[R] graph or svn

[Rolf Turner]

On 9/10/2007, at 12:04 PM, H. Paul Benton wrote:

> Hello all,
>
>     I'm having a spot of trouble. I have made a very nice distance
> matrix  from some comparison calculations. However, the matrix is  
> 3096 x
> 3096, so it's relatively large. Currently I'm using the svn package as
> it seems to work for my data. The graph package errors and says the
> "adjacency matrix must be symmetric for undirected graphs". I though
> 3096 x 3096 was symmetric??


	NO!!!!  That's ***square***, not symmetric.

	To be symmetric a matrix must satisfy a[i,j] = a[j,i] for all i and j.

	In terms of distance, that says that the distance from A to B is the  
same
	as the distance from B to A.  This is often (almost always?) expected
	of a distance measure.

	If your distance measure is or should be symmetric, then there is  
something
	wrong with your distance matrix.  It could simply be a matter of  
numerical
	noise or it could be a programming error.

	If it really makes sense that your distances are not symmetric, then  
you're
	stuck with using svn or something else that handles asymmetry.  I know
	nothing about this area so don't ask ***me***!

> However, the with the svn package the gplot command has been  
> running for
> 6hr's now and no end in sight :) . Is there another package that i can
> use or a way to speed up the analysis, or even another way of  
> displaying
> the data than the nodes and edges plot?

	Off hand I would've thought that ***any*** display base on a 3096 x  
3096
	matrix would be totally opaque no matter how it was structured.

	As the signature file of someone who posts regularly to this list says
	``What problem are you trying to solve?''

				cheers,

					Rolf Turner

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