[R] speeding read.table

[Fisher Dennis]

R 2.15.1
OS X

Colleagues,

I am reading a 1 GB file into R using read.table.  The file consists of 100 tables, each of which is headed by two lines of characters.  
The first of these lines is:
	TABLE NO.  1
The second is a list of column headers.

For example:
TABLE NO.  1
 COL1        COL2        COL3        COL4        COL5        COL6        COL7        COL8        COL9        COL10       COL11       COL12
  1.0010E+05  0.0000E+00  1.0000E+00  1.0000E+03 -1.0000E+00  1.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00
  1.0010E+05  1.0001E+01  1.0000E+00  1.0000E+03 -1.0000E+00  1.0000E+00  2.2737E-14 -2.2737E-14  0.0000E+00  1.9281E-08  0.0000E+00  0.0000E+00
  1.0010E+05  2.4000E+01  1.0000E+00  2.0000E+03 -1.0000E+00  1.0000E+00  5.7541E-15 -5.7541E-15  0.0000E+00  5.1115E-13  0.0000E+00  0.0000E+00

Later something similar appears:
TABLE NO.  1
 COL1        COL2        COL3        COL4        COL5        COL6        COL7        COL8        COL9        COL10       COL11       COL12
  1.0010E+05  0.0000E+00  1.0000E+00  1.0000E+03 -1.0000E+00  1.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00
  1.0010E+05  1.0001E+01  1.0000E+00  1.0000E+03 -1.0000E+00  1.0000E+00  2.2737E-14 -2.2737E-14  0.0000E+00  1.9281E-08  0.0000E+00  0.0000E+00
  1.0010E+05  2.4000E+01  1.0000E+00  2.0000E+03 -1.0000E+00  1.0000E+00  5.7541E-15 -5.7541E-15  0.0000E+00  5.1115E-13  0.0000E+00  0.0000E+00

I will use the term "problematic lines" to refer to the repeated occurrences of the two non-data lines 

read.table is not successful in reading the table because of these problematic lines (I get around the first "TABLE NO." line using the skip option)

My word-around has been to: 
	1.  read the table with readLines
	2.  remove the problematic lines
	3.  write the file to disk
	4.  read the file with read.table.
However, this process is slow.

I though about using "comment.char" as a means of avoiding reading the problematic lines.  However, comment.char does not accept ="[A-Z]" 

Are there any clever workarounds for this?

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