[STATSGRASS] Re: Connecting to databases on Windows using R

[Markus Neteler]

Craig,

it complains loudly even on Linux... sigh. Things changed again,
I'll have to update the indicated web page (how to use install.packages()
with bioconductor?).

Downloading and installing on command line should work (on Linux,
maybe even Cygwin).

Markus

On Thu, Mar 17, 2005 at 01:54:10PM -0700, Craig Aumann wrote:
> 
> Well I'm curious to know what R on Windows actually does with the
> following commands:
> 
> install.packages(contriburl="http://www.bioconductor.org/repository/devel/package/Source/","Rdbi")
> install.packages(contriburl="http://www.bioconductor.org/repository/devel/package/Source/","RdbiPgSQL")
> 
> Does it successully install the packages, or complain loudly?
> 
> 
> On Thu, 2005-03-17 at 13:30, Markus Neteler wrote:
> > Hi 
> > 
> > (for me) it's strange that Rdbi doesn't appear on CRAN but
> > I was already notified once not to discuss Rdbi questions on 
> > the R Mailing lists... (so better to ask here :-)
> > 
> > Anyway, I have compiled some usage instructions here:
> >  http://grass.itc.it/statsgrass/r_and_dbms.html
> > which should be more or less still valid. 
> > 
> > Maybe a bit helpful, also comparing speed of Rdbi and RODBC.
> > However, it doesn't cover MS-Win installation...
> > 
> > Best
> > 
> >  Markus
> > 
> > On Thu, Mar 17, 2005 at 11:33:02AM -0700, Craig Aumann wrote:
> > > See Teague's question below.  As a linux person, I don't know the answer
> > > to this so am forward this message to the list.  
> > > 
> > > Having looked also at  http://www.bioconductor.org/ - which links off of
> > > the main R web page, I see a Windows version of Rdbi (click "What is
> > > Bioconductor"  and scroll down till you find the heading: "Database
> > > Interaction").  I'm seeing a RDBI for Windows, but no windows version of
> > > RdbiPgsql which is a problem! 
> > > 
> > > Have you tried sending a message to the R-Help list about this - how do
> > > windows users access PGSQL databases from R?  (R website -> mailing
> > > lists.)  
> > > 
> > > On the CRAN site, just searching databases, I saw the following:
> > > DBI, RMySQL, RODBC, ROracle. Not sure if windows versions exist for any
> > > of these.   
> > > 
> > > Also have a look at the links in
> > > http://cran.r-project.org/doc/manuals/R-data.html .  
> > > 
> > > Afraid that's all I know about attaching to Databases on Windows - which
> > > ain't much I'm afraid. 
> > > 
> > > Cheers!
> > > Craig
> > > 
> > > 
> > > 
> > > 
> > > 
> > > 
> > > On Thu, 2005-03-17 at 10:40, Teague O'Mara wrote:
> > > > Hi Craig.  I came back across this email from awhile ago.  I'm attempting to
> > > > look at cluster of points in GRASS and have been using the script that Michael
> > > > Barton wrote, but I'd like to look at a few other things and it seems that using
> > > > R and my GRASS data will be much easier. I have been using R for basic
> > > > statistics, but am far from being fluent with it.  If you have a moment, can you
> > > > help me out with some R issues?  I'm using an XP machine with R 2.0.1.
> > > > 
> > > > I'm having a problem downloading and installing Rdbi and RdbiPgSQL.  I can't
> > > > find these two sets, or any SQL interface that will download from CRAN.  I was
> > > > able to download these directly from sourcforge (tar.gz format), but I'm not
> > > > sure what to do with them now.  Is it an issue with this version of R?
> > > > 
> > > > Thanks for any help you can offer.
> > > > 
> > > > Cheers--
> > > > Teague
> > > > 
> > > > 
> > > > 
> > > > Teague O'Mara
> > > > Department of Anthropology
> > > > Arizona State University
> > > > Box 872402
> > > > Tempe, AZ 85287-2402
> > > > 480.965.6213
> > > > 
> > > > 
> > > > Quoting Craig Aumann <caumann at ualberta.ca>:
> > > > 
> > > > > In glancing at your script, I wondered why you didn't just import the
> > > > > stuff into a statistical package like R and then use all the
> > > > > clustering
> > > > > routines it has.    See www.r-project.org
> > > > > 
> > > > > 
> > > > > 
> > > > > 
> > > > > ## Key commands in R are:
> > > > > 
> > > > > ## Load the packages to access the database, in particular the PgSQL
> > > > > ##
> > > > > database
> > > > > require(Rdbi)
> > > > > require(RdbiPgSQL)
> > > > > 
> > > > > ## Load some clustering routines
> > > > > 
> > > > > require(cluster)
> > > > > require(mclust)
> > > > > 
> > > > > 
> > > > > ### Connect to the database and read in a points data set "jogis"
> > > > > ## and read in the dataset "wells_att".  
> > > > > 
> > > > > 
> > > > > conn <- dbConnect(PgSQL(), dbname="jogis", user="caumann")
> > > > > wells <- dbReadTable(conn, "wells_att")
> > > > > dbDisconnect(conn)
> > > > > 
> > > > > ## Now you can apply any clustering or kernel smoothing technique you
> > > > > want to the dataset.  
> > > > > 
> > > > > If this is of any help, let me know and I can provide more details.  
> > > > > Cheers!
> > > > > Craig
> > > > > 
> > > > > 
> > > > 
> > > > 
> > > > 
> > > 
> > > _______________________________________________
> > > statsgrass mailing list
> > > statsgrass at grass.itc.it
> > > http://grass.itc.it/mailman/listinfo/statsgrass

-- 
Markus Neteler     <neteler itc it>       http://mpa.itc.it
ITC-irst -  Centro per la Ricerca Scientifica e Tecnologica
MPBA - Predictive Models for Biol. & Environ. Data Analysis
Via Sommarive, 18        -       38050 Povo (Trento), Italy