Hi Henrik, I am using your saveObject/loadObject to handle over 1000 matrices. It worked beautifully. Because I need to load those matrices often for evaluating a few functions on them and those matrices do not fit all in memory at once, is there a way to speed up the loading part? I tried save all the binary files to /dev/shm (shared memory section in linux) but the speed of loadObject on /dev/shm remains the same as on the disk.
Thanks Hao -----Original Message----- From: henrik.bengts...@gmail.com [mailto:henrik.bengts...@gmail.com] On Behalf Of Henrik Bengtsson Sent: Monday, November 02, 2009 12:34 AM To: David Winsemius Cc: r-help@r-project.org; jeffc Subject: Re: [R] save an object by dynamicly created name On Sun, Nov 1, 2009 at 9:18 PM, David Winsemius <dwinsem...@comcast.net> wrote: > > On Nov 1, 2009, at 11:28 PM, Henrik Bengtsson wrote: > >> On Sun, Nov 1, 2009 at 7:48 PM, David Winsemius <dwinsem...@comcast.net> >> wrote: >>> >>> On Nov 1, 2009, at 10:16 PM, Henrik Bengtsson wrote: >>> >>>> path <- "data"; >>>> dir.create(path); >>>> >>>> for (i in 1:10) { >>>> m <- i:5; >>>> filename <- sprintf("m%02d.Rbin", i); >>>> pathname <- file.path(path, filename); >>>> save(m, file=pathname); >>>> } >>>> >>> >>> That would result in each of the ten files containing an object with the >>> same name == "m". (Also on my system R data files have type Rdta.) So I >>> thought what was requested might have been a slight mod: >>> >>> path <- "~/"; >>> dir.create(path); >>> >>> for (i in 1:10) { >>> assign( paste("m", i, sep=""), i:5) >>> filename <- sprintf("m%02d.Rdta", i) >>> pathname <- file.path(path, filename) >>> obj =get(paste("m", i, sep="")) >>> save(obj, file=pathname) >>> } >> >> Then a more convenient solution is to use saveObject() and >> loadObject() of R.utils. saveObject() does not save the name of the >> object save. > > The OP asked for this outcome : > > " I would like to save m as m1, m2, m3 ..., > to file /home/data/m1, /home/data/m2, home/data/m3, ..." > > >> If you want to save multiple objects, the wrap them up >> in a list. > > I agree that a list would makes sense if it were to be stored in one file , > although it was not what requested. That comment was not for the OP, but for saveObject()/loadObject() in general. > But wouldn't that require assign()-ing a name before list()-wrapping? Nope, the whole point of using saveObject()/loadObject() is to save the objects/values without their names that you happens to choose in the current session, and to avoid overwriting existing ones in your next session. My example could also have been: library("R.utils"); saveObject(list(a=1,b=LETTERS,c=Sys.time()), file="foo.Rbin"); y <- loadObject("foo.Rbin"); z <- loadObject("foo.Rbin"); stopifnot(identical(y,z)); If you really want to attach the elements of the saved list, do: attachLocally(loadObject("foo.Rbin")); > str(a) num 1 > str(b) chr [1:26] "A" "B" "C" "D" "E" "F" "G" "H" "I" "J" ... > str(c) POSIXct[1:1], format: "2009-11-01 21:30:41" > > I suppose we ought to mention that the use of assign to create a variable is > a FAQ ... 7.21? Yep, I have now referred to it a sufficient number of times > to refer to it by number. > > http://cran.r-project.org/doc/FAQ/R-FAQ.html#How-can-I-turn-a-string-into-a- variable_003f My personal take on assign() and get() is that if you find yourself using them (at this level), there is a good chance there exists a better solution that you should use instead. My $.02 /H > > -- > David > >> loadObject() does not assign variable, but instead return >> them. Example: >> >> library("R.utils"); >> x <- list(a=1,b=LETTERS,c=Sys.time()); >> saveObject(x, file="foo.Rbin"); >> y <- loadObject("foo.Rbin"); >> stopifnot(identical(x,y)); > >> >> So, for the original example, I'd recommend: >> >> library("R.utils"); >> path <- "data"; >> mkdirs(path); >> >> for (i in 1:10) { >> m <- i:5; >> filename <- sprintf("m%02d.Rbin", i); >> saveObject(m, file=filename, path=path); >> } >> >> and loading the objects back as: >> >> for (i in 1:10) { >> filename <- sprintf("m%02d.Rbin", i); >> m <- loadObject(filename, path=path); >> print(m); >> } >> /Henrik >> >>> >>> -- >>> David. >>> >>>> /H >>>> >>>> On Sun, Nov 1, 2009 at 6:53 PM, jeffc <h...@andrew.cmu.edu> wrote: >>>>> >>>>> Hi, >>>>> >>>>> I would like to save a few dynamically created objects to disk. The >>>>> following is the basic flow of the code segment >>>>> >>>>> for(i = 1:10) { >>>>> m = i:5 >>>>> save(m, file = ...) ## ??? >>>>> } >>>>> To distinguish different objects to be saved, I would like to save m as >>>>> m1, >>>>> m2, m3 ..., to file /home/data/m1, /home/data/m2, home/data/m3, ... >>>>> >>>>> I tried a couple of methods on translating between object names and >>>>> strings >>>>> (below) but couldn't get it to work. >>>>> https://stat.ethz.ch/pipermail/r-help/2008-November/178965.html >>>>> http://tolstoy.newcastle.edu.au/R/help/04/08/2673.html >>>>> >>>>> Any suggestions would be appreciated. >>>>> >>>>> thanks >>>>> >>>>> Hao >>>>> >>>>> -- >>>>> View this message in context: >>>>> >>>>> http://old.nabble.com/save-an-object-by-dynamicly-created-name-tp26155437p26 155437.html >>>>> Sent from the R help mailing list archive at Nabble.com. >>>>> >>>>> ______________________________________________ >>>>> 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. >>>>> >>>> >>>> ______________________________________________ >>>> 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. >>> >>> David Winsemius, MD >>> Heritage Laboratories >>> West Hartford, CT >>> >>> ______________________________________________ >>> 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. >>> > > David Winsemius, MD > Heritage Laboratories > West Hartford, CT > > ______________________________________________ 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.
