Speeding reading of a large file

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