Hi, On Fri, Sep 14, 2012 at 4:26 PM, Dennis Murphy <djmu...@gmail.com> wrote: > Hi: > > This should give you some idea of what Steve is talking about: > > library(data.table) > dt <- data.table(x = sample(100000, 10000000, replace = TRUE), > y = rnorm(10000000), key = "x") > dt[, .N, by = x] > system.time(dt[, .N, by = x]) > > ...on my system, dual core 8Gb RAM running Win7 64-bit, >> system.time(dt[, .N, by = x]) > user system elapsed > 0.12 0.02 0.14 > > .N is an optimized function to find the number of rows of each data subset. > Much faster than aggregate(). It might take a little longer because you > have more columns that suck up space, but you get the idea. It's also about > 5-6 times faster if you set a key variable in the data table than if you > don't.
Well done, sir! (slight critique in that .N isn't a function, it's just a variable that is constantly reset within each by-subset/group) Also, don't forget to use the .SDcols parameter in [.data.table if you plan on only using a subset of the columns in side your "by" stuff. There's lots of documentation in the package `?data.table` and the vignettes/FAQ to help you tweak your usage, if you decide to take data.table route. HTH, -steve > > Dennis > > On Fri, Sep 14, 2012 at 12:26 PM, Sam Steingold <s...@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. >> >> -- >> Sam Steingold (http://sds.podval.org/) on Ubuntu 12.04 (precise) X >> 11.0.11103000 >> http://www.childpsy.net/ http://www.PetitionOnline.com/tap12009/ >> http://dhimmi.com http://think-israel.org http://iris.org.il >> WinWord 6.0 UNinstall: Not enough disk space to uninstall WinWord >> >> ______________________________________________ >> 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 >> and provide commented, minimal, self-contained, reproducible code. >> > > [[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 > and provide commented, minimal, self-contained, reproducible code. -- 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 ______________________________________________ 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 and provide commented, minimal, self-contained, reproducible code.
