Re: [R-sig-eco] NMDS with metaMDS from vegan following an example from Numerical Ecology with R

[Manuel Spínola]

Thank you very much Jari,

Using weakties = FALSE it works very well.  The results are similar to the
book.

Best,

Manuel

> e.mds = metaMDS(especies, distance = "bray", weakties = FALSE)
Run 0 stress 0.1088505
Run 1 stress 0.113103
Run 2 stress 0.1356066
Run 3 stress 0.1088552
... procrustes: rmse 0.1304834  max resid 0.4025236
Run 4 stress 0.1403525
Run 5 stress 0.3915359
Run 6 stress 0.1305611
Run 7 stress 0.1417557
Run 8 stress 0.1088584
... procrustes: rmse 0.001626811  max resid 0.007608109
*** Solution reached

Mensajes de aviso perdidos
In distfun(comm, method = distance, ...) :
  you have empty rows: their dissimilarities may be meaningless in method
“bray”

2012/6/12 Jari Oksanen <jari.oksa...@oulu.fi>

>
> On 13/06/2012, at 07:33 AM, Manuel Spínola wrote:
>
> > Dear list members,
> >
> > I am working on an NMDS using metaMDS from vegan with the Doubs fish data
> > from the book Numerical ecology with R.
> >
> >> especies <- read.csv("DoubsSpe.csv", row.names = 1)
> >> e.mds = metaMDS(especies, distance = "bray")
> > Run 0 stress 0.003706943
> > Run 1 stress 0.0004788424
> > ... New best solution
> > ... procrustes: rmse 0.009197047  max resid 0.01874812
> > Run 2 stress 0.0004600702
> > ... New best solution
> > ... procrustes: rmse 0.0002883791  max resid 0.0005590752
> > *** Solution reached
> >
> > Mensajes de aviso perdidos
> > In distfun(comm, method = distance, ...) :
> >  you have empty rows: their dissimilarities may be meaningless in method
> > „bray‰
> >>
> >
> > My results are "strange" (stress is too low and different to the one on
> the
> > book) and the plot is very different to the one that appears in the book.
> >
> Manuel,
>
> I'm too lazy to go to have a look at the book now (I'm sitting in my
> balcony sipping my morning coffee), but I assume that the difference is
> that metaMDS in your book was still based on MASS::isoMDS(), but the
> current vegan (from 2.0-0) uses its own monoMDS() function as a default.
> One difference is that isoMDS() expresses the stress per cent, and
> monoMDS() as parts of one, so that equal isoMDS() is 100x higher. Another
> difference is that monoMDS() implements treatment of tied dissimilarity
> values, and defaults to "weak" ties so that equal observed dissimilarities
> can be allowed to be at different ordination distances. If I remember
> correctly, these Doubs fish data are very simple so that monoMDS() really
> may be able to have nearly zero stress (which is suspect in general).
>
> For better correspondence to the book, you may first try setting 'weakties
> = FALSE' which will force tie treatment that is closer to isoMDS(), but
> still not identical. For true replication of the book results you should
> set 'engine = "isoMDS"'.
>
> As usual, these are documented features.
>
> Cheers, Jari Oksanen
> --
> Jari Oksanen, Dept Biology, Univ Oulu, 90014 Finland
> jari.oksa...@oulu.fi, Ph. +358 400 408593, http://cc.oulu.fi/~jarioksa
>
>
>
>


-- 
*Manuel Spínola, Ph.D.*
Instituto Internacional en Conservación y Manejo de Vida Silvestre
Universidad Nacional
Apartado 1350-3000
Heredia
COSTA RICA
mspin...@una.ac.cr
mspinol...@gmail.com
Teléfono: (506) 2277-3598
Fax: (506) 2237-7036
Personal website: Lobito de río <https://sites.google.com/site/lobitoderio/>
Institutional website: ICOMVIS <http://www.icomvis.una.ac.cr/>

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