[R-sig-eco] using metaMDS and getting error messages

[Jari Oksanen]

On 2/02/10 15:25 PM, "Aisyah" <aisyah.faruk at ioz.ac.uk> wrote:

> 
> Hi
> 
> Im currently trying to use the metaMDS function on MASS and keep getting
> this message. Im new at this and need some help.
> 
>> stream.mds<-metaMDS(stream)
> Using step-across dissimilarities:
> Too long or NA distances: 65 out of 105 (61.9%)
> Stepping across 105 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 stepacross(dis, trace = trace, ...) :
>   Disconnected data: Result will contain NAs
> 2: In metaMDSdist(comm, distance = distance, autotransform = autotransform,
> :
>   Data are disconnected, results may be meaningless
> 
> The data is abundance of different species in certain plots. I've
> standardized the data using the wisconsin function.
> 
Aisyah,

I think the diagnostic message more or less tells you what is the problem:
the data are disconnected. This means that there are some plots or groups of
plots that have nothing in common with some other plots. It is impossible to
define the relationship of these disconnected plots with other plots. You
should handle your disconnected blocks separately, or in mild cases, remove
the plots that have nothing in common with others. In principle, such plots
could be anywhere outside the configuration of other points.

You can use function distconnected() in vegan to find connected groups
within disconnected data.

Cheers, Jari Oksanen