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?
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
you could try the following:
n <- nrow(X)
k <- n * (n - 1) / 2
Y <- matrix(NA, k, n)
ind.up <- which(upper.tri(X), arr.ind = TRUE)
ind.lo <- which(lower.tri(X), arr.ind = TRUE)
Y[cbind(1:k, ind.lo[, 1])] <- X[ind.up]
Y[cbind(1:k, ind.lo[, 2])] <- X[ind.lo]
Y
I hope it helps.
Best,
Dimitris
----
Dimitris Rizopoulos
Ph.D. Student
Biostatistical Centre
School of Public Health
Catholic University of Leuven
Address: Kapucijnenvoer 35, Leuven, Belgium
Tel: +32/(0)16/336899
Fax: +32/(0)16/337015
Web: http://med.kuleuven.be/biostat/
http://www.student.kuleuven.be/~m0390867/dimitris.htm
----- Original Message -----
From: "Robin Hankin" <r.hankin at noc.soton.ac.uk>
To: "R program" <R-help at r-project.org>
Sent: Wednesday, September 12, 2007 4:32 PM
Subject: [R] vectorize a matrix conversion
> 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?
>
> 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
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm
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 > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > 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