[R-sig-eco] metaMDS: unrealistic good stress

Daniel daniel_ho at web.de
Tue Feb 3 16:55:24 CET 2009


Hello,

i'm using metaMDS to ordinate trait mean data of plants in different 
ecosystems.
I used different calibrations but the stress differs only  between 0,001 
an 0,1e-19.
I have never seen such a good stress, so I wonder about possible 
mistakes, but i cannot find one.

Data looks like that:

plots      trait1      trait2      traits3
1            2,4           0,2         20
2            0,5           0,3         21 
.                .               .            .
300          .               .            .

My standard calibration is:
metaMDS(test
,distance = "euclidean"   # because metric data
, k = 3                                 # because I have 3 traits, but I 
couldn't plot a scree plot
, trymax = 3-5                     # not more, because too large dataset
, autotransform =TRUE
, noshare =1    # Ordination may be very difficult if a large proportion 
of sites have no shared species. In this case, the results may be 
improved with stepacross dissimilarities, or flexible shortest paths 
among all sites. No manipilation: noshare=1.0
,trace = TRUE         # will monitor the final stresses
,plot = TRUE       
,zerodist="add"         
)

thanks for helping me out

Daniel

-----------------------------------------------------------------
Daniel Hornstein  
University of Bayreuth, Germany
Department of Disturbance Ecology

phone: 0921//55-2173



More information about the R-sig-ecology mailing list