From ihaka@stat.auckland.ac.nz  Mon Apr 20 01:44:00 1998
From: ihaka@stat.auckland.ac.nz (Ross Ihaka)
Date: Mon, 20 Apr 1998 12:44:00 +1200 (NZST)
Subject: RFC: large database interface
In-Reply-To: <3539DBAD.76AD3DC1@delos.lf.net>
References: <Pine.LNX.3.96.980301144403.7917A-100000@buffy>
 <3539DBAD.76AD3DC1@delos.lf.net>
Message-ID: <199804200044.MAA16425@stat1.stat.auckland.ac.nz>

Egon Schmid writes:
 > Thomas Lumley wrote:
 > > 
 > > I have been playing with a large database interface for R, and have
 > > written one complete but useless demonstration and one incomplete but
 > > potentially useful example (with memory mapping of a fixed-format ASCII
 > > file). The idea is to make the file appear like a matrix or data frame but
 > > not have to read it into the R heap.
 > > 
 > > A description and code can be found at
 > > http://www.biostat.washington.edu/~thomas/Rdb.html
 > >                                           Rdb.nw  (noweb literate program)
 > >                                           Rdb.c
 > >                                           Rdb.R
 > > 
 > > Comments?

This looks very interesting.  It would be nice if the such an
interface were written in a way that could be customized to a variety
of applications.  Being able to read spreadsheets is one thing which
comes to mind.  It might be nice (for example) to have a rather
complex initialization procedure which inspects the dataset thoroughly
and determines things like variable types (if the database does not
contain this information).

Egon Schmid writes:
 > Well, there is a web interface through the Apache module PHP Hypertext
 > Preprocessor. At http://www.php.net/ there are plenty more database
 > interfaces.
 > 
 > Personaly I think it would a great idea to interface large datasets with
 > netCDF 
 >
 > "Why not use an existing database management system for storing
 > array-oriented data? Relational database software is not suitable for
 > the kinds of data access supported by the netCDF interface.
 > 

Hmm. Over the past week I have been looking at NetCDF because GMT
(The Generic Mapping Tools)
	http://www.soest.hawaii.edu/wessel/gmt.html
use NetCDF to store their maps.

[ The maps are rather better than the Becker and Wilks ones because
  they are based on the World Vector Shoreline as well as the CIA WDB
  that B&W use.  They also have the maps prepared pretty well for
  plotting.  The only place where B&W are better is in the naming
  of places ... ]

I wasn't thinking about pulling the data from these maps into R, but
rather just rendering them on a graphics device so that they could
then be added to.

I suspect that when I've done that I'll probably know enough to create
an R/NetCDF link, perhaps using a framework of the type Thomas
proposes.
	Ross
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RFC: large database interface
Ross Ihaka