[Vegan-commits] Non metric multidimensional scaling

[Eleanor Spratt]

To All,

I want to use vegan package to plot an ordination for my data. I have
three habitat types and collected 100 different species from these
habitats. My data frame has habitat and species as a columns. The
habitat column could be classes as categorical with three habitat
types named. The species columns are numbers (abundances) representing
the abundance per habitat.

The code I am wanting to use seems to be having some difficulties.

> NMMDS<-read.csv(file.choose(),header=T)
> library(vegan)
> ordination<-NMMDS[,1:101]        # select coloumns excl. env variables
> d<-dist(ordination)
> fit<-metaMDS(d,k=2)
Loading required package: MASS
Error in isoMDS(dist, k = k, trace = isotrace) :
  zero or negative distance between objects 63 and 65
In addition: Warning message:
package 'MASS' was built under R version 2.13.1

That is the error message- due to this I can't continue. I have
researched what that error message means, but it is not entirely
clear.

I then tried an alternative way, and this had a different error

> NMMDS<-read.csv(file.choose(),header=T)
> library(vegan)
> library (MASS)
> sol<-metaMDS(NMMDS)
Error in if (any(autotransform, noshare > 0, wascores) && any(comm < 0)) { :
  missing value where TRUE/FALSE needed
In addition: Warning message:
In Ops.factor(left, right) : < not meaningful for factors

What do you recommend?

Kind Regards

Eleanor