Howdy Folks,
I received the two data files from Duarte Viana, but I can't reproduce the
problem: it runs smoothly in my computer.
resp-read.table(resp.txt,header=F,sep=\t)
explan-read.table(explan.txt,header=F,sep=\t)
library(vegan)
Loading required package: permute
This is vegan 2.1-16
Hi,
Thanks Jari for your help.
I forgot to say that I am working in a Mac (OS X, 10.6.8) and was
using the vegan version 2.0-2 of 2011.
I've just updated vegan to version 2.0-3 and now it runs fine (with
the same results as Jari). I should have checked for a newer version
before asking for
Ivailo,
Some (but not all) vegan functions internally coerce the matrix like
input object to matrix using 'x - as.matrix(x)'. The as.matrix()
coercion method is defined for sparse matrices in the Matrix package,
and that is why it works for some (but not all) vegan functions. In
case it does not
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
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
