R help - Nov 2004 - Pairwise Distances -- How to vectorize the loop

R-List,

I'm trying to compute pairwise distances among pairs of observations, 
which each pair containing data from 2 groups. There are more than 
100000 unique pairs. I have programmed a distance function that has 
three parameters, a vector of covariates from the ith observation in 
Group 1, a vector of covarites from the jth observation in Group 2, and 
a weighting matrix.

I have used expand.grid to create a matrix containing all possible pairs 
of Keys (unique identifiers) from Group 1 and Group 2 and a placeholder 
for each pairwise distance in an effort to pre-allocate memory.

The data containing the covariates are currently in a matrix that looks 
like:

x1 x2 x3 ... xn Key Group

where x1,...,xn are the covariates of interest. The Key values 
correspond to the row number.

I'm trying to figure out a way to calculate all of the distances by 
vectorizing a loop. I'm trying to avoid the nested-loop paradigm. I'm 
sure I'm missing something quite obvious.

Any insights would be appreciated.

Best,

Tim

Hi
>From what you write it seems to me a work for outer(). Did you 
try it?

Cheers
Petr


On 15 Nov 2004 at 22:26, Timothy W. Victor wrote:
> R-List,
> 
> I'm trying to compute pairwise distances among pairs of observations,
> which each pair containing data from 2 groups. There are more than
> 100000 unique pairs. I have programmed a distance function that has
> three parameters, a vector of covariates from the ith observation in
> Group 1, a vector of covarites from the jth observation in Group 2,
> and a weighting matrix.
> 
> I have used expand.grid to create a matrix containing all possible
> pairs of Keys (unique identifiers) from Group 1 and Group 2 and a
> placeholder for each pairwise distance in an effort to pre-allocate
> memory.
> 
> The data containing the covariates are currently in a matrix that
> looks like:
> 
> x1 x2 x3 ... xn Key Group
> 
> where x1,...,xn are the covariates of interest. The Key values 
> correspond to the row number.
> 
> I'm trying to figure out a way to calculate all of the distances by
> vectorizing a loop. I'm trying to avoid the nested-loop paradigm.
I'm
> sure I'm missing something quite obvious.
> 
> Any insights would be appreciated.
> 
> Best,
> 
> Tim
> 
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Petr Pikal
petr.pikal at precheza.cz