[R] speeding read.table

[Jason Edgecombe]

On 10/18/2012 09:57 AM, Fisher Dennis wrote:
> 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?
>
Create a connection to a pipe, where pipe reads from the grep command. 
Grep can exlude the problematic lines. Use the pipe object as your 
connection in read.table.