R help - May 2007 - rewrite a data file use write.table(), count.fields() show different pattern, any suggestion appreciated.

Dear all:

I read in a tab delimited dataset, and then write it out as another
file as following: I did this simply to make sure I understand the
behavior of this command.

data<-read.table(file,header=F,sep="\t",fill=T,colClasses="character");
write.table(data,file="newdata.txt",eol="\n",sep="\t",quote=F,row.names=F);


cf1 <- count.fields(newdata.txt, sep="\t")
table(cf1)
13   17       23
10   126   5445

# is different to

cf2 <- count.fields(file,sep="\t")
13   17       23        33
10   106   5433      32

the worst problem is the maximal value of cf1 (33) is larger than the
maximal value of cf2 (23) which is the right number of fields for most
rows in the original file.

I need to use write.table for some important data manipulation work,
your suggestion is
highly appreciated.

Best Regards

If you write out unquoted fields, how do you know they do not contain 
tabs?

The default is quote=TRUE for a good reason.

On Tue, 22 May 2007, Yong Wang wrote:
> Dear all:
>
> I read in a tab delimited dataset, and then write it out as another
> file as following: I did this simply to make sure I understand the
> behavior of this command.
>
>
data<-read.table(file,header=F,sep="\t",fill=T,colClasses="character");
>
write.table(data,file="newdata.txt",eol="\n",sep="\t",quote=F,row.names=F);
>
>
> cf1 <- count.fields(newdata.txt, sep="\t")
> table(cf1)
> 13   17       23
> 10   126   5445
>
> # is different to
>
> cf2 <- count.fields(file,sep="\t")
> 13   17       23        33
> 10   106   5433      32
>
> the worst problem is the maximal value of cf1 (33) is larger than the
> maximal value of cf2 (23) which is the right number of fields for most
> rows in the original file.
>
> I need to use write.table for some important data manipulation work,
> your suggestion is
> highly appreciated.
>
> Best Regards
>
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

Thank you for the suggestion, Dr. Ripley

However, I am a little bit confused. My understanding is that you
suspect the should-be-quoted fields (factor or character fields)
contains tabs.

if this is the case,  count.fields()  should detect the tab,
read.table(sep="t\") should read with the same awareness, and if
write.table(sep"\t") write and seperate with tab those fields as
acknowldged by read.table(sep="t\"), the two field counts should be
the same.

anyway, I will try to redo it per your suggestion.

Regards
yong


On 5/22/07, Prof Brian Ripley <ripley at stats.ox.ac.uk>
wrote:
> If you write out unquoted fields, how do you know they do not contain
> tabs?
>
> The default is quote=TRUE for a good reason.
>
> On Tue, 22 May 2007, Yong Wang wrote:
>
> > Dear all:
> >
> > I read in a tab delimited dataset, and then write it out as another
> > file as following: I did this simply to make sure I understand the
> > behavior of this command.
> >
> >
data<-read.table(file,header=F,sep="\t",fill=T,colClasses="character");
> >
write.table(data,file="newdata.txt",eol="\n",sep="\t",quote=F,row.names=F);
> >
> >
> > cf1 <- count.fields(newdata.txt, sep="\t")
> > table(cf1)
> > 13   17       23
> > 10   126   5445
> >
> > # is different to
> >
> > cf2 <- count.fields(file,sep="\t")
> > 13   17       23        33
> > 10   106   5433      32
> >
> > the worst problem is the maximal value of cf1 (33) is larger than the
> > maximal value of cf2 (23) which is the right number of fields for most
> > rows in the original file.
> >
> > I need to use write.table for some important data manipulation work,
> > your suggestion is
> > highly appreciated.
> >
> > Best Regards
> >
> > ______________________________________________
> > R-help at stat.math.ethz.ch mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
> >
>
> --
> Brian D. Ripley,                  ripley at stats.ox.ac.uk
> Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
> University of Oxford,             Tel:  +44 1865 272861 (self)
> 1 South Parks Road,                     +44 1865 272866 (PA)
> Oxford OX1 3TG, UK                Fax:  +44 1865 272595
>