[R] Speeding reading of a large file

[Juliet Hannah]

Thanks, it does help. Is it possible to elaborate on how specifically
why this syntax
preserves dimensions. It this correct to just say that even though
lapply returns a list, x[] forces x to have the
same dimensions?

On Thu, Dec 6, 2012 at 11:53 AM, Rui Barradas <ruipbarradas at sapo.pt> wrote:
> Hello,
>
> Because x[] keeps the dimensions, unlike just x.
>
> Hope this helps,
>
> Rui Barradas
> Em 06-12-2012 16:24, Juliet Hannah escreveu:
>
>> All,
>>
>> Can someone describe what
>>
>>   x[]             <- lapply(x, as.numeric)
>>
>> I see that it is putting the list elements into a data frame. The
>> results for lapply are a list, so how does this become
>> a data frame.
>>
>> Thanks,
>>
>> Juliet
>>
>>
>> On Mon, Dec 3, 2012 at 5:49 PM, Fisher Dennis <fisher at plessthan.com>
>> wrote:
>>>
>>> Colleagues,
>>>
>>> This past week, I asked the following question:
>>>
>>>          I have a file that looks that this:
>>>
>>>          TABLE NO.  1
>>>           PTID        TIME        AMT         FORM        PERIOD
>>> IPRED       CWRES       EVID        CP          PRED        RES         WRES
>>>            2.0010E+03  3.9375E-01  5.0000E+03  2.0000E+00  0.0000E+00
>>> 0.0000E+00  0.0000E+00  1.0000E+00  0.0000E+00  0.0000E+00 0.0000E+00
>>> 0.0000E+00
>>>            2.0010E+03  8.9583E-01  5.0000E+03  2.0000E+00  0.0000E+00
>>> 3.3389E+00  0.0000E+00  1.0000E+00  0.0000E+00  3.5321E+00 0.0000E+00
>>> 0.0000E+00
>>>            2.0010E+03  1.4583E+00  5.0000E+03  2.0000E+00  0.0000E+00
>>> 5.8164E+00  0.0000E+00  1.0000E+00  0.0000E+00  5.9300E+00 0.0000E+00
>>> 0.0000E+00
>>>            2.0010E+03  1.9167E+00  5.0000E+03  2.0000E+00  0.0000E+00
>>> 8.3633E+00  0.0000E+00  1.0000E+00  0.0000E+00  8.7011E+00 0.0000E+00
>>> 0.0000E+00
>>>            2.0010E+03  2.4167E+00  5.0000E+03  2.0000E+00  0.0000E+00
>>> 1.0092E+01  0.0000E+00  1.0000E+00  0.0000E+00  1.0324E+01 0.0000E+00
>>> 0.0000E+00
>>>            2.0010E+03  2.9375E+00  5.0000E+03  2.0000E+00  0.0000E+00
>>> 1.1490E+01  0.0000E+00  1.0000E+00  0.0000E+00  1.1688E+01 0.0000E+00
>>> 0.0000E+00
>>>            2.0010E+03  3.4167E+00  5.0000E+03  2.0000E+00  0.0000E+00
>>> 1.2940E+01  0.0000E+00  1.0000E+00  0.0000E+00  1.3236E+01 0.0000E+00
>>> 0.0000E+00
>>>            2.0010E+03  4.4583E+00  5.0000E+03  2.0000E+00  0.0000E+00
>>> 1.1267E+01  0.0000E+00  1.0000E+00  0.0000E+00  1.1324E+01 0.0000E+00
>>> 0.0000E+00
>>>
>>>          The file is reasonably large (> 10^6 lines) and the two line
>>> header is repeated periodically in the file.
>>>          I need to read this file in as a data frame.  Note that the
>>> number of columns, the column headers, and the number of replicates of the
>>> headers are not known in advance.
>>>
>>> I received a number of replies, many of them quite useful.  Of these, one
>>> beat out all the others in my benchmarking using files ranging from 10^5 to
>>> 10^6 lines.
>>> That version, provided by Jim Holtman, was:
>>>          x               <- read.table(FILE, as.is = TRUE, skip=1,
>>> fill=TRUE, header = TRUE)
>>>          x[]             <- lapply(x, as.numeric)
>>>          x               <- x[!is.na(x[,1]), ]
>>>
>>> Other versions involved readLines, following by edits, following by cat
>>> (or write) to a temp file, then read.table again.
>>> The overhead with invoking readLines, write/cat, and read.table was
>>> substantially larger than the strategy of read.table / as.numeric / indexing
>>>
>>> Thanks for the input from many folks.
>>>
>>> Dennis
>>>
>>> Dennis Fisher MD
>>> P < (The "P Less Than" Company)
>>> Phone: 1-866-PLessThan (1-866-753-7784)
>>> Fax: 1-866-PLessThan (1-866-753-7784)
>>> www.PLessThan.com
>>>
>>> ______________________________________________
>>> R-help at 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 at 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.
>
>