[R] re ad.table() and setwd() in unix batch mode
I continually receive the error Error in file(file, r) : cannot open the connection, when running in batch mode, but not when inputing directly into R. Any ideas? Thanks! TB -- View this message in context: http://www.nabble.com/read.table%28%29-and-setwd%28%29-in-unix-batch-mode-tp24107008p24107008.html Sent from the R help mailing list archive at Nabble.com. __ 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.
Re: [R] re ad.table() and setwd() in unix batch mode
tbigdeli wrote: I continually receive the error Error in file(file, r) : cannot open the connection, when running in batch mode, but not when inputing directly into R. Have you given the full path name? If not, do you start both R instances from the same working directory? Otherwise, do you have the same credentials in both cases? Uwe Ligges Any ideas? Thanks! TB __ 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.
Re: [R] re ad.table() and setwd() in unix batch mode
My apologies for being overly brief before..
I submit an R script to batch mode as follows:
a list of files (object = 'files'). In each iteration, the next file is
read, alterations made, working directory changed, and output file written
out. R will take an inordinate amount of time processing the first file,
after which no files seem to be read-in. For batch mode, are my paths
inappropriate? Thanks!
setwd(/home/bigdelitb/chr20/merlin/sim/d5/ped)
files-read.table(d5.rf.list,stringsAsFactors=FALSE)
for(i in 1:length(files$V1)){
setwd(/home/bigdelitb/chr20/merlin/sim/d5/ped)
count - 1
name-files$V1[i]
ped - read.table(name,header=FALSE,stringsAsFactors=FALSE)
...
...
setwd(/home/bigdelitb/chr20/merlin/sim/d5/ped/pdt/)
write.table(ped,name,quote=FALSE,..)
}
Uwe Ligges-3 wrote:
tbigdeli wrote:
I continually receive the error
Error in file(file, r) : cannot open the connection, when running in
batch
mode, but not when inputing directly into R.
Have you given the full path name?
If not, do you start both R instances from the same working directory?
Otherwise, do you have the same credentials in both cases?
Uwe Ligges
Any ideas?
Thanks!
TB
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Sent from the R help mailing list archive at Nabble.com.
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Re: [R] re ad.table() and setwd() in unix batch mode
tbigdeli wrote:
My apologies for being overly brief before..
I submit an R script to batch mode as follows:
a list of files (object = 'files'). In each iteration, the next file is
read, alterations made, working directory changed, and output file written
out. R will take an inordinate amount of time processing the first file,
after which no files seem to be read-in. For batch mode, are my paths
inappropriate? Thanks!
setwd(/home/bigdelitb/chr20/merlin/sim/d5/ped)
files-read.table(d5.rf.list,stringsAsFactors=FALSE)
for(i in 1:length(files$V1)){
setwd(/home/bigdelitb/chr20/merlin/sim/d5/ped)
count - 1
name-files$V1[i]
ped - read.table(name,header=FALSE,stringsAsFactors=FALSE)
...
...
setwd(/home/bigdelitb/chr20/merlin/sim/d5/ped/pdt/)
write.table(ped,name,quote=FALSE,..)
}
1. This should do the same for interactive and batch mode given the
relevant things are not hidden in
2. You are running both inteactive and batch under the same user?
3. Why do you change working directories all the time, you could give
full path names instead.
4. 1:length(files$V1) is dangerous in loops (if length becomes 0),
hence use seq_along(files$V1)
Uwe Ligges
Uwe Ligges-3 wrote:
tbigdeli wrote:
I continually receive the error
Error in file(file, r) : cannot open the connection, when running in
batch
mode, but not when inputing directly into R.
Have you given the full path name?
If not, do you start both R instances from the same working directory?
Otherwise, do you have the same credentials in both cases?
Uwe Ligges
Any ideas?
Thanks!
TB
__
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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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.
Re: [R] re ad.table, row.names arg
Markus Loecher-4 wrote: Dear R users, I had somehow expected that read.table() would treat the column specified by the row.names argument as of class character. That seems to be the only sensible class allowed for a column containing row names. However, that does not seem to be the case, as the following example shows: x - cbind.data.frame(ID = c(010007787048271871, 1007109516820319, 10094843652996959, 010145176274075487), X1 = 1:4, X2 = 4:1) [...snip...] As a better alternative, why not move directly the first column in the rownames? rownames(x) - x$ID write.table(x[, -1], tmp.txt) y - read.table(tmp.txt, header=T) y X1 X2 010007787048271871 1 4 10071095168203192 3 10094843652996959 3 2 010145176274075487 4 1 In this case, X1 and X2 variables are read as numeric, while the first column is read as character and assigned directly to the rownames. HTH, Adrian -- View this message in context: http://www.nabble.com/read.table%2C-row.names-arg-tp23888975p23892826.html Sent from the R help mailing list archive at Nabble.com. __ 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.
[R] re ad.table
Hi, I ve been searching a lot in internet..but I can t find a solution Attached, you find a file. I need for each (Materiale, tpdv, UM) to find sum,avg and count My idea was to aggregate for the 3 parameters ..but I don t know how to get the numeric value (SUM,COUNT,AVG) I need. Can you help me? thank you http://www.nabble.com/file/p22905601/ordini2008_ex.txt ordini2008_ex.txt -- View this message in context: http://www.nabble.com/read.table-tp22905601p22905601.html Sent from the R help mailing list archive at Nabble.com. __ 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.
[R] re ad.table prn file
Dear Forum, I´ve imported a prn file with read.table (file(E:/test.prn),sep=\t,skip=3). My problem is now, that my file has a complicated structure: It is not tabstop seperated, it looks like that: JEAR JAN FEB MAR APR 1938154 912 19396 71014 19409 If there are default values, there is no seperation in the line, I want that the program seperates after every JAN, FEB (in detail after the 18., 24., 36 character). Is there a possibility to seperate after i.e.the 15. character? i tried with strsplit, but get no satisfying result. Please help me. I think I could do this with exel and export it with csv, but i would like to solve the problem with R. -- View this message in context: http://www.nabble.com/read.table-prn-file-tp22161342p22161342.html Sent from the R help mailing list archive at Nabble.com. __ 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.
Re: [R] re ad.table prn file
On Mon, Feb 23, 2009 at 05:18:28AM -0800, canadiangirl19 wrote: My problem is now, that my file has a complicated structure: It is not tabstop seperated, it looks like that: JEAR JAN FEB MAR APR 1938154 912 19396 71014 19409 If there are default values, there is no seperation in the line, I want that the program seperates after every JAN, FEB (in detail after the 18., 24., 36 character). Is there a possibility to seperate after i.e.the 15. character? i tried with strsplit, but get no satisfying result. Sounds like read.fwf may solve your problem. cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität München Wissenschaftszentrum Weihenstephan 85350 Freising, Germany http://mips.gsf.de/staff/pagel __ 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.
Re: [R] re ad.table prn file
I´ve tried with: write.fwf(test,file=E:/test.prn,widths=6), but get the error: Fehler in write.table(t(as.matrix(colnamesMy)), file = file, append = append, : unbenutzte(s) Argument(e) (widths = 6) My matrix hast only one column (so it is a vector), and many rows, I want to seperate the vector (after 6 character, I don´t know, is the width=6?) in a matrix with 5 columns. How can I do this? And with format.info I get no output. thanks in advance for helping me Philipp Pagel-5 wrote: On Mon, Feb 23, 2009 at 05:18:28AM -0800, canadiangirl19 wrote: My problem is now, that my file has a complicated structure: It is not tabstop seperated, it looks like that: JEAR JAN FEB MAR APR 1938154 912 19396 71014 19409 If there are default values, there is no seperation in the line, I want that the program seperates after every JAN, FEB (in detail after the 18., 24., 36 character). Is there a possibility to seperate after i.e.the 15. character? i tried with strsplit, but get no satisfying result. Sounds like read.fwf may solve your problem. cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität München Wissenschaftszentrum Weihenstephan 85350 Freising, Germany http://mips.gsf.de/staff/pagel __ 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. -- View this message in context: http://www.nabble.com/read.table-prn-file-tp22161342p22162335.html Sent from the R help mailing list archive at Nabble.com. __ 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.
Re: [R] re ad.table prn file
On Mon, Feb 23, 2009 at 06:24:33AM -0800, canadiangirl19 wrote: write.fwf(test,file=E:/test.prn,widths=6), but get the error: Fehler in write.table(t(as.matrix(colnamesMy)), file = file, append = append, : unbenutzte(s) Argument(e) (widths = 6) My matrix hast only one column (so it is a vector), and many rows, I want to seperate the vector (after 6 character, I don´t know, is the width=6?) in a matrix with 5 columns. How can I do this? And with format.info I get no output. Are you sure the above is your actual code? I didn't even know the function write.fwf existed. I was suggesting was to READ the file with read.fwf. Your reply seems to indicate that you are first reading the file by some other means and then trying to write it back to a file. If, for some obscure reason, you really cannot use read.fwf(), textConnection() would be an option. But it would probably only complicate things more than necessary. cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität München Wissenschaftszentrum Weihenstephan 85350 Freising, Germany http://mips.gsf.de/staff/pagel __ 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.
Re: [R] re ad.table prn file
It works thanks a lot Philipp Pagel-5 wrote: On Mon, Feb 23, 2009 at 06:24:33AM -0800, canadiangirl19 wrote: write.fwf(test,file=E:/test.prn,widths=6), but get the error: Fehler in write.table(t(as.matrix(colnamesMy)), file = file, append = append, : unbenutzte(s) Argument(e) (widths = 6) My matrix hast only one column (so it is a vector), and many rows, I want to seperate the vector (after 6 character, I don´t know, is the width=6?) in a matrix with 5 columns. How can I do this? And with format.info I get no output. Are you sure the above is your actual code? I didn't even know the function write.fwf existed. I was suggesting was to READ the file with read.fwf. Your reply seems to indicate that you are first reading the file by some other means and then trying to write it back to a file. If, for some obscure reason, you really cannot use read.fwf(), textConnection() would be an option. But it would probably only complicate things more than necessary. cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität München Wissenschaftszentrum Weihenstephan 85350 Freising, Germany http://mips.gsf.de/staff/pagel __ 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. -- View this message in context: http://www.nabble.com/read.table-prn-file-tp22161342p22176814.html Sent from the R help mailing list archive at Nabble.com. __ 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.
[R] re ad.table
Hi , I want to use the read.table to the following example 'data.txt' format: a b c d e f SPX LSZ 100 C 0 34.4 SPX LSZ 100 P 0 1.3 SPX LSZ 105 C 0 30.3 SPX LSZ 105 P 0 1.85 SPX LSZ 110 C 0 26.4 and I want to have the columns a,b,d read as the 'character' data, a the remaining columns as 'numeric'. What I did was: read.table(data.txt,header=T, colClasses=c(character,character,numeric,character, numeric,numeric), but I could not get what I want, since all values were in the 'character' format. I will apprecaite any suggestions. best, robert -- View this message in context: http://www.nabble.com/read.table-tp21090550p21090550.html Sent from the R help mailing list archive at Nabble.com. __ 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.
Re: [R] re ad.table
Seems to work for me: x - read.table(textConnection(a b c d e f + SPX LSZ 100 C 0 34.4 + SPX LSZ 100 P 0 1.3 + SPX LSZ 105 C 0 30.3 + SPX LSZ 105 P 0 1.85 + SPX LSZ 110 C 0 26.4), + header=T, colClasses=c(character,character,numeric,character, + numeric,numeric)) x a b c d e f 1 SPX LSZ 100 C 0 34.40 2 SPX LSZ 100 P 0 1.30 3 SPX LSZ 105 C 0 30.30 4 SPX LSZ 105 P 0 1.85 5 SPX LSZ 110 C 0 26.40 str(x) 'data.frame': 5 obs. of 6 variables: $ a: chr SPX SPX SPX SPX ... $ b: chr LSZ LSZ LSZ LSZ ... $ c: num 100 100 105 105 110 $ d: chr C P C P ... $ e: num 0 0 0 0 0 $ f: num 34.4 1.3 30.3 1.85 26.4 sessionInfo() R version 2.8.0 (2008-10-20) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] stats grDevices utils datasets graphics methods base other attached packages: [1] MASS_7.2-44 On Fri, Dec 19, 2008 at 7:35 AM, threshold r.kozar...@gmail.com wrote: Hi , I want to use the read.table to the following example 'data.txt' format: a b c d e f SPX LSZ 100 C 0 34.4 SPX LSZ 100 P 0 1.3 SPX LSZ 105 C 0 30.3 SPX LSZ 105 P 0 1.85 SPX LSZ 110 C 0 26.4 and I want to have the columns a,b,d read as the 'character' data, a the remaining columns as 'numeric'. What I did was: read.table(data.txt,header=T, colClasses=c(character,character,numeric,character, numeric,numeric), but I could not get what I want, since all values were in the 'character' format. I will apprecaite any suggestions. best, robert -- View this message in context: http://www.nabble.com/read.table-tp21090550p21090550.html Sent from the R help mailing list archive at Nabble.com. __ 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. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem that you are trying to solve? __ 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.
Re: [R] re ad.table
probably best just to change each variable one by one to the correct classification after you have read the data frame in. variable-as.character(variable) - Original Message - From: threshold r.kozar...@gmail.com To: r-help@r-project.org Sent: Friday, December 19, 2008 12:35 PM Subject: [R] re ad.table Hi , I want to use the read.table to the following example 'data.txt' format: a b c d e f SPX LSZ 100 C 0 34.4 SPX LSZ 100 P 0 1.3 SPX LSZ 105 C 0 30.3 SPX LSZ 105 P 0 1.85 SPX LSZ 110 C 0 26.4 and I want to have the columns a,b,d read as the 'character' data, a the remaining columns as 'numeric'. What I did was: read.table(data.txt,header=T, colClasses=c(character,character,numeric,character, numeric,numeric), but I could not get what I want, since all values were in the 'character' format. I will apprecaite any suggestions. best, robert -- View this message in context: http://www.nabble.com/read.table-tp21090550p21090550.html Sent from the R help mailing list archive at Nabble.com. __ 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. __ 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.
Re: [R] re ad.table problem
did you remark you obtain the half of rows (636615*2=1273230) ; maybe the columns aren't good sliced phoebe kong wrote: Dear all, I have problem when reading a table into R. The total row of read in table has is much less than the original saved table. I built a 1,273,230 by 6 data set named mydata2, it was saved in the following command, write.table(mydata2, mydata2.txt, row.name=F,col.name=T,quote=F,sep=\t) The next day I read in above saved text file into R, temp-read.table(mydata2.txt,header=T,sep=\t,na.strings=NA) However, the dimension of temp is 636,615 X 6. Do yo know why? Thanks in advanced, Sityee [[alternative HTML version deleted]] __ 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. -- View this message in context: http://www.nabble.com/read.table-problem-tp18370284p18379571.html Sent from the R help mailing list archive at Nabble.com. __ 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.
