error in MetaMDS
On 21/07/2013, at 03:02 AM, Elaine Kuo wrote:
Hello
I am trying to run MetaMDS but got the following error based on the code.
Please kindly indicate the error source and thank you.
Elaine
Code
# Compute the Simpson distance matrices for the dataset (3 hr using 4GB)
library(betapart)
dist.sim<-beta.pair(dataR, index.family="sor")
class(dist.sim)
betasim.sim<-dist.sim[["beta.sim"]]
class(betasim.sim)
# NMDS
library(vegan)
nms <- metaMDS(betasim.sim,trymax=100,zerodist="add",autotransform
=FALSE,k=2)
Error
Error in if (any(autotransform, noshare > 0, wascores) && any(comm < 0)) {
:
missing value where TRUE/FALSE needed
Elaine, I cannot reproduce this, and there is no information in the message to know what happens. Do you have missing values in betasim.sim? Are betasim.sim really dissimilarities? BTW, vegan has Simpson dissimilarity: use betadiver(x, "sim"). Cheers, Jari Oksanen