[R] read.table : how to condition on error while opening file?
Hi,
I'm using read.table in a loop, to read in multiple files. The problem
is that when a file is missing there is an error message and the loop is
broken; what I'd like to do is to test for the error and simply do
next instead of breaking the loop. Anybody knows how to do that?
Example:
filelist - c(file1.txt, file2.txt, file3.txt)
for (i in 1:3) {
if (read.table(filelist[i]) == ERROR LOADING FILE) {
# this is where I do not know how to write the condition
print(paste(error opening file , filelist[i], sep=))
next
} else {
tmp - read.table(filelist[i])
}
}
Cheers,
Stephane
--
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Limited, a charity registered in England with number 1021457 and a
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Re: [R] read.table : how to condition on error while opening file?
Hi Stephane,
see ?try
hth.
Stephane Bourgeois schrieb:
Hi,
I'm using read.table in a loop, to read in multiple files. The problem
is that when a file is missing there is an error message and the loop is
broken; what I'd like to do is to test for the error and simply do
next instead of breaking the loop. Anybody knows how to do that?
Example:
filelist - c(file1.txt, file2.txt, file3.txt)
for (i in 1:3) {
if (read.table(filelist[i]) == ERROR LOADING FILE) {
# this is where I do not know how to write the condition
print(paste(error opening file , filelist[i], sep=))
next
} else {
tmp - read.table(filelist[i])
}
}
Cheers,
Stephane
--
Eik Vettorazzi
Institut für Medizinische Biometrie und Epidemiologie
Universitätsklinikum Hamburg-Eppendorf
Martinistr. 52
20246 Hamburg
T ++49/40/42803-8243
F ++49/40/42803-7790
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] read.table : how to condition on error while opening file?
Hello Stephane,
here is something you could try,
filelist - c(file1.txt, file2.txt, file3.txt)
for (i in 1:3) {
tmpList-try(read.table(filelist[[i]]), silent=TRUE)
if(inherits(tmpList, try-error))
{print(paste(error opening file , filelist[[i]]))
} else {
tmp-read.table(filelist[[i]])-namelist[[i]]
}
}
There is though a problem that I didnt manage to fix, that is: if , suppose,
file1.txt exists, file2 doesn't exist
and file 3 exists,
the dataframe in file 1 will at first be called tmp, but then it will be
substituted by the data.frame in file 3...
It is as if you would do:
c(1,2,3,4)-tmp
and then do
c(1,6,7,8)-tmp
the second tmp will substitute the first one...
Hope this helps
Laura
Messaggio originale
Da: e.vettora...@uke.uni-hamburg.de
Data: 19.02.2009 17.23
A: Stephane Bourgeoiss...@sanger.ac.uk
Copia: r-help@r-project.org
Oggetto: Re: [R] read.table : how to condition on error while opening file?
Hi Stephane,
see ?try
hth.
Stephane Bourgeois schrieb:
Hi,
I'm using read.table in a loop, to read in multiple files. The problem
is that when a file is missing there is an error message and the loop is
broken; what I'd like to do is to test for the error and simply do
next instead of breaking the loop. Anybody knows how to do that?
Example:
filelist - c(file1.txt, file2.txt, file3.txt)
for (i in 1:3) {
if (read.table(filelist[i]) == ERROR LOADING FILE) {
# this is where I do not know how to write the condition
print(paste(error opening file , filelist[i], sep=))
next
} else {
tmp - read.table(filelist[i])
}
}
Cheers,
Stephane
--
Eik Vettorazzi
Institut für Medizinische Biometrie und Epidemiologie
Universitätsklinikum Hamburg-Eppendorf
Martinistr. 52
20246 Hamburg
T ++49/40/42803-8243
F ++49/40/42803-7790
__
R-help@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.
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
