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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