I guess the mail list precludes attachments then, makes sense. I have sent the modified source directly to anyone who has asked.
I had a look at the light-weight data.frame class post (http://tolstoy.newcastle.edu.au/R/devel/05/05/0837.html) : > Now the transcript itself: > # the motivation: subscription of a data.frame is *much* (almost 20 times) slower than that of a list > # compare > n = 1e6 > i = seq(n) > x = data.frame(a=seq(n), b=seq(n)) > system.time(x[i,], gcFirst=TRUE) [1] 1.01 0.14 1.14 0.00 0.00 > > x = list(a=seq(n), b=seq(n)) > system.time(lapply(x, function(col) col[i]), gcFirst=TRUE) [1] 0.06 0.00 0.06 0.00 0.00 > > # the solution: define methods for the light-weight data.frame class > lwdf = function(...) structure(list(...), class = "lwdf") > ... But if I have understood correctly I think the time difference here is just down to the rownames. The rownames are 1:n stored in character form. This takes the most time and space in this example, but are never used. I'm not sure why 1:n in character form would ever be useful in fact. Running the example above with my modifications appears to fix the problem ie negligible time difference. I needed to make a one line change to [.data.frame, and I've sent that to anyone who requested the code. I can see the problem : > apropos("data.frame") [1] "[.data.frame" "as.matrix.data.frame" "data.frame" "dim.data.frame" [5] "format.data.frame" "print.data.frame" ".__C__data.frame" "aggregate.data.frame" [9] "$<-.data.frame" "Math.data.frame" "Ops.data.frame" "Summary.data.frame" [13] "[.data.frame" "[<-.data.frame" "[[.data.frame" "[[<-.data.frame" [17] "as.data.frame" "as.data.frame.AsIs" "as.data.frame.Date" "as.data.frame.POSIXct" [21] "as.data.frame.POSIXlt" "as.data.frame.array" "as.data.frame.character" "as.data.frame.complex" [25] "as.data.frame.data.frame" "as.data.frame.default" "as.data.frame.factor" "as.data.frame.integer" [29] "as.data.frame.list" "as.data.frame.logical" "as.data.frame.matrix" "as.data.frame.model.matrix" [33] "as.data.frame.numeric" "as.data.frame.ordered" "as.data.frame.package_version" "as.data.frame.raw" [37] "as.data.frame.table" "as.data.frame.ts" "as.data.frame.vector" "as.list.data.frame" [41] "as.matrix.data.frame" "by.data.frame" "cbind.data.frame" "data.frame" [45] "dim.data.frame" "dimnames.data.frame" "dimnames<-.data.frame" "duplicated.data.frame" [49] "format.data.frame" "is.data.frame" "is.na.data.frame" "mean.data.frame" [53] "merge.data.frame" "print.data.frame" "rbind.data.frame" "row.names.data.frame" [57] "row.names<-.data.frame" "rowsum.data.frame" "split.data.frame" "split<-.data.frame" [61] "stack.data.frame" "subset.data.frame" "summary.data.frame" "t.data.frame" [65] "transform.data.frame" "unique.data.frame" "unstack.data.frame" "xpdrows.data.frame" > But I think the changes would be quick to make. Is anything else effected? Do any test suites exist to confirm R hasn't broken? On the face of it allowing data frames to have null row names seems a small change, and would make them consistent with matrices, with large time and space benefits. However, I can see the argument for a new class instead for safety. Whats the consenus? -----Original Message----- From: Hin-Tak Leung [mailto:[EMAIL PROTECTED] Sent: 09 December 2005 18:41 To: Gabor Grothendieck Cc: Matthew Dowle; r-devel@r-project.org; Peter Dalgaard Subject: Re: [Rd] [R] data.frame() size Gabor Grothendieck wrote: > There was nothing attached in the copy that came through > to me. I like to see that patch also. > By the way, there was some discussion earlier this year > on a light-weight data.frame class but I don't think anyone ever > posted any code. It may have been me. I am working on a bit-packed data.frame which only uses 2-bits per unit of data, so it is 4 units per RAWSXP. (work in progress, nothing to show). So I am very interested to see the patch. Yes, I took a couple of weeks reading/learning where have all the memory gone in data.frame. The rowname/column names allocation is a bit stupid. Each rowname and each column name is a full R object, so there is a 32(or 28) byte overhead just from managing that, before the STRSXP for the actual string, which is another X bytes. so for an 1 x N data.frame with integers for content, the the content is 4-byte * N, but the rowname/columnname is 32 * N -ish. (a 9x increase). Word is 32-bit on most people's machines, and I am counting the extra one from which you have to keep the address of each SEXPREC somewhere, so it is 7+1 = 8, if I understand it correctly. Here is the relevant comment, quoted verbatum from around line 225 of "src/include/Rinternals.h": /* The generational collector uses a reduced version of SEXPREC as a header in vector nodes. The layout MUST be kept consistent with the SEXPREC definition. The standard SEXPREC takes up 7 words on most hardware; this reduced version should take up only 6 words. In addition to slightly reducing memory use, this can lead to more favorable data alignment on 32-bit architectures like the Intel Pentium III where odd word alignment of doubles is allowed but much less efficient than even word alignment. */ Hin-Tak Leung > On 12/9/05, Matthew Dowle <[EMAIL PROTECTED]> wrote: > >>Hi, >> >>Please see below for post on r-help regarding data.frame() and the >>possibility of dropping rownames, for space and time reasons. I've >>made some changes, attached, and it seems to be working well. I see >>the expected space (90% saved) and time (10 times faster) savings. >>There are no doubt some bugs, and needs more work and testing, but I >>thought I would post first at this stage. >> >>Could some changes along these lines be made to R ? I'm happy to help >>with testing and further work if required. In the meantime I can work >>with overloaded functions which fixes the problems in my case. >> >>Functions effected : >> >> dim.data.frame >> format.data.frame >> print.data.frame >> data.frame >> [.data.frame >> as.matrix.data.frame >> >>Modified source code attached. >> >>Regards, >>Matthew >> >> >>-----Original Message----- >>From: Matthew Dowle >>Sent: 09 December 2005 09:44 >>To: 'Peter Dalgaard' >>Cc: 'r-help@stat.math.ethz.ch' >>Subject: RE: [R] data.frame() size >> >> >> >>That explains it. Thanks. I don't need rownames though, as I'll only >>ever use integer subscripts. Is there anyway to drop them, or even >>better not create them in the first place? The memory saved (90%) by >>not having them and 10 times speed up would be very useful. I think I >>need a data.frame rather than a matrix because I have columns of >>different types in real life. >> >> >>>rownames(d) = NULL >> >>Error in "dimnames<-.data.frame"(`*tmp*`, value = list(NULL, c("a", "b" : >> invalid 'dimnames' given for data frame >> >> >>-----Original Message----- >>From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of >>Peter Dalgaard >>Sent: 08 December 2005 18:57 >>To: Matthew Dowle >>Cc: 'r-help@stat.math.ethz.ch' >>Subject: Re: [R] data.frame() size >> >> >>Matthew Dowle <[EMAIL PROTECTED]> writes: >> >> >>>Hi, >>> >>>In the example below why is d 10 times bigger than m, according to >>>object.size ? It also takes around 10 times as long to create, which >>>fits with object.size() being truthful. gcinfo(TRUE) also indicates >>>a great deal more garbage collector activity caused by data.frame() >>>than matrix(). >>> >>>$ R --vanilla >>>.... >>> >>>>nr = 1000000 >>>>system.time(m<<-matrix(integer(1), nrow=nr, ncol=2)) >>> >>>[1] 0.22 0.01 0.23 0.00 0.00 >>> >>>>system.time(d<<-data.frame(a=integer(nr), b=integer(nr))) >>> >>>[1] 2.81 0.20 3.01 0.00 0.00 # 10 times longer >>> >>> >>>>dim(m) >>> >>>[1] 1000000 2 >>> >>>>dim(d) >>> >>>[1] 1000000 2 # same dimensions >>> >>> >>>>storage.mode(m) >>> >>>[1] "integer" >>> >>>>sapply(d, storage.mode) >>> >>> a b >>>"integer" "integer" # same storage.mode >>> >>> >>>>object.size(m)/1024^2 >>> >>>[1] 7.629616 >>> >>>>object.size(d)/1024^2 >>> >>>[1] 76.29482 # but 10 times bigger >>> >>> >>>>sum(sapply(d, object.size))/1024^2 >>> >>>[1] 7.629501 # or is it ? If its not >>>really 10 times bigger, why 10 times longer above ? >> >>Row names!! >> >> >> >>>r <- as.character(1:1e6) >>>object.size(r) >> >>[1] 72000056 >> >>>object.size(r)/1024^2 >> >>[1] 68.6646 >> >>'nuff said? >> >>-- >> O__ ---- Peter Dalgaard Øster Farimagsgade 5, Entr.B >> c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K >> (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 >>~~~~~~~~~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 >> >> >> >> >>______________________________________________ >>R-devel@r-project.org mailing list >>https://stat.ethz.ch/mailman/listinfo/r-devel >> >> >> > > > ______________________________________________ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
