[R] self-defined distance function to be computed on matrix

[R. Michael Weylandt]

Hi zz,

The help file for the dist() function ( ?dist) says that

"Missing values are allowed, and are excluded from all computations
     involving the rows within which they occur"

so if you can cajole this into any of the standard distance metrics,
you could do something like:

x[x == 0] <- NA

before dist(x, method = ??)

It's not quite clear to me how your distance metric is defined
(perhaps give it symbolically, or at least on an output that's not all
+/- 1 where it's hard to see what comes from where) but if you
clarify, I can help you think through that.

Cheers,
Michael

On Thu, Aug 30, 2012 at 12:48 PM, zz <czhang at uams.edu> wrote:
> Hello,
>
> I have a self-defined function to be computed on each column in a matrix.
> The basic idea is to ignore the elements that have value of 0 during
> computation.
>
> I should be able to write my own function but it could be computational
> expensive, so I'd love to ask if anyone may have suggestions on how to
> implement it more efficiently.  Thanks in advance.
>
> For example, there are three vectors in the matrix, which are
> A       B       C
> 1       0       1
> -1      1       1
> -1      -1      1
> 1       0       -1
>
> Distance(AB) = (-1X1+(-1)X(-1))/de(AB) , and
> de(AB) = sqrt(square(-1)+square(-1)) X sqrt(square(1)+square(-1))
>
> Distance(BC) = (1X1+(-1)X1)/de(BC) ,and
> de(BC) = sqrt(square(1)+square(-1)) X sqrt(square(1)+square(1))
>
> Distance(AC) = (1X1+(-1)X1+(-1)X1+1X(-1))/de(AC), and
> de(BC) = sqrt(square(1)+square(-1)+square(-1)+square(1)) X
> sqrt(square(1)+square(1)+square(1)+square(-1))
>
> As you may see, the numerator is basically the dot product of the two
> vectors; this function actually is more like the cosine function in R, but
> with some variations.
>
> I would need to compute the distance between any two vectors in a matrix.
> It would be ideal if the results could be the output that produces by some R
> distance function.
>
> Thanks.
>
>
>
>
>
>
>
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