R help - May 2010 - Where is the construction of a dist object from raw data described?

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()?

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

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
> 
> ______________________________________________
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