Skip to content

Ordination with vegan's metaMDS

2 messages · Michele Tobias, Tyler Smith

Original
Michele Tobias
# 
I have plant cover data for a number of sample plots and would like to 
do an ordination plot with the vegan package's metaMDS.  The problem is 
that some of my plots have matching data (for example, two plots have 5% 
cover by one species and nothing else).  Because of this, the 
dissimilarity measure between these is zero and the ordination doesn't 
work.  It gives me this message: "Error in metaMDSdist(comm, distance = 
distance, autotransform = autotransform,  : Zero dissimilarities are not 
allowed".
Does anyone have any suggestions on how to work with this?  Thank you 
for your help!

cheers,
Michele
Tyler Smith
# 
Michele Tobias <mmtobias at ucdavis.edu>
writes:
You can add the option zerodist = "add", which will add a small value to
all zero distances. See the help page for metaMDS.

Cheers,

Tyler