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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