[R-sig-eco] 2 questions about NMDS in vegan

[Manuel Spínola]

Dear list members,

I am trying to run an NMDS with 9 standardized variables regarding to 
water quality and I got the following message:

 > aguae.mds <- metaMDS(aguae, dist="euclidean", k=2, zerodist="add")
Using step-across dissimilarities:
Too long or NA distances: 564 out of 666 (84.7%)
Stepping across 666 dissimilarities...
Error in isoMDS(dist, k = k, trace = isotrace) :
 an initial configuration must be supplied with NA/Infs in 'd'
In addition: Warning messages:
1: In metaMDSdist(comm, distance = distance, autotransform = 
autotransform,  :
 Zero dissimilarities changed into 0.0759809585356366
2: In stepacross(dis, trace = trace, ...) :
 Disconnected data: Result will contain NAs
3: In metaMDSdist(comm, distance = distance, autotransform = 
autotransform,  :
 Data are disconnected, results may be meaningless

1) Should I do not standardize the variables?

2) In a plot for a nmds with fitted environmental variables (function 
envfit) how can I change the name of the labels of the vectors (arrows)?

Thank you very much in advance.
Best,

Manuel Spínola

-- 
Manuel Spínola, Ph.D.
Instituto Internacional en Conservación y Manejo de Vida Silvestre
Universidad Nacional
Apartado 1350-3000
Heredia
COSTA RICA
mspinola at una.ac.cr
mspinola10 at gamil.com
Teléfono: (506) 2277-3598
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