[R] vectorize a matrix conversion

[Charles C. Berry]

On Wed, 12 Sep 2007, Robin Hankin wrote:

> Hello
>
>
> I have X, an n-by-n  matrix and want to convert it to Y, an
>  n(n-1)/2 -by- n matrix such that each row of Y
> corresponds to an element of the upper diagonal
> of X.   Say row k of Y corresponds to [i,j] with i\neq j.
>
> Then Y[i,k] = X[i,j] and Y[j,k] = X[j,i].
> and Y[-c(i,j),k] = NA.
>
> How to do this vectorizedly?
>

If I follow you:

   upper.indexes <- which( lower.tri( X ), arr.ind=TRUE )
   from.mat <- rbind( upper.indexes, upper.indexes[ , 2:1 ] )
   to.mat <- cbind( rep( 1:nrow(upper.indexes), 2 ), as.vector( upper.indexes[, 2:1] ) )
   Y[ to.mat ] <- X[ from.mat ]

HTH,

Chuck


> Example follows:
>
>
>
> > X
>      [,1] [,2] [,3] [,4]
> [1,]   NA   10    8    7
> [2,]   10   NA    7   12
> [3,]   12   13   NA    8
> [4,]   13    8   12   NA
> > Y
>      [,1] [,2] [,3] [,4]
> [1,]   10   10   NA   NA
> [2,]   12   NA    8   NA
> [3,]   13   NA   NA    7
> [4,]   NA   13    7   NA
> [5,]   NA    8   NA   12
> [6,]   NA   NA   12    8
> >
>
> [matrix X corresponds to an all-play-all competition amongst 4
> individuals,
> entry [i,j] corresponding to the  number of times individual "i" won
> when competing against individual "j".  Thus individual 2 beat
> individual
> 3 seven times and individual 3 beat individual 2 thirteen times.
> Note X[i,j] + X[j,i]=20 as there were 20 trials for each pair]
>
>
> Pitiful nonvectorized code follows.
>
> n <- nrow(X)
> Y <-  matrix(NA,n*(n-1)/2,n)
> k <- 1
> for(i in 1:(n-1)){
>   for(j in (i+1):n){
>     if( !(i==j)){
>       print(c(i,j,k))
>       Y[k,i] <- X[i,j]
>       Y[k,j] <- X[j,i]
>     }
>     k <- k+1
>   }
> }
>
>
>
>
>
> --
> Robin Hankin
> Uncertainty Analyst
> National Oceanography Centre, Southampton
> European Way, Southampton SO14 3ZH, UK
>  tel  023-8059-7743
>
> ______________________________________________
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

Charles C. Berry                            (858) 534-2098
                                             Dept of Family/Preventive Medicine
E mailto:cberry at tajo.ucsd.edu	            UC San Diego
http://famprevmed.ucsd.edu/faculty/cberry/  La Jolla, San Diego 92093-0901