Re: [R] Most often pairs of chars across grouping variable

From: Marc Schwartz <marc_schwartz_at_comcast.net>
Date: Tue, 29 Jul 2008 10:15:04 -0500

on 07/29/2008 09:51 AM svga_at_arcor.de wrote:
> Hi list,
>
> is there a package or function to compute the frequencies of pairs of
> chars in a variable across a grouping variable? Eg:
>
>
> d <- data.frame(ID=gl(2,3), F=c("A","B","C","A","C","D"))

>> d

> ID F 1 1 A 2 1 B 3 1 C 4 2 A 5 2 C 6 2 D
>
>
> Now I want to summarize the frequencies of all pairs A-B, A-C, A-D,
> B-C, B-D, C-D across ID:
>
> A B C D A - 1 2 1 B - - 1 0 C - - - 1
>
>
> here, the combination A-C is most frequent. The real problem behind
> that is that 'F' codes diagnoses and I search for the most often
> pairs of diagnoses.
>
> Thanks, Sven

I suspect that there might be something over in Bioconductor, but here is one approach:

 > table(data.frame(t(do.call(cbind,

                      tapply(d$F, d$ID,
                             function(x) combn(as.character(x), 2))))))
    X2
X1 B C D

   A 1 2 1
   B 0 1 0
   C 0 0 1

See ?combn to create the initial pairs from the data. This is done on a per ID basis using tapply. The result is transposed into a data frame and then table() is used to create the cross tabulation of the results.

HTH, Marc Schwartz



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