Hi All,
I have a problem with reading in multiple text files where some of the files
have no data and was hoping someone may be able to help me find a solution.
Each text file is a daily log of fish movement. However, on some occasions
no movements will be recorded on a particular day and therefore the text
file for that day is empty.
I'm currently using the following code to read the files:
a<-list.files()
x<-lapply(a,function(x){read.table(x,colClasses='character')}) #the
colClasses is to ensure zeros at the beginning of tag numbers are included
myData<-do.call(rbind, x)
This works fine as long as all the files being read have data in them, but
if one of the empty log files is included it returns the following error:
Error in read.table(x, colClasses = "character", blank.lines.skip =
TRUE) :
no lines available in input
Does anyone know of a way that I can overcome this (maybe skip empty files
somehow?) without having to manually trawl through the hundreds of files I
have to remove the empty ones?
Thanks in advance,
Paul
--
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Michael Sumner
2010-Aug-31 04:56 UTC
[R] Reading multiple text files where some files are empty
What about trimming the file list based on a minimum size? You can also use the arguments to list.files to get only certain patterns in file names, and otherwise you can put a condition in the function passed to lapply to return NULL, which will rbind ok, or process x in a similar way. a <- a[file.info(a)$size > 1] On Tue, Aug 31, 2010 at 2:47 PM, Paul <p.franklin at niwa.co.nz> wrote:> > Hi All, > > I have a problem with reading in multiple text files where some of the files > have no data and was hoping someone may be able to help me find a solution. > > Each text file is a daily log of fish movement. However, on some occasions > no movements will be recorded on a particular day and therefore the text > file for that day is empty. > > I'm currently using the following code to read the files: > > a<-list.files() > x<-lapply(a,function(x){read.table(x,colClasses='character')}) #the > colClasses is to ensure zeros at the beginning of tag numbers are included > myData<-do.call(rbind, x) > > This works fine as long as all the files being read have data in them, but > if one of the empty log files is included it returns the following error: > > Error in read.table(x, colClasses = "character", blank.lines.skip = TRUE) : > ?no lines available in input > > Does anyone know of a way that I can overcome this (maybe skip empty files > somehow?) without having to manually trawl through the hundreds of files I > have to remove the empty ones? > > Thanks in advance, > Paul > > -- > View this message in context: http://r.789695.n4.nabble.com/Reading-multiple-text-files-where-some-files-are-empty-tp2401035p2401035.html > Sent from the R help mailing list archive at Nabble.com. > > ______________________________________________ > R-help at r-project.org 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. >-- Michael Sumner Institute for Marine and Antarctic Studies, University of Tasmania Hobart, Australia e-mail: mdsumner at gmail.com
Jeff Newmiller
2010-Aug-31 05:31 UTC
[R] Reading multiple text files where some files are empty
Perhaps ?try can help... "Paul" <p.franklin at niwa.co.nz> wrote:> >Hi All, > >I have a problem with reading in multiple text files where some of the files >have no data and was hoping someone may be able to help me find a solution. > >Each text file is a daily log of fish movement. However, on some occasions >no movements will be recorded on a particular day and therefore the text >file for that day is empty. > >I'm currently using the following code to read the files: > >a<-list.files() >x<-lapply(a,function(x){read.table(x,colClasses='character')}) #the >colClasses is to ensure zeros at the beginning of tag numbers are included >myData<-do.call(rbind, x) > >This works fine as long as all the files being read have data in them, but >if one of the empty log files is included it returns the following error: > >Error in read.table(x, colClasses = "character", blank.lines.skip = TRUE) : > no lines available in input > >Does anyone know of a way that I can overcome this (maybe skip empty files >somehow?) without having to manually trawl through the hundreds of files I >have to remove the empty ones? > >Thanks in advance, >Paul > >-- >View this message in context: http://r.789695.n4.nabble.com/Reading-multiple-text-files-where-some-files-are-empty-tp2401035p2401035.html >Sent from the R help mailing list archive at Nabble.com. > >______________________________________________ >R-help at r-project.org 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.--------------------------------------------------------------------------- Jeff Newmiller The ..... ..... Go Live... DCN:<jdnewmil at dcn.davis.ca.us> Basics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/Batteries O.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k --------------------------------------------------------------------------- Sent from my phone. Please excuse my brevity.