20 -0.09446486 -0.61943616 > >>>>>>> 21 0.15010553 -0.31995009 > >>>>>>> 22 0.41540872 -0.29507200 > >>>>>>> 23 0.42573367 -0.12321584 > >>>>>>> 24 0.48081354 -0.02121688 > >>>>>>>> min(nmds$stress) > >>>>>>> [*1] 0.2787161* > >>>>>>>> nmds$r2[which.min(nmds$stress)] > >>>>>>> [1] 0.6338372 > >>>>>>> > >>>>>>> Is it possible I got so different stress values?? > >>>>>>> > >>>>>>> Thanks for replying, > >>>>>>> > >>>>>>> _______________________________________________ > >>>>>>> R-sig-ecology mailing list > >>>>>>> R-sig-ecology@r-project.org > >>>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology > >>>>>> > >>>>>> -- > >>>>>> > %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% > >>>>>> Dr. Gavin Simpson [t] +44 (0)20 7679 0522 > >>>>>> ECRC, UCL Geography, [f] +44 (0)20 7679 0565 > >>>>>> Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk > >>>>>> Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ > >>>>>> UK. WC1E 6BT. [w] http://www.freshwaters.org.uk > >>>>>> > %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% > >>>>>> > >>>>>> > >>>>>> > >>>>> > >>>>> > >>>>> > >>>>> *----- Do not print this email unless you really need to. Save paper > >>> and > >>>>> protect the environment! -----* > >>>>> > >>>>> [[alternative HTML version deleted]] > >>>>> > >>>>> _______________________________________________ > >>>>> R-sig-ecology mailing list > >>>>> R-sig-ecology@r-project.org > >>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology > >>>> > >>>> -- > >>>> %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% > >>>> Dr. Gavin Simpson [t] +44 (0)20 7679 0522 > >>>> ECRC, UCL Geography, [f] +44 (0)20 7679 0565 > >>>> Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk > >>>> Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ > >>>> UK. WC1E 6BT. [w] http://www.freshwaters.org.uk > >>>> %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% > >>>> > >>>> > >>>> > >>> > >>> [[alternative HTML version deleted]] > >>> > >>> > >>> _______________________________________________ > >>> R-sig-ecology mailing list > >>> R-sig-ecology@r-project.org > >>> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology > >>> > >>> > >> > >> [[alternative HTML version deleted]] > >> > >> _______________________________________________ > >> R-sig-ecology mailing list > >> R-sig-ecology@r-project.org > >> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology > > > > -- > > %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% > > Dr. Gavin Simpson [t] +44 (0)20 7679 0522 > > ECRC, UCL Geography, [f] +44 (0)20 7679 0565 > > Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk > > Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ > > UK. WC1E 6BT. [w] http://www.freshwaters.org.uk > > %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% > > > > _______________________________________________ > > R-sig-ecology mailing list > > R-sig-ecology@r-project.org > > https://stat.ethz.ch/mailman/listinfo/r-sig-ecology > > -- > Jari Oksanen, Dept Biology, Univ Oulu, 90014 Finland > jari.oksa...@oulu.fi, Ph. +358 400 408593, http://cc.oulu.fi/~jarioksa > > _______________________________________________ > R-sig-ecology mailing list > R-sig-ecology@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-ecology > [[alternative HTML version deleted]] _______________________________________________ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
