[R] Seeking a more efficient way to read in a file
jim holtman
jholtman at gmail.com
Thu Jan 3 02:31:39 CET 2008
After you read in the first line, read the rest of the file with a single scan:
rest <- scan(..., sep="\t", what=0, skip=1)
index <- 1 # used to march through 'rest'
for (i in 1:3000){
for (j in 1:i){
malt[i,j] <- rest[index]
index <- index+1
}
}
There are probably faster ways, but this should go quicker since most
of your previous time was spent in the reading.
On Jan 2, 2008 6:05 PM, Talbot Katz <topkatz at msn.com> wrote:
>
> Hi.
>
> I have a matrix stored in a large, tab-delimited flat file. The first row contains column names. Because the matrix is symmetric, the file has lower triangular format, so the second row contains one number, the third row two numbers, etc. In general, row k+1 contains k numbers; the matrix has 3000 rows, so the file has 3001 rows. The file has variable length records, so each row ends with its last piece of data. I read in the file and produced the full symmetric matrix as follows:
>
> > mana01 <- scan( file = "C:/mat.dat", sep = "\t", nlines = 1, what = "character" )Read 3000 items> nco <- length( mana01 )> malt <- matrix(0, nrow = nco, ncol = nco )> colnames( malt ) <- mana01> rownames( malt ) <- mana01> for ( i in 1:3000 ) { malt[ i, (1:i) ] <- scan( file="C:/mat.dat", skip = i, n = i, quiet = TRUE ) }
> > mat <- malt + t( malt ) - diag( diag( malt ) )>
>
> The for loop took a couple of hours to complete. I suspect there's a much faster way to do this. Any suggestions? Thanks!
>
> -- TMK --212-460-5430 home917-656-5351 cell
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--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
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