R help - Dec 2009 - read.csv to read output of system()?

Dear list,

I have a file that is comma delimited but contains some erroneous
non-delimiter commas. I would like to replace these commas with
semicolons and then read the correct file into R as a data frame.

I want to do this from within R, without changing the original data
file.

My current idea of how to do this would be to use system("sed ...")
and feed the result to read.csv(), but I cannot figure out how to
combine the two.

Minimal example:

system("echo \"one,two,three\" > file.csv") # create
mockup file
read.csv(file=system("sed -e 's/,/;/' file.csv"))  # this does
not work

I think the answer must be in ?connections, maybe pipe() but I have
fiddled with these and cannot figure it out.

Marianne

-- 
Marianne Promberger PhD, King's College London
http://promberger.info
R version 2.10.0 (2009-10-26)
Ubuntu 9.04

On Dec 12, 2009, at 7:54 AM, Marianne Promberger wrote:
> Dear list,
>
> I have a file that is comma delimited but contains some erroneous
> non-delimiter commas. I would like to replace these commas with
> semicolons and then read the correct file into R as a data frame.
>
> I want to do this from within R, without changing the original data
> file.
>
> My current idea of how to do this would be to use system("sed
...")
> and feed the result to read.csv(), but I cannot figure out how to
> combine the two.
>
> Minimal example:
>
> system("echo \"one,two,three\" > file.csv") # create
mockup file
> read.csv(file=system("sed -e 's/,/;/' file.csv"))  # this
does not
> work
>
> I think the answer must be in ?connections, maybe pipe() but I have
> fiddled with these and cannot figure it out.
You need to figure out how to do multiple replacements unless it is  
only the first comma that you are targeting:

 > readLines(pipe("sed -e 's/,/;/' ~/file.csv"))
[1] "one;two,three"

>
> Marianne
>
> -- 
> Marianne Promberger PhD, King's College London
> http://promberger.info

David Winsemius, MD
Heritage Laboratories
West Hartford, CT