Dear Christos, Thanks for your reply. Actually, I should have been more careful with language: its not really a sparse matrix, but rather a ragged array that results from a more compact representation we though of for the hidden states in a Hidden Markov Model in many runs of MCMC. However, it might make sense for us to check sparseMatrix and see how its done there.
Thanks, R On Thu, Feb 28, 2008 at 7:49 PM, Christos Hatzis <[EMAIL PROTECTED]> wrote: > Ramon, > > If you are looking for a solution to your specific application (as opposed > to a general compression/ decompression mechanism), it might be worth > checking out the Matrix package, which has facilities for storing and > manipulating sparse matrices. The sparseMatrix class stores matrices in the > triplet representation (i.e. only indices and values of the non-zero > elements) and this affords great compression ratios, depending on the size > and degree of sparseness of the matrix. > > -Christos > > > > > -----Original Message----- > > From: [EMAIL PROTECTED] > > [mailto:[EMAIL PROTECTED] On Behalf Of Ramon Diaz-Uriarte > > Sent: Thursday, February 28, 2008 1:18 PM > > To: [EMAIL PROTECTED] > > Subject: [R] compress data on read, decompress on write > > > > Dear All, > > > > I'd like to be able to have R store (in a list component) a > > compressed data set, and then write it out uncompressed. > > gzcon and gzfile work in exactly the opposite direction. What > > would be a good way to handle this? > > > > Details: > > ---------- > > > > We have a package that uses C; part of the C output is a > > large sparse matrix. This is never manipulated directly by R, > > but always by the C code. However, we need to store that data > > somewhere (inside an R > > object) for further calls to the functions in our package. > > We'd like to store that matrix as part of the R object (say, > > as an element of a list). Ideally, it would be stored in as > > compressed a way as possible. > > Then, when we need to use that information, it would be > > decompressed and passed to the C function. > > > > I guess one way to do it is to have C deal with the > > compression and uncompression (e.g., using zlib or the bzip2 > > libraries) and then use readBin, etc, from R. But, if I can, > > I'd like to avoid our C code having to call zlib, etc, so as > > to make our package easily portable. > > > > > > Thanks, > > > > R. > > > > -- > > Ramon Diaz-Uriarte > > Statistical Computing Team > > Structural Biology and Biocomputing Programme Spanish > > National Cancer Centre (CNIO) http://ligarto.org/rdiaz > > > > ______________________________________________ > > R-help@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. > > > > > > > -- Ramon Diaz-Uriarte Statistical Computing Team Structural Biology and Biocomputing Programme Spanish National Cancer Centre (CNIO) http://ligarto.org/rdiaz ______________________________________________ R-help@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.
