[R] Where is the construction of a dist object from raw data described?

[Gavin Simpson]

On Wed, 2010-05-19 at 10:10 -0400, Steven Lembark wrote:
> Any reference to the appropriate documentation would
> be most appreciated.
> 
> I am using the TSP module for clustering of HIV
> genetic sequences. The distances have already been
> computed and available as either upper-triangular
> or square, i.e.:
> 
>     a  1 2 3
>     b  4 5
>     c  6
>     d
> 
> or 
> 
>     a 0 1 2 3
>     b 1 0 4 5
>     c 2 4 0 6
>     d 3 5 6 0
> 
> The TSP modules takes in a "dist" object.
> 
> Catch: The only way I can see to get a dist
> object is with dist(), which computes the 
> distances for itself rather than taking them
> as-is.
> 
> Q: How does one convert either of the strucutres
>    above into a "dist" object without having to 
>    first feed them through dist()?

as.dist() will convert the square matrix into a dist object

I'm not sure of a convenient way of importing data in the "upper" form
you show without having to go via a matrix, or build the dist object by
hand, so if this really is an either/or situation and the square form is
always available and it is not a problem loading the dissimilarity
matrix into RAM, I'd stick with as.dist.

HTH

G

> 
> I can easily split the labels into a seprate
> output file, leaving me with the rownames 
> and colnames values for the result in a separate
> place if that makes explaining how to get the 
> numeric values into a dist any easier.
> 
> Google, searching r-project.org, and the R
> Nutshell book all lead me back to dist() or 
> daisy().
> 
> thanks
> 
> --
> Steven Lembark                                          85-09 90th St.
> Workhorse Computing                               Woodhaven, NY, 11421
> lembark at wrkhors.com                                    +1 888 359 3508
> 
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

-- 
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
 Dr. Gavin Simpson             [t] +44 (0)20 7679 0522
 ECRC, UCL Geography,          [f] +44 (0)20 7679 0565
 Pearson Building,             [e] gavin.simpsonATNOSPAMucl.ac.uk
 Gower Street, London          [w] http://www.ucl.ac.uk/~ucfagls/
 UK. WC1E 6BT.                 [w] http://www.freshwaters.org.uk
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%