Hola!
I am programming a class (S3) "symarray" for
storing the results of functions symmetric in its
k arguments. Intended use is for association indices
for more than two variables, for instance coresistivity
against antibiotics.
There is one programming problem I haven't solved, making an inverse
of the index function indx() --- se code below. It could for instance
return the original k indexes in strictly increasing order, to make
indx() formally invertible.
Any ideas?
Kjetil
Code:
# Implementing an S3 class for symarrays with array rank r for dimension
# [k, k, ..., k] with k>=r repeated r times. We do not store the diagonal.
# Storage requirement is given by {r, k}= choose(k, r)
# where r=array rank, k=maximum index
symarray <- function(data=NA, dims=c(1,1)){
r <- dims[1]
k <- dims[2]
if(r > k) stop("symarray needs dimension larger than array
rank")
len <- choose(k, r)
out <- data[1:len]
attr(out, "dims") <- dims
class(out) <- "symarray"
out
}
# Index calculation:
indx <- function(inds, k){
r <- length(inds)
if(r==1) return(inds) else {
if(inds[1]==1) {
return( indx(inds[-1]-1, k-1 ) ) } else {
return( indx(c(inds[1]-1, seq(from=k-r+2, by=1, to=k)), k) +
indx( inds[-1]-inds[1], k-inds[1] ))
}
}
} # end indx
# Methods for assignment and indexing:
"[.symarray" <- function(x, inds, drop=FALSE){
dims <- attr(x, "dims")
k <- dims[2]
inds <- indx(inds, k)
res <- NextMethod("[", x)
res
}
"[<-.symarray" <- function(x, inds, value){
dims <- attr(x, "dims")
k <- dims[2]
inds <- indx(inds, k)
res <- NextMethod("[<-", x)
res
}
I'm not sure I understand your question, but are you asking how to
index choose(k, r) objects? Almost 3 years ago, I asked a question like
this. Andy Liaw referred me to nchoosek(vsn)
(http://finzi.psych.upenn.edu/R/Rhelp02a/archive/12518.html). This
produces a matrix of dimension (r, choose(k, r)). With this matrix, you
could convert an integer between 1 and choose(k, r) into an r-vector by
table look-up. Reading the code for nchoosek might help you further if
this does not seem appropriate for you.
I found this just now using 'RSiteSearch("all subsets of a
size")',
which produced 102 hits. Another one that looked like it might help you
is "http://finzi.psych.upenn.edu/R/Rhelp02a/archive/1717.html".
Hope this helps,
Spencer Graves
Kjetil Brinchmann Halvorsen wrote:> Hola!
>
> I am programming a class (S3) "symarray" for
> storing the results of functions symmetric in its
> k arguments. Intended use is for association indices
> for more than two variables, for instance coresistivity
> against antibiotics.
>
> There is one programming problem I haven't solved, making an inverse
> of the index function indx() --- se code below. It could for instance
> return the original k indexes in strictly increasing order, to make
> indx() formally invertible.
>
> Any ideas?
>
> Kjetil
>
>
> Code:
>
>
> # Implementing an S3 class for symarrays with array rank r for dimension
> # [k, k, ..., k] with k>=r repeated r times. We do not store the
diagonal.
>
> # Storage requirement is given by {r, k}= choose(k, r)
> # where r=array rank, k=maximum index
>
> symarray <- function(data=NA, dims=c(1,1)){
> r <- dims[1]
> k <- dims[2]
> if(r > k) stop("symarray needs dimension larger than array
rank")
> len <- choose(k, r)
> out <- data[1:len]
> attr(out, "dims") <- dims
> class(out) <- "symarray"
> out
> }
>
> # Index calculation:
>
> indx <- function(inds, k){
> r <- length(inds)
> if(r==1) return(inds) else {
> if(inds[1]==1) {
> return( indx(inds[-1]-1, k-1 ) ) } else {
> return( indx(c(inds[1]-1, seq(from=k-r+2, by=1, to=k)), k) +
> indx( inds[-1]-inds[1], k-inds[1] ))
> }
> }
> } # end indx
>
> # Methods for assignment and indexing:
>
> "[.symarray" <- function(x, inds, drop=FALSE){
> dims <- attr(x, "dims")
> k <- dims[2]
> inds <- indx(inds, k)
> res <- NextMethod("[", x)
> res
> }
>
> "[<-.symarray" <- function(x, inds, value){
> dims <- attr(x, "dims")
> k <- dims[2]
> inds <- indx(inds, k)
> res <- NextMethod("[<-", x)
> res
> }
>
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html
On Mon, 29 May 2006, Martin Maechler wrote:>>>>>> "SpG" == Spencer Graves <spencer.graves at pdf.com> >>>>>> on Sun, 28 May 2006 16:21:53 -0700 writes: > > SpG> I'm not sure I understand your question, but > SpG> are you asking how to index choose(k, r) objects? > SpG> Almost 3 years ago, I asked a question like this. Andy > SpG> Liaw referred me to nchoosek(vsn) > SpG> (http://finzi.psych.upenn.edu/R/Rhelp02a/archive/12518.html). > SpG> This produces a matrix of dimension (r, choose(k, r)). > SpG> With this matrix, you could convert an integer between > SpG> 1 and choose(k, r) into an r-vector by table look-up. > SpG> Reading the code for nchoosek might help you further if > SpG> this does not seem appropriate for you. > > Note that *if* the above is the answer, > I'd rather recommend to use combn() from package "combinat", > since a (slightly improved) version of combn() has been part of R-devel > (to become R 2.4.0 in October) for a while. Also, combn() from > "combinat" precedes nchoosek() historically and is also faster.And if the problem is large enough to bog down combn() (e.g. choose(25,12) combinations) look at this approach: http://article.gmane.org/gmane.comp.lang.r.general/62065> > Martin Maechler, ETH Zurich > > SpG> I found this just now using 'RSiteSearch("all > SpG> subsets of a size")', which produced 102 hits. Another > SpG> one that looked like it might help you is > SpG> "http://finzi.psych.upenn.edu/R/Rhelp02a/archive/1717.html". > > SpG> Hope this helps, Spencer Graves > > SpG> Kjetil Brinchmann Halvorsen wrote: > >> Hola! > >> > >> I am programming a class (S3) "symarray" for storing the > >> results of functions symmetric in its k > >> arguments. Intended use is for association indices for > >> more than two variables, for instance coresistivity > >> against antibiotics. > >> > >> There is one programming problem I haven't solved, making > >> an inverse of the index function indx() --- se code > >> below. It could for instance return the original k > >> indexes in strictly increasing order, to make indx() > >> formally invertible. > >> > >> Any ideas? > >> > >> Kjetil > >> > >> > >> Code: > >> > >> > >> # Implementing an S3 class for symarrays with array rank > >> r for dimension # [k, k, ..., k] with k>=r repeated r > >> times. We do not store the diagonal. > >> > >> # Storage requirement is given by {r, k}= choose(k, r) # > >> where r=array rank, k=maximum index > >> > >> symarray <- function(data=NA, dims=c(1,1)){ r <- dims[1] > >> k <- dims[2] if(r > k) stop("symarray needs dimension > >> larger than array rank") len <- choose(k, r) out <- > >> data[1:len] attr(out, "dims") <- dims class(out) <- > >> "symarray" out } > >> > >> # Index calculation: > >> > >> indx <- function(inds, k){ r <- length(inds) if(r==1) > >> return(inds) else { if(inds[1]==1) { return( > >> indx(inds[-1]-1, k-1 ) ) } else { return( > >> indx(c(inds[1]-1, seq(from=k-r+2, by=1, to=k)), k) + > >> indx( inds[-1]-inds[1], k-inds[1] )) } } } # end indx > >> > >> # Methods for assignment and indexing: > >> > >> "[.symarray" <- function(x, inds, drop=FALSE){ dims <- > >> attr(x, "dims") k <- dims[2] inds <- indx(inds, k) res <- > >> NextMethod("[", x) res } > >> > >> "[<-.symarray" <- function(x, inds, value){ dims <- > >> attr(x, "dims") k <- dims[2] inds <- indx(inds, k) res <- > >> NextMethod("[<-", x) res } > >> > >> ______________________________________________ > >> R-help at stat.math.ethz.ch mailing list > >> https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do > >> read the posting guide! > >> http://www.R-project.org/posting-guide.html > > SpG> ______________________________________________ > SpG> R-help at stat.math.ethz.ch mailing list > SpG> https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do > SpG> read the posting guide! > SpG> http://www.R-project.org/posting-guide.html > > > > > [ Part 3.15: "Included Message" ] >Charles C. Berry (858) 534-2098 Dept of Family/Preventive Medicine E mailto:cberry at tajo.ucsd.edu UC San Diego http://biostat.ucsd.edu/~cberry/ La Jolla, San Diego 92093-0717