specifying a "chord" distance matrix in metaMDS

Hi all,

I have been running principal coordinates analysis on a "chord" distance
matrix (stand normalized for some) using cmdscale. I am trying now to do
this with metaMDS but running into some issues.

I can execute the code by specifying the distance matrix, and it works
fine...

obj.nmds<-metaMDS(dist.mat, k=4)

FYI, I got the chord distance matrix as follows:

dist.mat<-vegdist(decostand(as.matrix(orig.dat), "norm"),"euclidean")

I get a solution, and can get at all the site scores in the object dist.mat.
However, I also want species scores, which means I need to specify the
starting dataset in the command.

My question is: how do I specify the chord distance as a command in metaMDS?
I've tried a bunch of things that don't work. I know my code should
eventually look something like:

obj2.nmds<-metaMDS(orig.dat, distance = "something that specifies chord
distance", k=4, zerodist="add", autotransform = FALSE, wascores=TRUE)

It's the "something that specifies chord distance" that I'm having trouble
with. R seems to want a string descriptor there, and I want to give it the
call to vegdist but it doesn't look like it wants to let me. If I try and
submit the call to vegdist, e.g.,

obj2.nmds<-metaMDS(orig.dat, distance =
vegdist(decostand(as.matrix(orig.dat), "norm"),"euclidean"), k=4,
zerodist="add", autotransform = FALSE, wascores=TRUE)


I get an error saying "invalid distance method".

Surely there's a way around this, but it seems like a coding issue which is
why I'm not including example data.

Any thoughts?

Mike

PS- I also gather from reading other posts that I should loop this 50 times
or so to make sure I don't end up on some local solution?

Thanks Jari- however, when I try this code, it gives me some results for
runs with stresses, says I have a solution reached, and then I get an error:

Error in cov.wt(x, x.w) : weights must be non-negative and not all zero

I'm assuming this is saying I have either zeros or negative values in my
distance matrix? Which I shouldn't- when I specify the distance matrix
outside of metaMDS, it's all values between 0 and root 2, and I don't see
any zero values.