[R] Alternatives to merge for large data sets?

Prof Brian Ripley ripley at stats.ox.ac.uk
Thu Sep 7 10:57:58 CEST 2006

Which version of R?

Please try 2.4.0 alpha, as it has a different and more efficient 
algorithm for the case of 1-1 matches.

On Wed, 6 Sep 2006, Adam D. I. Kramer wrote:

> Hello,
> I am trying to merge two very large data sets, via
> pubbounds.prof <-
> merge(x=pubbounds,y=prof,by.x="user",by.y="userid",all=TRUE,sort=FALSE)
> which gives me an error of
> Error: cannot allocate vector of size 2962 Kb
> I am reasonably sure that this is correct syntax.
> The trouble is that pubbounds and prof are large; they are data frames which
> take up 70M and 11M respectively when saved as .Rdata files.
> I understand from various archive searches that "merge can't handle that,"
> because merge takes n^2 memory, which I do not have.

Not really true (it has been changed since those days).  Of course, if you 
have multiple matches it must do so.

> My question is whether there is an alternative to merge which would carry
> out the process in a slower, iterative manner...or if I should just bite the
> bullet, write.table, and use a perl script to do the job.
> Thankful as always,
> Adam D. I. Kramer

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

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