[R] aggregate() runs out of memory

[Sam Steingold]

Thanks Steve,
what is the analogue of .N for min and max?
i.e., what is the data.table's version of
aggregate(infl$delay,by=list(infl$share.id),FUN=min)
aggregate(infl$delay,by=list(infl$share.id),FUN=max)
thanks!
Sam.

On Fri, Sep 14, 2012 at 3:40 PM, Steve Lianoglou
<mailinglist.honeypot at gmail.com> wrote:
> Hi,
>
> On Fri, Sep 14, 2012 at 3:26 PM, Sam Steingold <sds at gnu.org> wrote:
>> I have a large data.frame Z (2,424,185,944 bytes, 10,256,441 rows, 17 columns).
>> I want to get the result of
>> table(aggregate(Z$V1, FUN = length, by = list(id=Z$V2))$x)
>> alas, aggregate has been running for ~30 minute, RSS is 14G, VIRT is
>> 24.3G, and no end in sight.
>> both V1 and V2 are characters (not factors).
>> Is there anything I could do to speed this up?
>> Thanks.
>
> You might find you'll get a lot of mileage out of data.table when
> working with such large data.frames ...
>
> To get something close to what you're after, you can try:
>
> R> library(data.table)
> R> Z <- as.data.table(Z)
> R> setkeyv(Z, 'V2')
> R> agg <- Z[, list(count=.N), by='V2']
>
> From here you might
>
> R> tab1 <- table(agg$count)
>
> I think that'll get you where you want to be ... I'm ashamed to say
> that I haven't really done much w/ aggregate since I mostly have used
> plyr and data.table like stuff, so I might be missing your end goal --
> providing a reproducible example with a small data.frame from you can
> help here (for me at least).
>
> HTH,
> -steve
>
> --
> Steve Lianoglou
> Graduate Student: Computational Systems Biology
>  | Memorial Sloan-Kettering Cancer Center
>  | Weill Medical College of Cornell University
> Contact Info: http://cbio.mskcc.org/~lianos/contact



--
Sam Steingold <http://sds.podval.org> <http://www.childpsy.net/>