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Martin Møller Skarbiniks Pedersen

2017-Sep-08 08:48 UTC

[R] Optimize code to read text-file with digits

Hi,

  Every day I try to write some small R programs to improve my R-skills.
  Yesterday I wrote a small program to read the digits from "A Million
Random Digits" from RAND.
  My code works but it is very slow and I guess the code is not optimal.

The digits.txt file downloaded from
https://www.rand.org/pubs/monograph_reports/MR1418.html
contains 20000 lines which looks like this:
00000   10097 32533  76520 13586  34673 54876  80959 09117  39292 74945
00001   37542 04805  64894 74296  24805 24037  20636 10402  00822 91665
00002   08422 68953  19645 09303  23209 02560  15953 34764  35080 33606
00003   99019 02529  09376 70715  38311 31165  88676 74397  04436 27659
00004   12807 99970  80157 36147  64032 36653  98951 16877  12171 76833

My program which is slow looks like this:

filename <- "digits.txt"
lines <- readLines(filename)

numbers <- vector('numeric')
for (i in 1:length(lines)) {

    # remove first column
    lines[i] <- sub("[^ ]+ +","",lines[i])

    # remove spaces
    lines[i] <- gsub(" ","",lines[i])

    # split the characters and convert them into numbers
    numbers <- c(numbers,as.numeric(unlist(strsplit(lines[i],""))))
}

Thanks for any advice how this program can be improved.

Regards
Martin M. S. Pedersen

	[[alternative HTML version deleted]]

PIKAL Petr

2017-Sep-08 09:25 UTC

head link

[R] Optimize code to read text-file with digits

Hi

see in line
> -----Original Message-----
> From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of Martin
> Moller Skarbiniks Pedersen
> Sent: Friday, September 8, 2017 10:49 AM
> To: r-help at r-project.org
> Subject: [R] Optimize code to read text-file with digits
>
> Hi,
>
>   Every day I try to write some small R programs to improve my R-skills.
>   Yesterday I wrote a small program to read the digits from "A Million
Random
> Digits" from RAND.
>   My code works but it is very slow and I guess the code is not optimal.
>
> The digits.txt file downloaded from
> https://www.rand.org/pubs/monograph_reports/MR1418.html
> contains 20000 lines which looks like this:
> 00000   10097 32533  76520 13586  34673 54876  80959 09117  39292 74945
> 00001   37542 04805  64894 74296  24805 24037  20636 10402  00822 91665
> 00002   08422 68953  19645 09303  23209 02560  15953 34764  35080 33606
> 00003   99019 02529  09376 70715  38311 31165  88676 74397  04436 27659
> 00004   12807 99970  80157 36147  64032 36653  98951 16877  12171 76833
>
> My program which is slow looks like this:
>
> filename <- "digits.txt"
> lines <- readLines(filename)
why you do not read a file as a whole e.g. by

lines<-read.table("digits.txt")

After that you do not need for cycle (but maybe I misunderstand what you really
want)

remove first column

lines <- lines[,-1]

And now I am lost.
Do you want each row convert into a numeric vector? It probably exceed the
precision of biggest number allowed.

Do you want to split each column to 5 numeric columns?
you can use something like

outer(lines[,1], 10^c(4:0), function(a, b) a %/% b %% 10)

to split the first column.

Or do you want one big numeric vector from all your numbers?

here you need to read values as character variables

lines<-read.table("digits.txt", colClasses="character")
numbers<-as.numeric(unlist(strsplit(as.character(lines[1,]),"")))
changes first row to numeric vector.

Anyway, can you explain what is your final goal?

Cheers
Petr

>
> numbers <- vector('numeric')
> for (i in 1:length(lines)) {
>
>     # remove first column
>     lines[i] <- sub("[^ ]+ +","",lines[i])
>
>     # remove spaces
>     lines[i] <- gsub(" ","",lines[i])
>
>     # split the characters and convert them into numbers
>     numbers <-
c(numbers,as.numeric(unlist(strsplit(lines[i],""))))
> }
>
> Thanks for any advice how this program can be improved.
>
> Regards
> Martin M. S. Pedersen
>
>       [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> 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.
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Martin Møller Skarbiniks Pedersen

2017-Sep-08 09:58 UTC

head link

[R] Optimize code to read text-file with digits

On 8 September 2017 at 11:25, PIKAL Petr <petr.pikal at precheza.cz>
wrote:
> > Moller Skarbiniks Pedersen
> My program which is slow looks like this:
> >
> > filename <- "digits.txt"
> > lines <- readLines(filename)
>
> why you do not read a file as a whole e.g. by
>
> lines<-read.table("digits.txt")
>
Good idea.
>
> And now I am lost.

[...]

>  Or do you want one big numeric vector from all your numbers?
here you need to read values as character variables>
Yes. That's what I am looking for.
>
> lines<-read.table("digits.txt",
colClasses="character")
>
numbers<-as.numeric(unlist(strsplit(as.character(lines[1,]),"")))
> changes first row to numeric vector.
>
>Do I still need to loop through all lines?
It is maybe even slower now.

numbers <- vector('numeric')
for (i in 1:nrows(lines)) {
  numbers <- c(numbers, as.numeric(unlist(strsplit(as.
character(lines[i,]),""))))
}

> Anyway, can you explain what is your final goal?
>
>A numeric vector of length 1 million. Each element should be one digit.

> Cheers
> Petr
>
>Thanks.
/Martin

	[[alternative HTML version deleted]]

peter dalgaard

2017-Sep-08 12:03 UTC

head link

[R] Optimize code to read text-file with digits

Simplest version that I can think of:

x <- scan("~/Downloads/digits.txt")
x <- x[-seq(1,220000,11)]
length(x) # 200000
hist(x)

Now, because it's Friday: 

How does one work out the theoretical distribution of the following table?
> table(table(factor(x,levels=0:99999)))
    0     1     2     3     4     5     6     7     8     9    10    11 
13497 27113 27010 18116  9122  3466  1186   366    99    22     1     1 
   12 
    1 

(I.e., out of 200000 random 5 digit numbers, 13497 numbers never occurred, 27113
numbers exactly once, and ... and 1 number occurred 12 times.)

-pd

> On 8 Sep 2017, at 10:48 , Martin M?ller Skarbiniks Pedersen <traxplayer
at gmail.com> wrote:
> 
> Hi,
> 
>  Every day I try to write some small R programs to improve my R-skills.
>  Yesterday I wrote a small program to read the digits from "A Million
> Random Digits" from RAND.
>  My code works but it is very slow and I guess the code is not optimal.
> 
> The digits.txt file downloaded from
> https://www.rand.org/pubs/monograph_reports/MR1418.html
> contains 20000 lines which looks like this:
> 00000   10097 32533  76520 13586  34673 54876  80959 09117  39292 74945
> 00001   37542 04805  64894 74296  24805 24037  20636 10402  00822 91665
> 00002   08422 68953  19645 09303  23209 02560  15953 34764  35080 33606
> 00003   99019 02529  09376 70715  38311 31165  88676 74397  04436 27659
> 00004   12807 99970  80157 36147  64032 36653  98951 16877  12171 76833
> 
> My program which is slow looks like this:
> 
> filename <- "digits.txt"
> lines <- readLines(filename)
> 
> numbers <- vector('numeric')
> for (i in 1:length(lines)) {
> 
>    # remove first column
>    lines[i] <- sub("[^ ]+ +","",lines[i])
> 
>    # remove spaces
>    lines[i] <- gsub(" ","",lines[i])
> 
>    # split the characters and convert them into numbers
>    numbers <-
c(numbers,as.numeric(unlist(strsplit(lines[i],""))))
> }
> 
> Thanks for any advice how this program can be improved.
> 
> Regards
> Martin M. S. Pedersen
> 
> 	[[alternative HTML version deleted]]
> 
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> 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.
-- 
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd.mes at cbs.dk  Priv: PDalgd at gmail.com

peter dalgaard

2017-Sep-08 12:37 UTC

head link

[R] Optimize code to read text-file with digits

> On 8 Sep 2017, at 14:03 , peter dalgaard <pdalgd at gmail.com> wrote:
> 
> x <- scan("~/Downloads/digits.txt")
> x <- x[-seq(1,220000,11)]
...and, come to think of it, if you really want the 1000000 random digits:

xx <- c(outer(x,10^(0:4), "%/%")) %% 10 

-- 
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd.mes at cbs.dk  Priv: PDalgd at gmail.com

William Dunlap

2017-Sep-08 15:28 UTC

head link

[R] Optimize code to read text-file with digits

Remove the for loop and all the [i]'s in your code and it will probably go
faster.  I.e., change

f0 <- function (lines)
{
    numbers <- vector("numeric")
    for (i in 1:length(lines)) {
        lines[i] <- sub("[^ ]+ +", "", lines[i])
        lines[i] <- gsub(" ", "", lines[i])
        numbers <- c(numbers, as.numeric(unlist(strsplit(lines[i],
            ""))))
    }
    numbers
}

to

f1 <- function (lines)
{
    lines <- sub("[^ ]+ +", "", lines)
    lines <- gsub(" ", "", lines)
    as.numeric(unlist(strsplit(lines, "")))
}

I haven't measured it, but the big time sink may come from f0 growing the
'numbers' vector bit by bit.  That can cause a lot of reallocations and
garbage collections.

Bill Dunlap
TIBCO Software
wdunlap tibco.com

On Fri, Sep 8, 2017 at 1:48 AM, Martin M?ller Skarbiniks Pedersen <
traxplayer at gmail.com> wrote:
> Hi,
>
>   Every day I try to write some small R programs to improve my R-skills.
>   Yesterday I wrote a small program to read the digits from "A Million
> Random Digits" from RAND.
>   My code works but it is very slow and I guess the code is not optimal.
>
> The digits.txt file downloaded from
> https://www.rand.org/pubs/monograph_reports/MR1418.html
> contains 20000 lines which looks like this:
> 00000   10097 32533  76520 13586  34673 54876  80959 09117  39292 74945
> 00001   37542 04805  64894 74296  24805 24037  20636 10402  00822 91665
> 00002   08422 68953  19645 09303  23209 02560  15953 34764  35080 33606
> 00003   99019 02529  09376 70715  38311 31165  88676 74397  04436 27659
> 00004   12807 99970  80157 36147  64032 36653  98951 16877  12171 76833
>
> My program which is slow looks like this:
>
> filename <- "digits.txt"
> lines <- readLines(filename)
>
> numbers <- vector('numeric')
> for (i in 1:length(lines)) {
>
>     # remove first column
>     lines[i] <- sub("[^ ]+ +","",lines[i])
>
>     # remove spaces
>     lines[i] <- gsub(" ","",lines[i])
>
>     # split the characters and convert them into numbers
>     numbers <-
c(numbers,as.numeric(unlist(strsplit(lines[i],""))))
> }
>
> Thanks for any advice how this program can be improved.
>
> Regards
> Martin M. S. Pedersen
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> 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]]

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