Also instead of 'splitting' the data frame, I split the indices and then use
those to access the information in the original dataframe.
On Tue, Dec 8, 2009 at 9:54 PM, Mark Kimpel <mwkim...@gmail.com> wrote:
> Hadley, Just as you were apparently writing I had the same thought and did
> exactly what you suggested, converting all columns except the one that I
> want split to character. Executed almost instantaneously without problem.
> Thanks! Mark
>
> Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry
> Indiana University School of Medicine
>
> 15032 Hunter Court, Westfield, IN 46074
>
> (317) 490-5129 Work, & Mobile & VoiceMail
> (317) 399-1219 Skype No Voicemail please
>
>
> On Tue, Dec 8, 2009 at 10:48 PM, hadley wickham <h.wick...@gmail.com>
> wrote:
>
> > Hi Mark,
> >
> > Why are you using factors? I think for this case you might find
> > characters are faster and more space efficient.
> >
> > Alternatively, you can have a look at the plyr package which uses some
> > tricks to keep memory usage down.
> >
> > Hadley
> >
> > On Tue, Dec 8, 2009 at 9:46 PM, Mark Kimpel <mwkim...@gmail.com> wrote:
> > > Charles, I suspect your are correct regarding copying of the
> attributes.
> > > First off, selectSubAct.df is my "real" data, which turns out to be of
> > the
> > > same dim() as myDataFrame below, but each column is make up of strings,
> > not
> > > simple letters, and there are many levels in each column, which I did
> not
> > > properly duplicate in my first example. I have ammended that below and
> > with
> > > the split the new object size is now not 10X the size of the original,
> > but
> > > 100X. My "real" data is even more complex than this, so I suspect that
> is
> > > where the problem lies. I need to search for a better solution to my
> > problem
> > > than split, for which I will start a separate thread if I can't figure
> > > something out.
> > >
> > > Thanks for pointing me in the right direction,
> > >
> > > Mark
> > >
> > > myDataFrame <- data.frame(matrix(paste("The rain in Spain",
> > > as.character(1:1400), sep = "."), ncol = 7, nrow = 399000))
> > > mySplitVar <- factor(paste("Rainy days and Mondays",
> > as.character(1:1400),
> > > sep = "."))
> > > myDataFrame <- cbind(myDataFrame, mySplitVar)
> > > object.size(myDataFrame)
> > > ## 12860880 bytes # ~ 13MB
> > > myDataFrame.split <- split(myDataFrame, myDataFrame$mySplitVar)
> > > object.size(myDataFrame.split)
> > > ## 1,274,929,792 bytes ~ 1.2GB
> > > object.size(selectSubAct.df)
> > > ## 52,348,272 bytes # ~ 52MB
> > > Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry
> > > Indiana University School of Medicine
> > >
> > > 15032 Hunter Court, Westfield, IN 46074
> > >
> > > (317) 490-5129 Work, & Mobile & VoiceMail
> > > (317) 399-1219 Skype No Voicemail please
> > >
> > >
> > > On Tue, Dec 8, 2009 at 10:22 PM, Charles C. Berry <
> cbe...@tajo.ucsd.edu
> > >wrote:
> > >
> > >> On Tue, 8 Dec 2009, Mark Kimpel wrote:
> > >>
> > >> I'm having trouble using split on a very large data-set with ~1400
> > levels
> > >>> of
> > >>> the factor to be split. Unfortunately, I can't reproduce it with the
> > >>> simple
> > >>> self-contained example below. As you can see, splitting the
> artificial
> > >>> dataframe of size ~13MB results in a split dataframe of ~ 144MB, with
> > an
> > >>> increase memory allocation of ~10 fold for the split object. If split
> > >>> scales
> > >>> linearly, then my actual 52MB dataframe should be easily handled by
> my
> > >>> 12GB
> > >>> of RAM, but it is not. instead, when I try to split selectSubAct.df
> on
> > one
> > >>> of its factors with 1473 levels, my memory is slowly gobbled up (plus
> 3
> > GB
> > >>> of swap) until I cancel the operation.
> > >>>
> > >>> Any ideas on what might be happening? Thanks, Mark
> > >>>
> > >>
> > >> Each element of myDataFrame.split contains a copy of the attributes of
> > the
> > >> parent data.frame.
> > >>
> > >> And probably it does scale linearly. But the scaling factor depends on
> > the
> > >> size of the attributes that get copied, I guess.
> > >>
> > >>
> > >>
> > >>
> > >>> myDataFrame <- data.frame(matrix(LETTERS, ncol = 7, nrow = 399000))
> > >>> mySplitVar <- factor(as.character(1:1400))
> > >>> myDataFrame <- cbind(myDataFrame, mySplitVar)
> > >>> object.size(myDataFrame)
> > >>> ## 12860880 bytes # ~ 13MB
> > >>> myDataFrame.split <- split(myDataFrame, myDataFrame$mySplitVar)
> > >>> object.size(myDataFrame.split)
> > >>> ## 144524992 bytes # ~ 144MB
> > >>>
> > >>
> > >> Note:
> > >>
> > >> only.attr <- lapply(myDataFrame.split,function(x)
> sapply(x,attributes))
> > >>>
> > >>>
> >
> (object.size(myDataFrame.split)-object.size(myDataFrame))/object.size(only.attr)
> > >>>
> > >> 1.03726179240978 bytes
> > >>
> > >>
> > >>>
> > >>
> > >> object.size(selectSubAct.df)
> > >>> ## 52,348,272 bytes # ~ 52MB
> > >>>
> > >>
> > >> What was this??
> > >>
> > >>
> > >> Chuck
> > >>
> > >>
> > >>> sessionInfo()
> > >>>>
> > >>> R version 2.10.0 Patched (2009-10-27 r50222)
> > >>> x86_64-unknown-linux-gnu
> > >>>
> > >>> locale:
> > >>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
> > >>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
> > >>> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
> > >>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
> > >>> [9] LC_ADDRESS=C LC_TELEPHONE=C
> > >>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> > >>>
> > >>> attached base packages:
> > >>> [1] stats graphics grDevices datasets utils methods base
> > >>>
> > >>> loaded via a namespace (and not attached):
> > >>> [1] tools_2.10.0
> > >>>
> > >>> Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry
> > >>> Indiana University School of Medicine
> > >>>
> > >>> 15032 Hunter Court, Westfield, IN 46074
> > >>>
> > >>> (317) 490-5129 Work, & Mobile & VoiceMail
> > >>> (317) 399-1219 Skype No Voicemail please
> > >>>
> > >>> [[alternative HTML version deleted]]
> > >>>
> > >>>
> > >>> ______________________________________________
> > >>> R-help@r-project.org mailing list
> > >>> https://stat.ethz.ch/mailman/listinfo/r-help
> > >>> PLEASE do read the posting guide
> > >>> http://www.R-project.org/posting-guide.html<http://www.r-project.org/posting-guide.html>
> > >>> and provide commented, minimal, self-contained, reproducible code.
> > >>>
> > >>>
> > >> Charles C. Berry (858) 534-2098
> > >> Dept of Family/Preventive
> > >> Medicine
> > >> E mailto:cbe...@tajo.ucsd.edu UC San Diego
> > >> http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego
> > 92093-0901
> > >>
> > >>
> > >>
> > >
> > > [[alternative HTML version deleted]]
> > >
> > > ______________________________________________
> > > R-help@r-project.org mailing list
> > > https://stat.ethz.ch/mailman/listinfo/r-help
> > > PLEASE do read the posting guide
> > http://www.R-project.org/posting-guide.html<http://www.r-project.org/posting-guide.html>
> > > and provide commented, minimal, self-contained, reproducible code.
> > >
> >
> >
> >
> > --
> > http://had.co.nz/
> >
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html<http://www.r-project.org/posting-guide.html>
> and provide commented, minimal, self-contained, reproducible code.
>
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem that you are trying to solve?
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and provide commented, minimal, self-contained, reproducible code.
