[R-sig-eco] question concerning nmds.min

[Ivailo]

2012/2/2 Gian Maria Niccolò Benucci <gian.benucci at gmail.com>:
> Hi all,
>
> I am trying to run a nmds with function nmds()
> Once I run the following code I wonder how to look to the R2 and stress
> value of the chosen configuration.
>
> iris.nmds <- nmds(iris.md, mindim=2, maxdim=2, nits=50)
>
> iris.nmin <- nmds.min(iris.nmds)
>
>
> Which among the 50 configuration the functions chose?
> How to look to its stress and R2 values?
>
>
> If I type iris.nmin I only got the X1 and X2 coordinates...
>
>
> Thanks in advance,
>
> Gian

Dear GIan,

try the following:

library(vegan)
data(dune)
sol <- metaMDS(dune)
sol

Call:
metaMDS(comm = dune)

global Multidimensional Scaling using monoMDS

Data:     dune
Distance: bray

Dimensions: 2
Stress:     0.1183195
Stress type 1, weak ties
Two convergent solutions found after 5 tries
Scaling: centring, PC rotation, halfchange scaling
Species: expanded scores based on 'dune'


Cheers,
Ivailo
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