Thanks, Greg. Yes, I'd store the compressed stuff as a raw data type. Best,
R. On Thu, Feb 28, 2008 at 11:54 PM, Gregory Warnes <[EMAIL PROTECTED]> wrote: > > You might look at storing the data using R's "raw" data type... > > -G > > > > > On Feb 28, 2008, at 5:38PM , Ramon Diaz-Uriarte wrote: > > > 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. > > -- 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.
