[R] Speeding reading of a large file

Juliet Hannah juliet.hannah at gmail.com
Thu Dec 6 17:24:13 CET 2012


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.



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
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