Re: [Rd] [R] data.frame() size

From: Matthew Dowle <mdowle_at_concordiafunds.com>
Date: Mon 12 Dec 2005 - 11:34:31 GMT

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:hin-tak.leung@cimr.cam.ac.uk] 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 <mdowle@concordiafunds.com> 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: pd@pubhealth.ku.dk [mailto:pd@pubhealth.ku.dk] 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 <mdowle@concordiafunds.com> 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             ุster Farimagsgade 5, Entr.B
>> c/ /'_ --- Dept. of Biostatistics     PO Box 2099, 1014 Cph. K
>> (*) \(*) -- University of Copenhagen   Denmark          Ph:  (+45)
35327918
>>~~~~~~~~~~ - (p.dalgaard@biostat.ku.dk)                  FAX: (+45)
35327907
>>
>>
>>
>>
>>______________________________________________
>>R-devel@r-project.org mailing list 
>>https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>>
>>

>
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