R devel - Apr 2012 - csv version of data in an R object

For a package, I need to write a csv version of a data set to an R
object. Right now, I use:

    out <- capture.output(
                          write.table(x,
                                      sep = ",",
                                      na = "?",
                                      file = "",
                                      quote = FALSE,
                                      row.names = FALSE,
                                      col.names = FALSE))

To me, this is fairly slow; 131 seconds for a data frame with 8100
rows and 1400 columns.

The data will be in a data frame; I know write.table() would be faster
with a matrix. I was looking into converting the data frame to a
character matrix using as.matrix() or, better yet, format() prior to
the call above. However, I'm not sure what an appropriate value of
'digits' should be so that the character version of numeric data has
acceptable fidelity.

I also tried using a text connection and sink() as shown in
?textConnection but there was no speedup.

Any suggestions or ideas?

Thanks,

Max

> sessionInfo()
R version 2.14.0 (2011-10-31)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

loaded via a namespace (and not attached):
[1] tools_2.14.0

On Sat, Apr 21, 2012 at 3:28 PM, Max Kuhn <mxkuhn at gmail.com>
wrote:
> For a package, I need to write a csv version of a data set to an R
> object. Right now, I use:
>
> ? ?out <- capture.output(
> ? ? ? ? ? ? ? ? ? ? ? ? ?write.table(x,
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?sep = ",",
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?na = "?",
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?file = "",
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?quote = FALSE,
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?row.names = FALSE,
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?col.names = FALSE))
>
> To me, this is fairly slow; 131 seconds for a data frame with 8100
> rows and 1400 columns.
>
> The data will be in a data frame; I know write.table() would be faster
> with a matrix. I was looking into converting the data frame to a
> character matrix using as.matrix() or, better yet, format() prior to
> the call above. However, I'm not sure what an appropriate value of
> 'digits' should be so that the character version of numeric data
has
> acceptable fidelity.
>
> I also tried using a text connection and sink() as shown in
> ?textConnection but there was no speedup.
>
 You could try a loop over each row, and use 'paste' to join each
element in a row by commas. Then use 'paste' again to join everything
you've got (a vector of rows) by a '\n' character.

something like:
paste(apply(x,1,paste,collapse=","),collapse="\n")   #
untested

you probably also want to stick a final \n on it.

Is it faster? I don't know!

Barry