Hello, I'd like to use DBI to store lm objects in a database. I've to analyze many of linear models and I cannot store them in a single R-session (not enough memory). Also it'd be nice to have them persistent. Maybe it's possible to create a compact binary representation of the object (the kind of format created created by "save"), so that one doesn't need to write a conversion routine for these objects (or maybe there's already a conversion available for lm?). I assume that the data do not need to be analyzed with a any other software than R. I'm happy for any suggestions and links to get some more info on this. kid regards, Arne -- Arne Muller, Ph.D. Toxicogenomics, Aventis Pharma arne dot muller domain=aventis com
On Thu, 13 May 2004 Arne.Muller at aventis.com wrote:> I'd like to use DBI to store lm objects in a database. I've to analyze > many of linear models and I cannot store them in a single R-session (not > enough memory). Also it'd be nice to have them persistent. > > Maybe it's possible to create a compact binary representation of the > object (the kind of format created created by "save"), so that one > doesn't need to write a conversion routine for these objects (or maybe > there's already a conversion available for lm?). I assume that the data > do not need to be analyzed with a any other software than R.?serialize. It's exactly the "save" format. -- Brian D. Ripley, ripley at stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UK Fax: +44 1865 272595
Arne, There are several database access packages for R. I use RMySQL, but there are several others (ODBC, etc.). However, as far as I know (and I may be wrong), there is not a persistence API for R objects (in a relational DB sense), but you could certainly deconstruct the objects and store their parts for later reconstruction of the objects. I guess another option would be a scheme of saved results (files) indexed in some way so that you could get the results, but I can't think of a way to make this fast. Sean On 5/13/04 11:11 AM, "Arne.Muller at aventis.com" <Arne.Muller at aventis.com> wrote:> Hello, > > I'd like to use DBI to store lm objects in a database. I've to analyze many of > linear models and I cannot store them in a single R-session (not enough > memory). Also it'd be nice to have them persistent. > > Maybe it's possible to create a compact binary representation of the object > (the kind of format created created by "save"), so that one doesn't need to > write a conversion routine for these objects (or maybe there's already a > conversion available for lm?). I assume that the data do not need to be > analyzed with a any other software than R. > > I'm happy for any suggestions and links to get some more info on this. > > kid regards, > > Arne > > -- > Arne Muller, Ph.D. > Toxicogenomics, Aventis Pharma > arne dot muller domain=aventis com > > ______________________________________________ > R-help at stat.math.ethz.ch mailing list > https://www.stat.math.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html >
Thanks for your reply. I think I'll go for Prof Ripley's suggestion to use "serialize", since I don't need to query attributes of the objects via SQL. So a crude BLOB will do ... thanks, Arne -- Arne Muller, Ph.D. Toxicogenomics, Aventis Pharma arne dot muller domain=aventis com> -----Original Message----- > From: Sean Davis [mailto:sdavis2 at mail.nih.gov] > Sent: 13 May 2004 17:22 > To: Muller, Arne PH/FR; r-help > Subject: Re: [R] storage of lm objects in a database > > > Arne, > > There are several database access packages for R. I use > RMySQL, but there > are several others (ODBC, etc.). However, as far as I know > (and I may be > wrong), there is not a persistence API for R objects (in a > relational DB > sense), but you could certainly deconstruct the objects and > store their > parts for later reconstruction of the objects. I guess > another option would > be a scheme of saved results (files) indexed in some way so > that you could > get the results, but I can't think of a way to make this fast. > > Sean > > On 5/13/04 11:11 AM, "Arne.Muller at aventis.com" > <Arne.Muller at aventis.com> > wrote: > > > Hello, > > > > I'd like to use DBI to store lm objects in a database. I've > to analyze many of > > linear models and I cannot store them in a single R-session > (not enough > > memory). Also it'd be nice to have them persistent. > > > > Maybe it's possible to create a compact binary > representation of the object > > (the kind of format created created by "save"), so that one > doesn't need to > > write a conversion routine for these objects (or maybe > there's already a > > conversion available for lm?). I assume that the data do > not need to be > > analyzed with a any other software than R. > > > > I'm happy for any suggestions and links to get some more > info on this. > > > > kid regards, > > > > Arne > > > > -- > > Arne Muller, Ph.D. > > Toxicogenomics, Aventis Pharma > > arne dot muller domain=aventis com > > > > ______________________________________________ > > R-help at stat.math.ethz.ch mailing list > > https://www.stat.math.ethz.ch/mailman/listinfo/r-help > > PLEASE do read the posting guide!http://www.R-project.org/posting-guide.html>