Thread: R and postgres
I'd like to get R to talk to postgresql, but my head's spinning among a web of broken links, way outdated web pages, project deprecation announcements and a terrible signal:link ratio.
Rdbi and RdbiPgSQL seem to be the answer, despite both being apparently defunct projects.
What is the Right Thing for a guy who wants R to talk to postgresql?
Thanks, and send aspirin,
Reece
Rdbi and RdbiPgSQL seem to be the answer, despite both being apparently defunct projects.
What is the Right Thing for a guy who wants R to talk to postgresql?
Thanks, and send aspirin,
Reece
-- Reece Hart, http://harts.net/reece/, GPG:0x25EC91A0 |
On Monday 06 November 2006 04:58 pm, Reece Hart wrote: > I'd like to get R to talk to postgresql, but my head's spinning among a > web of broken links, way outdated web pages, project deprecation > announcements and a terrible signal:link ratio. > > Rdbi and RdbiPgSQL seem to be the answer, despite both being apparently > defunct projects. > > What is the Right Thing for a guy who wants R to talk to postgresql? > > Thanks, and send aspirin, > Reece You might want to take a look at PL/R a procedural language for R in Postgres. http://www.joeconway.com/plr/ -- Adrian Klaver aklaver@comcast.net
On Mon, 2006-11-06 at 19:13 -0800, Adrian Klaver wrote:
PL/R is indeed neat, but I want to go the other way: within R, fetch data from postgres and manipulate it (plot, histogram, etc). I appreciate that I could expose this through postgres, but that's a little awkward for prototyping and I'm not keen to add load to my postgres box.
-Reece
You might want to take a look at PL/R a procedural language for R in Postgres.
http://www.joeconway.com/plr/
PL/R is indeed neat, but I want to go the other way: within R, fetch data from postgres and manipulate it (plot, histogram, etc). I appreciate that I could expose this through postgres, but that's a little awkward for prototyping and I'm not keen to add load to my postgres box.
-Reece
-- Reece Hart, http://harts.net/reece/, GPG:0x25EC91A0 |
On Monday 06 November 2006 07:38 pm, Reece Hart wrote: > On Mon, 2006-11-06 at 19:13 -0800, Adrian Klaver wrote: > > You might want to take a look at PL/R a procedural language for R in > > Postgres. > > http://www.joeconway.com/plr/ > > PL/R is indeed neat, but I want to go the other way: within R, fetch > data from postgres and manipulate it (plot, histogram, etc). I > appreciate that I could expose this through postgres, but that's a > little awkward for prototyping and I'm not keen to add load to my > postgres box. > > -Reece Sorry, I did not read the message closely enough. A quick perusal of the R docs helped me understand the issue a little better. The only solution I can see at this point is to have an intermediate step. There are two ways I can see to do this. The first is to use the copy command to create a csv file. The read.table() function would then be used in R to import the data. The second is use the program pg2xbase http://www.klaban.torun.pl/prog/pg2xbase/ to create a DBF file and use read.dbf() to input the file. -- Adrian Klaver aklaver@comcast.net
I assume you've seen pl/R? http://www.joeconway.com/plr/ On Mon, 6 Nov 2006, Reece Hart wrote: > I'd like to get R to talk to postgresql, but my head's spinning among a > web of broken links, way outdated web pages, project deprecation > announcements and a terrible signal:link ratio. > > Rdbi and RdbiPgSQL seem to be the answer, despite both being apparently > defunct projects. > > What is the Right Thing for a guy who wants R to talk to postgresql? > > Thanks, and send aspirin, > Reece > > -- > Reece Hart, http://harts.net/reece/, GPG:0x25EC91A0 > >
Reece Hart wrote: > I'd like to get R to talk to postgresql, but my head's spinning among a > web of broken links, way outdated web pages, project deprecation > announcements and a terrible signal:link ratio. > > Rdbi and RdbiPgSQL seem to be the answer, despite both being apparently > defunct projects. > > What is the Right Thing for a guy who wants R to talk to postgresql? I think you want this: http://bioconductor.org/packages/1.9/bioc/html/RdbiPgSQL.html The bioconductor project is now maintaining RdbiPgSQL. I think many people also use RODBC to connect R with Postgres. Joe
I use RODBC which is available from http://cran.r-project.org/ I'm not sure if this will do what you want, or whether it has the features of Rdbi you need, but it gets the job done for me. I can open a "channel", execute a SQL statement (typically a Select) and read the results back into a R dataframe. There is a nice way to dump a dataframe back into a table which is created for you, with columns and datatypes as appropriate. Hope this helps. TJ O'Donnell http://www.gnova.com/ > I'd like to get R to talk to postgresql, but my head's spinning among a > web of broken links, way outdated web pages, project deprecation > announcements and a terrible signal:link ratio. > > Rdbi and RdbiPgSQL seem to be the answer, despite both being apparently > defunct projects. > > What is the Right Thing for a guy who wants R to talk to postgresql?
On Tue, 2006-11-07 at 00:22 -0800, Joe Conway wrote:
Joe-
I almost sent you an off-list email before I posted because I just knew you'd know the answer.
Thank you.
-Reece
I think you want this:
http://bioconductor.org/packages/1.9/bioc/html/RdbiPgSQL.html
The bioconductor project is now maintaining RdbiPgSQL. I think many
people also use RODBC to connect R with Postgres.
Joe-
I almost sent you an off-list email before I posted because I just knew you'd know the answer.
Thank you.
-Reece
-- Reece Hart, http://harts.net/reece/, GPG:0x25EC91A0 |
Reece Hart wrote: > On Tue, 2006-11-07 at 00:22 -0800, Joe Conway wrote: > >> I think you want this: >> http://bioconductor.org/packages/1.9/bioc/html/RdbiPgSQL.html >> >> The bioconductor project is now maintaining RdbiPgSQL. I think many >> people also use RODBC to connect R with Postgres. > > I almost sent you an off-list email before I posted because I just knew > you'd know the answer. Wouldn't be a problem with me, but better to post so the answer gets into the archives for others to find later. Glad I could help. Joe