[R] read.table
Hi, I want to read a ascii-file using the function read.table. With 'skip' and 'nrows' I can select the rows to read from this file. Is there a way to select columns (in the selected rows)? Thanks, Ingo __ R-help@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.
Re: [R] read.table
Ingo Holz wrote: Hi, I want to read a ascii-file using the function read.table. With 'skip' and 'nrows' I can select the rows to read from this file. Is there a way to select columns (in the selected rows)? Yes, use the colClasses argument. (I won't rewrite the help page here; I expect that you can read it once you know where to look.) -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-help@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.
[R] read.table opening a website incl Password
Dear all, in the past I have been able to access websites with data directly. For example the following code works nicely mydata - read.table(http://www.lifetable.de/data/MPIDR/POL_2004.txt;, header=TRUE) But what happens if I need a username and password (a different site)? How do I do that? Or is it not possible to this in R? I tried something like this mydata.frame - read.table(myusr:[EMAIL PROTECTED]/adir/afile.txt) but it did not work. I'd appreciate any hints. My platform is Win32 (and I am actually running R 2.3.1, but I guess (hope!) this is not the reason. At least I checked the NEWS file whether any changes appeared since 2.3.1 which could affect this behavior). Thanks, Roland __ R-help@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.
Re: [R] read.table opening a website incl Password
Roland Rau wrote: Dear all, in the past I have been able to access websites with data directly. For example the following code works nicely mydata - read.table(http://www.lifetable.de/data/MPIDR/POL_2004.txt;, header=TRUE) But what happens if I need a username and password (a different site)? How do I do that? Or is it not possible to this in R? I tried something like this mydata.frame - read.table(myusr:[EMAIL PROTECTED]/adir/afile.txt) but it did not work. I'd appreciate any hints. My platform is Win32 (and I am actually running R 2.3.1, but I guess (hope!) this is not the reason. At least I checked the NEWS file whether any changes appeared since 2.3.1 which could affect this behavior). In what way did it not work? The following seems to work for me: read.table(ftp://myusr:[EMAIL PROTECTED]/mydir/test.dat) Thanks, Roland __ R-help@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. -- Chuck Cleland, Ph.D. NDRI, Inc. 71 West 23rd Street, 8th floor New York, NY 10010 tel: (212) 845-4495 (Tu, Th) tel: (732) 512-0171 (M, W, F) fax: (917) 438-0894 __ R-help@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.
Re: [R] read.table opening a website incl Password
On Wed, 16 May 2007, Roland Rau wrote: Dear all, in the past I have been able to access websites with data directly. For example the following code works nicely mydata - read.table(http://www.lifetable.de/data/MPIDR/POL_2004.txt;, header=TRUE) But what happens if I need a username and password (a different site)? How do I do that? Or is it not possible to this in R? I tried something like this mydata.frame - read.table(myusr:[EMAIL PROTECTED]/adir/afile.txt) but it did not work. Well, it could not. You need ftp:// or http:// for this to be a URL. This ought to work for ftp:, but AFAIK not for http:. You could always try --internet2: if it works in IE, it will probably also work in R. I'd appreciate any hints. My platform is Win32 (and I am actually running R 2.3.1, but I guess (hope!) this is not the reason. At least I checked the NEWS file whether any changes appeared since 2.3.1 which could affect this behavior). Thanks, Roland __ R-help@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, [EMAIL PROTECTED] 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, UKFax: +44 1865 272595 __ R-help@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.
Re: [R] read.table opening a website incl Password
Chuck, Roland is trying to read from a web site instead of a ftp site. I have also gotten this to work: read.table(ftp://myusr:[EMAIL PROTECTED]/mydir/test.dat) But when I try to do the same thing from the SEC's ftp site I get an error, so beyond R, there may be some internet settings that need to be fiddled with. Maybe I can tag onto Roland's question and ask for hints on what configuration options are available? Thanks, Roger -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Chuck Cleland Sent: Wednesday, May 16, 2007 1:08 PM To: Roland Rau Cc: r-help@stat.math.ethz.ch Subject: Re: [R] read.table opening a website incl Password Roland Rau wrote: Dear all, in the past I have been able to access websites with data directly. For example the following code works nicely mydata - read.table(http://www.lifetable.de/data/MPIDR/POL_2004.txt;, header=TRUE) But what happens if I need a username and password (a different site)? How do I do that? Or is it not possible to this in R? I tried something like this mydata.frame - read.table(myusr:[EMAIL PROTECTED]/adir/afile.txt) but it did not work. I'd appreciate any hints. My platform is Win32 (and I am actually running R 2.3.1, but I guess (hope!) this is not the reason. At least I checked the NEWS file whether any changes appeared since 2.3.1 which could affect this behavior). In what way did it not work? The following seems to work for me: read.table(ftp://myusr:[EMAIL PROTECTED]/mydir/test.dat) Thanks, Roland __ R-help@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. -- Chuck Cleland, Ph.D. NDRI, Inc. 71 West 23rd Street, 8th floor New York, NY 10010 tel: (212) 845-4495 (Tu, Th) tel: (732) 512-0171 (M, W, F) fax: (917) 438-0894 __ R-help@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. ** * This message is for the named person's use only. It may contain confidential, proprietary or legally privileged information. No right to confidential or privileged treatment of this message is waived or lost by any error in transmission. If you have received this message in error, please immediately notify the sender by e-mail, delete the message and all copies from your system and destroy any hard copies. You must not, directly or indirectly, use, disclose, distribute, print or copy any part of this message if you are not the intended recipient. __ R-help@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.
Re: [R] read.table opening a website incl Password
Dear all, so far I tried various things but I did not really succeed: - starting R with --internet2 - using url() - using read.table(http://myusr:[EMAIL PROTECTED]/adir/afile.txt) I just have an idea what the problem could be for me: The username is actually an email address. So the '@'-character has some ambiguous meaning in my setting. Sorry that I did not think of that beforehand. Thank you very much for your help, Roland Prof Brian Ripley wrote: On Wed, 16 May 2007, Roland Rau wrote: Dear all, in the past I have been able to access websites with data directly. For example the following code works nicely mydata - read.table(http://www.lifetable.de/data/MPIDR/POL_2004.txt;, header=TRUE) But what happens if I need a username and password (a different site)? How do I do that? Or is it not possible to this in R? I tried something like this mydata.frame - read.table(myusr:[EMAIL PROTECTED]/adir/afile.txt) but it did not work. Well, it could not. You need ftp:// or http:// for this to be a URL. This ought to work for ftp:, but AFAIK not for http:. You could always try --internet2: if it works in IE, it will probably also work in R. I'd appreciate any hints. My platform is Win32 (and I am actually running R 2.3.1, but I guess (hope!) this is not the reason. At least I checked the NEWS file whether any changes appeared since 2.3.1 which could affect this behavior). Thanks, Roland __ R-help@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. __ R-help@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.
[R] read.table
sorry, I don't undersatnd what happens Annee_O;Id_Essai;Id_Rep;Id_Geno;Id_Cult;Lib_Geno;St_Cult;Id_Par;X_Par;Y_Par;Id_Cara;Surf_O;Val_O;Ori_O;Stade_O;Date_O;Id_Bloc;Id_TrT1 2004;1006003;1;55094;1012988;XF 338/1;;1;1;1;137;;9.4;P;;09/09/2004;1;0 2004;1006003;1;55094;1012988;XF 338/1;;1;1;1;193;;189;P;;01/01/2004;1;0 2004;1006003;1;55094;1012988;XF 338/1;;1;1;1;103;14.95;85;P;;09/09/2004;1;0 2004;1006003;1;55094;1012988;XF 338/1;;1;1;1;177;;55.1;P;;05/10/2004;1;0 2004;1006003;1;55094;1012988;XF 338/1;;1;1;1;138;14.95;6.3;P;;09/09/2004;1;0 2004;1006003;1;55094;1012988;XF 338/1;;1;1;1;308;;140;P;;05/08/2004;1;0 2004;1006003;1;55096;1012999;Dally/1;;2;2;1;137;;8.9;P;;09/09/2004;1;0 2004;1006003;1;55096;1012999;Dally/1;;2;2;1;193;;192;P;;01/01/2004;1;0 2004;1006003;1;55096;1012999;Dally/1;;2;2;1;103;14.95;87;P;;09/09/2004;1;0 that's the begining of my table and I'm trying to read it from R but I can't actually to read it I write this script donAP - read.table(C:/Documents and Settings/melyakhlifi/Mes documents/feuilles excel/copi_donnees3.csv,header=TRUE,sep=;,quote=,dec=.) Erreur dans scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : la ligne 656 n'avait pas 18 éléments there's some errors and I don't understand why? ___ [[alternative HTML version deleted]] __ R-help@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.
Re: [R] read.table
elyakhlifi mustapha wrote: sorry, I don't undersatnd what happens Annee_O;Id_Essai;Id_Rep;Id_Geno;Id_Cult;Lib_Geno;St_Cult;Id_Par;X_Par;Y_Par;Id_Cara;Surf_O;Val_O;Ori_O;Stade_O;Date_O;Id_Bloc;Id_TrT1 2004;1006003;1;55094;1012988;XF 338/1;;1;1;1;137;;9.4;P;;09/09/2004;1;0 2004;1006003;1;55094;1012988;XF 338/1;;1;1;1;193;;189;P;;01/01/2004;1;0 2004;1006003;1;55094;1012988;XF 338/1;;1;1;1;103;14.95;85;P;;09/09/2004;1;0 2004;1006003;1;55094;1012988;XF 338/1;;1;1;1;177;;55.1;P;;05/10/2004;1;0 2004;1006003;1;55094;1012988;XF 338/1;;1;1;1;138;14.95;6.3;P;;09/09/2004;1;0 2004;1006003;1;55094;1012988;XF 338/1;;1;1;1;308;;140;P;;05/08/2004;1;0 2004;1006003;1;55096;1012999;Dally/1;;2;2;1;137;;8.9;P;;09/09/2004;1;0 2004;1006003;1;55096;1012999;Dally/1;;2;2;1;193;;192;P;;01/01/2004;1;0 2004;1006003;1;55096;1012999;Dally/1;;2;2;1;103;14.95;87;P;;09/09/2004;1;0 that's the begining of my table and I'm trying to read it from R but I can't actually to read it I write this script donAP - read.table(C:/Documents and Settings/melyakhlifi/Mes documents/feuilles excel/copi_donnees3.csv,header=TRUE,sep=;,quote=,dec=.) Erreur dans scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : la ligne 656 n'avait pas 18 �l�ments there's some errors and I don't understand why? The obvious question is what line 656 (+/- a couple of lines) actually contains... x - readLines(C:/Documents and Settings/melyakhlifi/Mes documents/feuilles excel/copi_donnees3.csv) length(x) x[656] x[653:658] # (if long enough) -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-help@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.
Re: [R] read.table with more than one sep
Try this: # test data Input - 4547;1970.01.01 00:00-1970.01.01 01:00; noData 4547;1970.01.01 00:00-1970.01.01 01:00; noData # replace next line with Lines - readLines(myfile.dat) Lines - readLines(textConnection(Input)) Lines - gsub([;-], , Lines) read.table(textConnection(Lines)) On 4/19/07, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote: Dear List, somebody knows, if the following operation can be done in an easier way? The data rows which should be read into R look like that: 4547;1970.01.01 00:00-1970.01.01 01:00; noData Unitil now we are doing this procedure: 1. Dividing columns which are separated by ; = temp - read.table(file ,sep=';', na.strings='noData', strip.white=TRUE) = write(temp, temp.txt) 2. Dividing colums which are separated by - = temp - read.table(temp.txt ,sep='-', na.strings='noData', strip.white=TRUE) = write(temp, temp.txt) 3. Dividing colums which are separated by = temp - read.table(temp.txt ,sep=' ', na.strings='noData', strip.white=TRUE) I can imagine that there should be a way to do this more efficient. Thanks for help in advance. Jan Schwanbeck University of Berne Institute of Geography __ R-help@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. __ R-help@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.
Re: [R] read.table for a subset of data
Feng,
I had the same question as you, how to read a subset of data, and the same
reaction as Wensui when I discovered that read.table could not. Even if my
computer's memory were up to it, I am troubled by the idea of reading in 1.8
GB of data (in my case) to get just 4,000 numbers, for instance, particularly
if I'm then going to iterating through the entire dataset in 4,000-number
chunks.
I ended up defining a NetCDF format to hold my data using the RNetCDF
package, since that package's var.get.nc() function is perfectly able to read
subsets of a NetCDF variable. Furthermore, NetCDF files allow data to be
matrices and even higher order arrays, from which you can then retrieve any
chunk by including var.get.nc 'start' and 'count' arguments in the form of
vectors of length equal to the number of array dimensions. Once a NetCDF
format is defined, all else is painless. One limitation is that the RNetCDF
package only supports version 3 of the NetCDF library, a version that puts a
2 GB limit on a variable's size. Version 4 removes this limitation; I'm
hopeful some day that an R package will be an interface to the NetCDF version
4 library.
John Thaden
Message: 22
Date: Sun, 11 Mar 2007 21:33:04 -0500
From: jim holtman [EMAIL PROTECTED]
Subject: Re: [R] read.table for a subset of data
To: Wensui Liu [EMAIL PROTECTED]
Cc: r-help r-help@stat.math.ethz.ch
Message-ID:
[EMAIL PROTECTED]
Content-Type: text/plain
If you know what 10 rows to read, then you can 'skip' to them, but it the
system still has to read each line at a time.
I have a 200,000 line csv file of numerics that takes me 4 seconds to read
in with 'read.csv' using 'colClasses', so I would guess your 100K line file
would take half of that. Is 2 seconds of time a waste of resources?
On 3/11/07, Wensui Liu [EMAIL PROTECTED] wrote:
Jim,
Glad to see your reply.
Refering to your email, what if I just want to read 10 rows from a csv
table with 10 rows? Do you think it a waste of resource to read
the whole table in?
Anything thought?
wensui
On 3/11/07, jim holtman [EMAIL PROTECTED] wrote:
Why cann't you read in the whole data set and then create the
subsets? This
is easily done with 'split'. If the data is too large, then consider a
data
base.
On 3/11/07, gnv shqp [EMAIL PROTECTED] wrote:
Hi R-experts,
I have data from four conditions of an experiment. I tried to create
four
subsets of the data with read.table, for example,
read.table(Experiment.csv,subset=(condition==1))
. I found a similar post in the archive, but the answer to that post
was
no. Any new ideas about reading subsets of data with read.table?
Thanks!
Feng
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__
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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.
Re: [R] read.table for a subset of data
If you are iterating through the dataset 4000 numbers/lines at a time, you
can do this by opening the dataset as a connection and then
reading/processing 4000 lines at a time
myFile - open('dataset', 'r')
while (TRUE){
input - scan(myFile, what=0, n=4000)
if (length(input) == 0) break
.process the data
}
But if you want to randomly select which lines, then some type of database
is better.
On 3/12/07, Thaden, John J [EMAIL PROTECTED] wrote:
Feng,
I had the same question as you, how to read a subset of data, and the
same
reaction as Wensui when I discovered that read.table could not. Even if
my
computer's memory were up to it, I am troubled by the idea of reading in
1.8
GB of data (in my case) to get just 4,000 numbers, for instance,
particularly
if I'm then going to iterating through the entire dataset in 4,000-number
chunks.
I ended up defining a NetCDF format to hold my data using the RNetCDF
package, since that package's var.get.nc() function is perfectly able to
read
subsets of a NetCDF variable. Furthermore, NetCDF files allow data to be
matrices and even higher order arrays, from which you can then retrieve
any
chunk by including var.get.nc 'start' and 'count' arguments in the form of
vectors of length equal to the number of array dimensions. Once a NetCDF
format is defined, all else is painless. One limitation is that the
RNetCDF
package only supports version 3 of the NetCDF library, a version that puts
a
2 GB limit on a variable's size. Version 4 removes this limitation; I'm
hopeful some day that an R package will be an interface to the NetCDF
version
4 library.
John Thaden
Message: 22
Date: Sun, 11 Mar 2007 21:33:04 -0500
From: jim holtman [EMAIL PROTECTED]
Subject: Re: [R] read.table for a subset of data
To: Wensui Liu [EMAIL PROTECTED]
Cc: r-help r-help@stat.math.ethz.ch
Message-ID:
[EMAIL PROTECTED]
Content-Type: text/plain
If you know what 10 rows to read, then you can 'skip' to them, but it the
system still has to read each line at a time.
I have a 200,000 line csv file of numerics that takes me 4 seconds to read
in with 'read.csv' using 'colClasses', so I would guess your 100K line
file
would take half of that. Is 2 seconds of time a waste of resources?
On 3/11/07, Wensui Liu [EMAIL PROTECTED] wrote:
Jim,
Glad to see your reply.
Refering to your email, what if I just want to read 10 rows from a csv
table with 10 rows? Do you think it a waste of resource to read
the whole table in?
Anything thought?
wensui
On 3/11/07, jim holtman [EMAIL PROTECTED] wrote:
Why cann't you read in the whole data set and then create the
subsets? This
is easily done with 'split'. If the data is too large, then consider
a
data
base.
On 3/11/07, gnv shqp [EMAIL PROTECTED] wrote:
Hi R-experts,
I have data from four conditions of an experiment. I tried to
create
four
subsets of the data with read.table, for example,
read.table(Experiment.csv,subset=(condition==1))
. I found a similar post in the archive, but the answer to that
post
was
no. Any new ideas about reading subsets of data with read.table?
Thanks!
Feng
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contact the sender by reply e-mail and destroy all copies of the original
message.
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem you are trying to solve?
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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.
[R] read.table for a subset of data
Hi R-experts, I have data from four conditions of an experiment. I tried to create four subsets of the data with read.table, for example, read.table(Experiment.csv,subset=(condition==1)) . I found a similar post in the archive, but the answer to that post was no. Any new ideas about reading subsets of data with read.table? Thanks! Feng [[alternative HTML version deleted]] __ R-help@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.
Re: [R] read.table for a subset of data
as far as I've know, I don't think you can do so with read.table. But I am also thinking about RODBC and wondering if you could assign a DSN to your .csv file and then use sql to fetch the subset. On 3/11/07, gnv shqp [EMAIL PROTECTED] wrote: Hi R-experts, I have data from four conditions of an experiment. I tried to create four subsets of the data with read.table, for example, read.table(Experiment.csv,subset=(condition==1)) . I found a similar post in the archive, but the answer to that post was no. Any new ideas about reading subsets of data with read.table? Thanks! Feng [[alternative HTML version deleted]] __ R-help@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. -- WenSui Liu A lousy statistician who happens to know a little programming (http://spaces.msn.com/statcompute/blog) __ R-help@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.
Re: [R] read.table for a subset of data
Why cann't you read in the whole data set and then create the subsets? This is easily done with 'split'. If the data is too large, then consider a data base. On 3/11/07, gnv shqp [EMAIL PROTECTED] wrote: Hi R-experts, I have data from four conditions of an experiment. I tried to create four subsets of the data with read.table, for example, read.table(Experiment.csv,subset=(condition==1)) . I found a similar post in the archive, but the answer to that post was no. Any new ideas about reading subsets of data with read.table? Thanks! Feng [[alternative HTML version deleted]] __ R-help@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. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem you are trying to solve? [[alternative HTML version deleted]] __ R-help@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.
Re: [R] read.table for a subset of data
Jim, Glad to see your reply. Refering to your email, what if I just want to read 10 rows from a csv table with 10 rows? Do you think it a waste of resource to read the whole table in? Anything thought? wensui On 3/11/07, jim holtman [EMAIL PROTECTED] wrote: Why cann't you read in the whole data set and then create the subsets? This is easily done with 'split'. If the data is too large, then consider a data base. On 3/11/07, gnv shqp [EMAIL PROTECTED] wrote: Hi R-experts, I have data from four conditions of an experiment. I tried to create four subsets of the data with read.table, for example, read.table(Experiment.csv,subset=(condition==1)) . I found a similar post in the archive, but the answer to that post was no. Any new ideas about reading subsets of data with read.table? Thanks! Feng [[alternative HTML version deleted]] __ R-help@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. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem you are trying to solve? [[alternative HTML version deleted]] __ R-help@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. -- WenSui Liu A lousy statistician who happens to know a little programming (http://spaces.msn.com/statcompute/blog) __ R-help@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.
Re: [R] read.table for a subset of data
If you know what 10 rows to read, then you can 'skip' to them, but it the system still has to read each line at a time. I have a 200,000 line csv file of numerics that takes me 4 seconds to read in with 'read.csv' using 'colClasses', so I would guess your 100K line file would take half of that. Is 2 seconds of time a waste of resources? On 3/11/07, Wensui Liu [EMAIL PROTECTED] wrote: Jim, Glad to see your reply. Refering to your email, what if I just want to read 10 rows from a csv table with 10 rows? Do you think it a waste of resource to read the whole table in? Anything thought? wensui On 3/11/07, jim holtman [EMAIL PROTECTED] wrote: Why cann't you read in the whole data set and then create the subsets? This is easily done with 'split'. If the data is too large, then consider a data base. On 3/11/07, gnv shqp [EMAIL PROTECTED] wrote: Hi R-experts, I have data from four conditions of an experiment. I tried to create four subsets of the data with read.table, for example, read.table(Experiment.csv,subset=(condition==1)) . I found a similar post in the archive, but the answer to that post was no. Any new ideas about reading subsets of data with read.table? Thanks! Feng [[alternative HTML version deleted]] __ R-help@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. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem you are trying to solve? [[alternative HTML version deleted]] __ R-help@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. -- WenSui Liu A lousy statistician who happens to know a little programming (http://spaces.msn.com/statcompute/blog) -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem you are trying to solve? [[alternative HTML version deleted]] __ R-help@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.
[R] read.table
hi, how could I let the colname be the numbers instead of X plus numbers when I use read.table. Or there is an alternative way? thanks -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you always know? No, I did not. But I believed... ---Matrix III __ R-help@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.
Re: [R] read.table
On Thu, 2006-10-19 at 16:10 -0400, Weiwei Shi wrote: hi, how could I let the colname be the numbers instead of X plus numbers when I use read.table. Or there is an alternative way? thanks Sounds like you have imported the data, perhaps using 'header = TRUE' either without an actual header row of column names or perhaps an incomplete or improper (not syntactically valid) header row. If you are getting X's (and not V's) pre-pended to the column names, that sounds like the result of make.names() on your data. See ?make.names If you don't have a header row in the imported data set, you can use the 'colnames' argument in read.table() to explicitly provide them. Just be sure to set 'header = FALSE'. If there is a header row, but it is problematic, set 'header = FALSE' AND 'skip = 1', which will skip over the first row in the incoming file. See ?read.table HTH, Marc Schwartz __ R-help@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.
Re: [R] read.table
thanks. i know how to go around it but i feel read.table should have something like that to disable the process of adding X to the header :) On 10/19/06, Marc Schwartz [EMAIL PROTECTED] wrote: On Thu, 2006-10-19 at 16:10 -0400, Weiwei Shi wrote: hi, how could I let the colname be the numbers instead of X plus numbers when I use read.table. Or there is an alternative way? thanks Sounds like you have imported the data, perhaps using 'header = TRUE' either without an actual header row of column names or perhaps an incomplete or improper (not syntactically valid) header row. If you are getting X's (and not V's) pre-pended to the column names, that sounds like the result of make.names() on your data. See ?make.names If you don't have a header row in the imported data set, you can use the 'colnames' argument in read.table() to explicitly provide them. Just be sure to set 'header = FALSE'. If there is a header row, but it is problematic, set 'header = FALSE' AND 'skip = 1', which will skip over the first row in the incoming file. See ?read.table HTH, Marc Schwartz -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you always know? No, I did not. But I believed... ---Matrix III __ R-help@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.
Re: [R] read.table
On Thu, 2006-10-19 at 17:06 -0400, Weiwei Shi wrote: thanks. i know how to go around it but i feel read.table should have something like that to disable the process of adding X to the header :) You could try setting 'check.names = FALSE' to see what you end up with in terms of column names. That will effectively disable the use of make.names() to validate/adjust the incoming column names. The risk here is unknown depending upon the root etiology of the problem. HTH, Marc Schwartz __ R-help@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.
Re: [R] read.table() and scientific notation
January == January Weiner [EMAIL PROTECTED] writes: Dear all, I am having troubles importing values written as scientific notation using read.table(). I'm sure this is a frequent problem, as many people in my lab have this problem as well, so I'm sure that I just have troubles googling for the right solution. The problem is, that, given a file like that: a 1 2e-4 b 2 3e-8 ... Note: this is advocacy for education in clear quantitative language and is a border-line off topic rant... The other day I read a paper from a student who used notation like 2e-4 in the text - blech! I sent it back for revisions. Lately I have noticed here and in other places this tendency to use floating point notation (also referred to as exponential notation) where scientific notation is appropriate, and vice versa. The notation 2e-4 is a convenient way to express floating point numbers with a simple text string, but it is certainly not scientific notation. No wonder you had trouble googling it! Mike __ R-help@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.
Re: [R] read.table() and scientific notation
Note: this is advocacy for education in clear quantitative
language and is a border-line off topic rant...
The other day I read a paper from a student who used notation
like 2e-4 in the text - blech! I sent it back for revisions.
You have sent it back for revisions just because the student used a
version of the scientific notation that can be routinely found in
literature? Hm. I am _teaching_ my students to understand the
scientific notation in the form 1e-20 etc. - for example, because
many programs in the field (including R) are representing real numbers
using this version of scientific notation. I wouldn't penalize a
student for using it in a scientific text. That's what the proof
reading is for (if the editors are picky).
Lately I have noticed here and in other places this tendency to
use floating point notation (also referred to as exponential
notation) where scientific notation is appropriate, and vice
versa. The notation 2e-4 is a convenient way to express floating
point numbers with a simple text string, but it is certainly not
scientific notation.
Depends how formal and picky you wish to be. 2e-4 is the same as
$2\times10^{-4}$ to me as it is for most people, I guess (e.g. look at
the Wikipedia entry).
No wonder you had trouble googling it!
Nope. The problem with googling is that most of the pages you get when
googling for R do not refer to R as the statistical language.
Cheers,
January
--
January Weiner 3 -+---
Division of Bioinformatics, University of Muenster | Schloßplatz 4
(+49)(251)8321634 | D48149 Münster
http://www.uni-muenster.de/Evolution/ebb/ | Germany
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[R] read.table() and scientific notation
Dear all, I am having troubles importing values written as scientific notation using read.table(). I'm sure this is a frequent problem, as many people in my lab have this problem as well, so I'm sure that I just have troubles googling for the right solution. The problem is, that, given a file like that: a 1 2e-4 b 2 3e-8 ... the third column gets imported as a factor, or a string if I set the as.is parameter of read.table to TRUE for this column. However, I just want a simple numeric vector :-) I'm sure there is a simple trick for this. If you can point me to the right function, or manual, I think I should be able to find out the details myself. Thanks in advance, January -- January Weiner 3 -+--- Division of Bioinformatics, University of Muenster | Schloßplatz 4 (+49)(251)8321634 | D48149 Münster http://www.uni-muenster.de/Biologie.Botanik/ebb/| Germany __ R-help@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.
Re: [R] read.table() and scientific notation
Your example does not exhibit that behavior when I try it (below). Can you provide a reproducible example following the style shown here: Lines - a 1 2e-4 + b 2 3e-8 DF - read.table(textConnection(Lines)) str(DF) 'data.frame': 2 obs. of 3 variables: $ V1: Factor w/ 2 levels a,b: 1 2 $ V2: int 1 2 $ V3: num 2e-04 3e-08 R.version.string # Windows XP [1] R version 2.4.0 (2006-10-03) On 10/10/06, January Weiner [EMAIL PROTECTED] wrote: Dear all, I am having troubles importing values written as scientific notation using read.table(). I'm sure this is a frequent problem, as many people in my lab have this problem as well, so I'm sure that I just have troubles googling for the right solution. The problem is, that, given a file like that: a 1 2e-4 b 2 3e-8 ... the third column gets imported as a factor, or a string if I set the as.is parameter of read.table to TRUE for this column. However, I just want a simple numeric vector :-) I'm sure there is a simple trick for this. If you can point me to the right function, or manual, I think I should be able to find out the details myself. Thanks in advance, January -- January Weiner 3 -+--- Division of Bioinformatics, University of Muenster | Schloßplatz 4 (+49)(251)8321634 | D48149 Münster http://www.uni-muenster.de/Biologie.Botanik/ebb/| Germany __ R-help@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. __ R-help@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.
Re: [R] read.table() and scientific notation
On FC5 Linux: gannet% cat foo.dat a 1 2e-4 b 2 3e-8 gannet% R ... read.table(foo.dat) V1 V2V3 1 a 1 2e-04 2 b 2 3e-08 sapply(read.table(foo.dat), class) V1V2V3 factor integer numeric so please tell us your environment and give a reproducible example. (This is using the OS function strtod, so it might be a deficiency in your OS's implementation of ISO C.) On Tue, 10 Oct 2006, January Weiner wrote: Dear all, I am having troubles importing values written as scientific notation using read.table(). I'm sure this is a frequent problem, as many people in my lab have this problem as well, so I'm sure that I just have troubles googling for the right solution. The problem is, that, given a file like that: a 1 2e-4 b 2 3e-8 ... the third column gets imported as a factor, or a string if I set the as.is parameter of read.table to TRUE for this column. However, I just want a simple numeric vector :-) I'm sure there is a simple trick for this. If you can point me to the right function, or manual, I think I should be able to find out the details myself. Thanks in advance, January -- Brian D. Ripley, [EMAIL PROTECTED] 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, UKFax: +44 1865 272595 __ R-help@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.
Re: [R] read.table() and scientific notation
Oh, thanks, that was hint enough :-) I see it now. I turns that R does not understand e-10 ...which stands for 1e-10 and is produced by some of the bioinformatic applications that I use (notably BLAST). However, R instead of being verbose on that just assumes that the whole column is a string. Is there a way to enforce a specific conversion in R (for example, to be able to see where the errors are?). January -- January Weiner 3 -+--- Division of Bioinformatics, University of Muenster | Schloßplatz 4 (+49)(251)8321634 | D48149 Münster http://www.uni-muenster.de/Biologie.Botanik/ebb/| Germany __ R-help@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.
Re: [R] read.table() and scientific notation
I think the colClasses argument to read.table() is what you need. Either that, or explicitly cast columns in the data.frame that's returned by read.table(). That's how you get data types that aren't directly supported by read.table(), like various date formats. - Martin January Weiner wrote: Oh, thanks, that was hint enough :-) I see it now. I turns that R does not understand e-10 ...which stands for 1e-10 and is produced by some of the bioinformatic applications that I use (notably BLAST). However, R instead of being verbose on that just assumes that the whole column is a string. Is there a way to enforce a specific conversion in R (for example, to be able to see where the errors are?). January __ R-help@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.
Re: [R] read.table() and scientific notation
On Tue, 10 Oct 2006, January Weiner wrote: Oh, thanks, that was hint enough :-) I see it now. I turns that R does not understand e-10 ...which stands for 1e-10 and is produced by some of the bioinformatic applications that I use (notably BLAST). And that is not standard C notation. However, R instead of being verbose on that just assumes that the whole column is a string. Is there a way to enforce a specific conversion in R (for example, to be able to see where the errors are?). Please study ?read.table, especially 'colClasses'. -- Brian D. Ripley, [EMAIL PROTECTED] 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, UKFax: +44 1865 272595 __ R-help@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.
Re: [R] read.table() and scientific notation
A cheeky solution by subverting the coerce mechanism and read.table:
# install a coerce function which can fix the e+10 syntax for an
imaginary class myDouble:
setAs(character, myDouble, function(from)as.double(sub('^(-?)
e','\\11e',from)))
Warning message:
in the method signature for function 'coerce' no definition for
class: “myDouble” in: matchSignature(signature, fdef, where)
# load some data:
Lines - scan(sep=\n, what=)
a 1 3e-8
b 2 1e+10
c 3 e-10
d 4 e+3
e 5 e+1
# process it without using the imaginary class - use a real double
instead to see what happens:
# Note I've used textConnection(Lines) here, where your filename
would go
T - read.table(textConnection(Lines), colClasses=list
(character, integer, double))
Error in scan(file, what, nmax, sep, dec, quote, skip, nlines,
na.strings, :
scan() expected 'a real', got 'e-10'
# process it, specifying the imaginary class myDouble.
T - read.table(textConnection(Lines), colClasses=list
(character, integer, myDouble))
T
V1 V2V3
1 a 1 3e-08
2 b 2 1e+10
3 c 3 1e-10
4 d 4 1e+03
5 e 5 1e+01
lapply(T, class)
$V1
[1] character
$V2
[1] integer
$V3
[1] numeric
Someone's bound to shoot me down for hackery here :-)
-Alex
On 10 Oct 2006, at 11:43, January Weiner wrote:
Dear all,
I am having troubles importing values written as scientific notation
using read.table(). I'm sure this is a frequent problem, as many
people in my lab have this problem as well, so I'm sure that I just
have troubles googling for the right solution.
The problem is, that, given a file like that:
a 1 2e-4
b 2 3e-8
...
the third column gets imported as a factor, or a string if I set the
as.is parameter of read.table to TRUE for this column. However, I just
want a simple numeric vector :-) I'm sure there is a simple trick for
this. If you can point me to the right function, or manual, I think I
should be able to find out the details myself.
Thanks in advance,
January
--
January Weiner 3 -+---
Division of Bioinformatics, University of Muenster | Schloßplatz 4
(+49)(251)8321634 | D48149 Münster
http://www.uni-muenster.de/Biologie.Botanik/ebb/| Germany
__
R-help@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.
__
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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.
[R] read.table() features {was difficult data ..}
Gabor == Gabor Grothendieck [EMAIL PROTECTED] on Mon, 3 Jul 2006 16:58:14 -0400 writes: Gabor Try this: Gabor # test data Gabor # read in header separately so R does not make column names unique Gabor Lines - AAA BBB CCC DDD AAA BBB Gabor 0 2 1 2 0 0 Gabor 2 3 7 6 0 1 Gabor 1.54 9 9 6 0 Gabor 1.06 1011 3 3 Gabor Gabor DF - read.table(textConnection(Lines), skip = 1) Gabor names(DF) - scan(textConnection(Lines), what = , nlines = 1) Hmm, this is unnecessarily slightly complicated. Instead, rather make use of read.table()'s capabilities, by DF - read.table(textConnection(Lines), check.names=FALSE, header=TRUE) ## ^ Martin Maechler, ETH Zurich __ R-help@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
[R] read.table with data in specific formats
Dear R Users Does anyone know how to read a text with a specific format? I know that has to do with two functions: read.table and sprintf but not sure how to put them together. Say that I have a text file called data.txt, and I would to read it according with %.14f %.10f %2.5f, which includes three columns. Thank you very much. Yihsu Chen The Johns Hopkins University __ R-help@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
Re: [R] read.table with data in specific formats
read.table segments rows by separators, not by format of entry. Suppose your data.txt is like: 1.00 2.01 3.003 4.10 5.22 6.333 7.22 8.88 9.99 Then read.table(data.txt, sep = ) Best Regards XiaoQuoting YIHSU CHEN [EMAIL PROTECTED]: Dear R Users Does anyone know how to read a text with a specific format? I know that has to do with two functions: read.table and sprintf but not sure how to put them together. Say that I have a text file called data.txt, and I would to read it according with %.14f %.10f %2.5f, which includes three columns. Thank you very much. Yihsu Chen The Johns Hopkins University __ R-help@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 *** Xiao Liu Stanford University Medical Center Department of Developmental Biology 279 Campus Drive Stanford, CA 94305-5329 (650)725-7612(L) __ R-help@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
[R] read.table (Error in file(file, r) : unable to open connection)
G’day, I am trying to read in a table and am getting an error message stating that R is unable to open a connection to the file. ➢ Avonvegen- read.table(Y:\Study Sites\Avon\nonspatial\datafiles\archive\Avon_VegEnh.dat , sep=,, na.string=-, header=TRUE) Error in file(file, r) : unable to open connection In addition: Warning message: cannot open file 'Y:Study SitesAvon onspatialdatafilesrchiveAvon_VegEnh.dat ', reason 'Invalid argument' I have checked that the AvonVegEnh.dat is spelt correctly and has no hidden extensions. I have checked that the folder is accessible. I have moved the datafile and changed the script to try reading from the local drive with no success. I have used the same syntax on a similar file (same field structure but different data) with no problems before and now it doesn't read either. Does anyone have any ideas? Thanks, david __ R-help@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
Re: [R] read.table (Error in file(file, r) : unable to open connection)
See 2.16 of the R Windows FAQ. On 5/8/06, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote: G'day, I am trying to read in a table and am getting an error message stating that R is unable to open a connection to the file. ➢ Avonvegen- read.table(Y:\Study Sites\Avon\nonspatial\datafiles\archive\Avon_VegEnh.dat , sep=,, na.string=-, header=TRUE) Error in file(file, r) : unable to open connection In addition: Warning message: cannot open file 'Y:Study SitesAvon onspatialdatafilesrchiveAvon_VegEnh.dat ', reason 'Invalid argument' I have checked that the AvonVegEnh.dat is spelt correctly and has no hidden extensions. I have checked that the folder is accessible. I have moved the datafile and changed the script to try reading from the local drive with no success. I have used the same syntax on a similar file (same field structure but different data) with no problems before and now it doesn't read either. Does anyone have any ideas? Thanks, david __ R-help@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 __ R-help@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
Re: [R] read.table (Error in file(file, r) : unable to open connection)
I guess you use R under windows,then use \\ instead of \. or use file.choose() to choose the file directly. 2006/5/9, [EMAIL PROTECTED] [EMAIL PROTECTED]: G'day, I am trying to read in a table and am getting an error message stating that R is unable to open a connection to the file. ➢ Avonvegen- read.table(Y:\Study Sites\Avon\nonspatial\datafiles\archive\Avon_VegEnh.dat , sep=,, na.string=-, header=TRUE) Error in file(file, r) : unable to open connection In addition: Warning message: cannot open file 'Y:Study SitesAvon onspatialdatafilesrchiveAvon_VegEnh.dat ', reason 'Invalid argument' I have checked that the AvonVegEnh.dat is spelt correctly and has no hidden extensions. I have checked that the folder is accessible. I have moved the datafile and changed the script to try reading from the local drive with no success. I have used the same syntax on a similar file (same field structure but different data) with no problems before and now it doesn't read either. Does anyone have any ideas? Thanks, david __ R-help@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 -- 黄荣贵 Deparment of Sociology Fudan University __ R-help@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
[R] Read.table
Hi, I have some column vector in txt or xls and I need to load into R as numeric vector. I use the read.table (X=read.table(123.txt) command but the program say that X is not a numeric vector Where is the problem? Matías University of Oviedo, Spain [[alternative HTML version deleted]] __ R-help@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
Re: [R] Read.table
Matias Mayor Fernandez wrote: Hi, I have some column vector in txt or xls and I need to load into R as numeric vector. I use the read.table (X=read.table(123.txt”) command but the program say that “X is not a numeric vector” No, I think you got: Error: syntax error in (X=read.table(123.txt or you have used another call without the syntax error in it. In any case, please be more specific what you did. You might also want to copy the first few lines of file 123.txt in your mail. Uwe Ligges Where is the problem? Matías University of Oviedo, Spain [[alternative HTML version deleted]] __ R-help@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 __ R-help@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
Re: [R] Read.table
From: Uwe Ligges Matias Mayor Fernandez wrote: Hi, I have some column vector in txt or xls and I need to load into R as numeric vector. I use the read.table (X=read.table(123.txt) command but the program say that X is not a numeric vector No, I think you got: Error: syntax error in (X=read.table(123.txt or you have used another call without the syntax error in it. In any case, please be more specific what you did. You might also want to copy the first few lines of file 123.txt in your mail. Besides, if Matias only has one column of data and want that read in as a vector, scan() is really more appropriate. Andy Uwe Ligges Where is the problem? Matías University of Oviedo, Spain [[alternative HTML version deleted]] -- -- __ R-help@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 __ R-help@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 __ R-help@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
Re: [R] Read.table
On 3/8/06 8:31 AM, Liaw, Andy [EMAIL PROTECTED] wrote: From: Uwe Ligges Matias Mayor Fernandez wrote: Hi, I have some column vector in txt or xls and I need to load into R as numeric vector. I use the read.table (X=read.table(123.txt) command but the program say that X is not a numeric vector See here if you want to think of your data as a single-column table: http://cran.r-project.org/doc/manuals/R-data.html#Spreadsheet_002dlike-data Sean __ R-help@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
[R] read.table missing values
Dear R users, I'm trying to read data from a tab-delimited text file to R, but I have problems with missing values. R gives this kind of error messages: line 1 did not have 9 elements. Could someone tell me how I can deal with missing values in this case? Thanks a lot in advance, Istvan __ R-help@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
Re: [R] read.table missing values
Does using read.delim instead of read.table fix your problem? Sean On 2/22/06 7:40 AM, I.Szentirmai [EMAIL PROTECTED] wrote: Dear R users, I'm trying to read data from a tab-delimited text file to R, but I have problems with missing values. R gives this kind of error messages: line 1 did not have 9 elements. Could someone tell me how I can deal with missing values in this case? Thanks a lot in advance, Istvan __ R-help@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 __ R-help@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
Re: [R] read.table missing values
might be, but I have already found another solution: reat.table(file,sep=\t) Thanks, Istvan On Wed, 22 Feb 2006 07:54:49 -0500 Sean Davis [EMAIL PROTECTED] wrote: Does using read.delim instead of read.table fix your problem? Sean On 2/22/06 7:40 AM, I.Szentirmai [EMAIL PROTECTED] wrote: Dear R users, I'm trying to read data from a tab-delimited text file to R, but I have problems with missing values. R gives this kind of error messages: line 1 did not have 9 elements. Could someone tell me how I can deal with missing values in this case? Thanks a lot in advance, Istvan __ R-help@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 __ R-help@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
Re: [R] read.table missing values
I have experienced a similar problem when saving Excel data in this format. When any of the variables, except the last, contained missing values, there was not a problem. However, the problem occurred when the last variable contained missing values. My guess is that the last delimiter was left off? The fill option worked in my case. Use the option with care and double check the dataset. HTH Matthew McIntosh -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of I.Szentirmai Sent: Wednesday, February 22, 2006 7:04 AM To: r-help Subject: Re: [R] read.table missing values might be, but I have already found another solution: reat.table(file,sep=\t) Thanks, Istvan On Wed, 22 Feb 2006 07:54:49 -0500 Sean Davis [EMAIL PROTECTED] wrote: Does using read.delim instead of read.table fix your problem? Sean On 2/22/06 7:40 AM, I.Szentirmai [EMAIL PROTECTED] wrote: Dear R users, I'm trying to read data from a tab-delimited text file to R, but I have problems with missing values. R gives this kind of error messages: line 1 did not have 9 elements. Could someone tell me how I can deal with missing values in this case? Thanks a lot in advance, Istvan __ R-help@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 __ R-help@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 __ R-help@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
Re: [R] read.table
Diethelm Wuertz wrote: Thanks a lot that works fine! Next problem, if I would have my own package, and the file test.csv would be located in the data directory How to use the function data to get data(test) Also put in the data subdirectory the file test.R with the commands to read test.csv Kjetil resulting in: test %y-%m-%d VALUE 1 1999-01-01 100 2 2000-12-31 999 Again Thanks in advance Diethelm Wuertz Phil Spector wrote: Look at the check.names= argument to read.table -- you want to set it to FALSE. But rememeber that you'l have to put quotes around the name whenever you use it, as in x$'%y-%m-%d' - Phil Spector Statistical Computing Facility Department of Statistics UC Berkeley [EMAIL PROTECTED] On Tue, 14 Feb 2006, Diethelm Wuertz wrote: I have a file named test.csv with the following 3 lines: %y-%m-%d;VALUE 1999-01-01;100 2000-12-31;999 read.table(test.csv, header = TRUE, sep = ;) delivers: X.y..m..d VALUE 1 1999-01-01 100 2 2000-12-31 999 I would like to see the following ... %y-%m-%d VALUE 1 1999-01-01 100 2 2000-12-31 999 Note, readLines(test.csv, 1) delivers [1] %y-%m-%d;VALUE Is this possible ??? Thanks DW __ R-help@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 __ R-help@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 __ R-help@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
[R] read.table
Hi it appears to me that read.table is very slow for reading large data files (mine are 200,000 rows). Is there a better way? Thanks! Max -- Maximilian O. Kauer, Ph.D. Department of Genetics, White lab 333 Cedar St, NSB 386 PO Box 208005 New Haven, CT 06510 __ R-help@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
Re: [R] read.table
?scan is much faser. Also, read.table has a colClasses optional argument which can be used to speed up the reading of large files significantly. read.table has a pretty good help section well worth reading. read.table(file, header = FALSE, sep = , quote = \', dec = ., row.names, col.names, as.is = FALSE, na.strings = NA, colClasses = NA, nrows = -1, skip = 0, check.names = TRUE, fill = !blank.lines.skip, strip.white = FALSE, blank.lines.skip = TRUE, comment.char = #, allowEscapes = FALSE) 2006/2/14, Max Kauer [EMAIL PROTECTED]: Hi it appears to me that read.table is very slow for reading large data files (mine are 200,000 rows). Is there a better way? Thanks! Max -- Maximilian O. Kauer, Ph.D. Department of Genetics, White lab 333 Cedar St, NSB 386 PO Box 208005 New Haven, CT 06510 __ R-help@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 [[alternative HTML version deleted]] __ R-help@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
[R] read.table
I have a file named test.csv with the following 3 lines: %y-%m-%d;VALUE 1999-01-01;100 2000-12-31;999 read.table(test.csv, header = TRUE, sep = ;) delivers: X.y..m..d VALUE 1 1999-01-01 100 2 2000-12-31 999 I would like to see the following ... %y-%m-%d VALUE 1 1999-01-01 100 2 2000-12-31 999 Note, readLines(test.csv, 1) delivers [1] %y-%m-%d;VALUE Is this possible ??? Thanks DW __ R-help@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
Re: [R] read.table
?read.table The documentation has the parameter 'check.names'. On 2/13/06, Diethelm Wuertz [EMAIL PROTECTED] wrote: I have a file named test.csv with the following 3 lines: %y-%m-%d;VALUE 1999-01-01;100 2000-12-31;999 read.table(test.csv, header = TRUE, sep = ;) delivers: X.y..m..d VALUE 1 1999-01-01 100 2 2000-12-31 999 I would like to see the following ... %y-%m-%d VALUE 1 1999-01-01 100 2 2000-12-31 999 Note, readLines(test.csv, 1) delivers [1] %y-%m-%d;VALUE Is this possible ??? Thanks DW __ R-help@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 -- Jim Holtman Cincinnati, OH +1 513 247 0281 What the problem you are trying to solve? [[alternative HTML version deleted]] __ R-help@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
Re: [R] read.table
You can do it manually by reading in the headers separately: headers - read.table(test, header = FALSE, nrow = 1, sep = ;, as.is = TRUE) read.table(test, header = FALSE, skip = 1, sep = ;, col.names = headers) On 2/13/06, Diethelm Wuertz [EMAIL PROTECTED] wrote: I have a file named test.csv with the following 3 lines: %y-%m-%d;VALUE 1999-01-01;100 2000-12-31;999 read.table(test.csv, header = TRUE, sep = ;) delivers: X.y..m..d VALUE 1 1999-01-01 100 2 2000-12-31 999 I would like to see the following ... %y-%m-%d VALUE 1 1999-01-01 100 2 2000-12-31 999 Note, readLines(test.csv, 1) delivers [1] %y-%m-%d;VALUE Is this possible ??? Thanks DW __ R-help@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 __ R-help@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
Re: [R] read.table
Thanks a lot that works fine! Next problem, if I would have my own package, and the file test.csv would be located in the data directory How to use the function data to get data(test) resulting in: test %y-%m-%d VALUE 1 1999-01-01 100 2 2000-12-31 999 Again Thanks in advance Diethelm Wuertz Phil Spector wrote: Look at the check.names= argument to read.table -- you want to set it to FALSE. But rememeber that you'l have to put quotes around the name whenever you use it, as in x$'%y-%m-%d' - Phil Spector Statistical Computing Facility Department of Statistics UC Berkeley [EMAIL PROTECTED] On Tue, 14 Feb 2006, Diethelm Wuertz wrote: I have a file named test.csv with the following 3 lines: %y-%m-%d;VALUE 1999-01-01;100 2000-12-31;999 read.table(test.csv, header = TRUE, sep = ;) delivers: X.y..m..d VALUE 1 1999-01-01 100 2 2000-12-31 999 I would like to see the following ... %y-%m-%d VALUE 1 1999-01-01 100 2 2000-12-31 999 Note, readLines(test.csv, 1) delivers [1] %y-%m-%d;VALUE Is this possible ??? Thanks DW __ R-help@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 __ R-help@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
Re: [R] read.table
On Tue, 14 Feb 2006, Diethelm Wuertz wrote: Thanks a lot that works fine! Next problem, if I would have my own package, and the file test.csv would be located in the data directory How to use the function data to get data(test) resulting in: test %y-%m-%d VALUE 1 1999-01-01 100 2 2000-12-31 999 I think you might be stuck in a particular mindset about this. Does the .csv file have to be called test.csv? If not then if it is called data.csv say, you can have in your data directory a file test.R with the code: read.table(data.csv, header = TRUE, sep = ;, check.names = FALSE) Alternatively you can have the data in the file test.R, plus the code to read it in as desired. Creating a data structure and reading it back in with dput and dget is one way to do this. See page 11 of the Writing R Extensions manual for the possible formats of files in the data directory: The data subdirectory is for additional data files the package makes available for loading using data(). Currently, data files can have one of three types as indicated by their extension: plain R code (.R or .r), tables (.tab, .txt, or .csv), or save() images (.RData or .rda). (All ports of R use the same binary (XDR) format and can read compressed images. Use images saved with save(, compress = TRUE) to save space.) Note that R code should be self-sufficient and not make use of extra functionality provided by the package, so that the data file can also be used without having to load the package. David Scott _ David Scott Department of Statistics, Tamaki Campus The University of Auckland, PB 92019 AucklandNEW ZEALAND Phone: +64 9 373 7599 ext 86830 Fax: +64 9 373 7000 Email: [EMAIL PROTECTED] Graduate Officer, Department of Statistics __ R-help@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
[R] read.table problem
Dear R useRs,
I have big (23000 rows), vertical bar delimited file:
e.g.
A1|Text a,Text b, Text c|345
A2|Text bla|456
...
..
.
Try using
A - read.table('filename.txt', header=FALSE,sep='\|')
process stop at line 11975 with warning message:
number of items read is not a multiple of the number of columns
I have no problems with processing similar file, which is only 1
rows long?
Any suggestion what's the problem here. Thank's in advance.
Cheers, Andrej
__
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PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] read.table problem
Andrej Kastrin [EMAIL PROTECTED] writes:
Dear R useRs,
I have big (23000 rows), vertical bar delimited file:
e.g.
A1|Text a,Text b, Text c|345
A2|Text bla|456
...
..
.
Try using
A - read.table('filename.txt', header=FALSE,sep='\|')
process stop at line 11975 with warning message:
number of items read is not a multiple of the number of columns
I have no problems with processing similar file, which is only 1
rows long?
Any suggestion what's the problem here. Thank's in advance.
Well, the most obvious suspect is the file...
You might try
table(count.fields('filename.txt',sep='|'))
(There's no point in escaping the vertical bar)
Also, beware of quote symbols in the file, and possibly consider using
fill=TRUE.
--
O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B
c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907
__
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Re: [R] read.table problem
Hello,
Well... the error message is explicit enough: number of items read is
not a multiple of the number of columns means that you do not have the
right number of items around line 11975 (not the same number as in the
11974 previous lines)! This is an error in you file.
Best,
Philippe Grosjean
Andrej Kastrin wrote:
Dear R useRs,
I have big (23000 rows), vertical bar delimited file:
e.g.
A1|Text a,Text b, Text c|345
A2|Text bla|456
...
..
.
Try using
A - read.table('filename.txt', header=FALSE,sep='\|')
process stop at line 11975 with warning message:
number of items read is not a multiple of the number of columns
I have no problems with processing similar file, which is only 1
rows long?
Any suggestion what's the problem here. Thank's in advance.
Cheers, Andrej
__
R-help@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
__
R-help@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
Re: [R] read.table problem
By the way, you might find this sed one-liner useful:
sed -n '11981q;11970,11980p' filename.txt
It will print the offending line and its neighbors. If you're on
Windows you need to install Windows Services For Unix or Cygwin.
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Andrej Kastrin
Sent: Wednesday, January 25, 2006 3:08 AM
To: r-help
Subject: [R] read.table problem
Dear R useRs,
I have big (23000 rows), vertical bar delimited file:
e.g.
A1|Text a,Text b, Text c|345
A2|Text bla|456
...
..
.
Try using
A - read.table('filename.txt', header=FALSE,sep='\|')
process stop at line 11975 with warning message:
number of items read is not a multiple of the number of columns
I have no problems with processing similar file, which is only 1
rows long?
Any suggestion what's the problem here. Thank's in advance.
Cheers, Andrej
__
R-help@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
__
R-help@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
[R] read.table error
Hey, Once again I ask for some quick help. Here is some code: ovendata- read.table(ovens.dat,header=TRUE) attach(ovendata) print(ovendata) Here is the .dat file: DOne Two Three FourFiveSeven Eight 1130254 252 375 384 252 375 876 127 250 250 384 386 251 378 875 Here is the R Console output: ovendata- read.table(ovens.dat,header=TRUE) Warning message: incomplete final line found by readTableHeader on 'ovens.dat' attach(ovendata) The following object(s) are masked from ovendata ( position 3 ) : D Eight Five Four One Seven Three Two The following object(s) are masked from ovendata ( position 4 ) : D Eight Five Four One Seven Three Two The following object(s) are masked from ovendata ( position 5 ) : Eight Five Four One Seven Three Two The following object(s) are masked from package:stats : D print(ovendata) D One Two Three Four Five Seven Eight 1 1130 254 252 375 384 252 375 876 2 127 250 250 384 386 251 378 875 I've never seen anything like theis before. What's going on? Eric __ R-help@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
[R] read.table without sep
Hello all,
I have a data file table.txt which i have attached. I am trying to pass the
columns as arguments to a function totnorm where i am displaying a total
normalization plot. The function is given below:
totnorm-function(x,y){scale-sum(x)/sum(y);xlab-colnames(x);ylab-colnames(y);x1-x[[1]];y1-scale*y[[1]];plot(x1,y1,xlab=xlab,ylab=ylab,col=6,
col.lab=4);}
i tried doing this:
data-read.table(alldata.txt,header=TRUE,sep=\t)
a-data[1]
b-data[2]
totnorm(a,b)
The problem i am facing is- xlab and ylab contain the column names of
data[1] and data[2], but data[1][[1]] which is assigned to x1 has different
data which does not correspond to the colname(data[1]). Stating more
clearly, the colnames and the coldata don't match. I tried usind
read.tablewithout sep attribute, as given below:
data1-read.table(alldata.txt,header=TRUE)
But this statement is not getting executed using Rserve when i make a
connection to R and try to execute it from a java servlet. I don't know why
it was doing so, so thought it would be better to fix this on R side, i.e,
try to use the sep attribue in read.table and still make the colnames and
coldata point to the same col#.
Please suggest a solution.
Thanks,
Vasu.
14A_U133A_StatPairs 14A_U133A_Detection 14B_U133A_Signal
88A_U133A_Signal88B_U133A_Signal183A_U133A_Signal
183B_U133A_Signal
AFFX-BioB-5_at 403.0 409.3 611.5 569.2 536.6 580.2
AFFX-BioB-M_at 757.3 574.4 826.7 595.3 755.2 956.0
AFFX-BioB-3_at 284.4 327.3 421.6 336.6 391.3 412.6
AFFX-BioC-5_at 2314.2 1685.3 2264.7 2204.1 2233.1 2458.4
AFFX-BioC-3_at 1574.5 1273.0 1484.6 1321.2 1474.7 1774.1
AFFX-BioDn-5_at 2333.7 1796.8 2464.5 2372.5 2095.9 2735.7
AFFX-BioDn-3_at 13673.9 11463.9 13624.7 14513.9 12934.1 16293.1
AFFX-CreX-5_at 17778.8 15248.8 19977.2 19613.4 18609.1 18988.2
AFFX-CreX-3_at 31056.6 24869.9 30773.4 32918.6 34412.1 33954.6
AFFX-DapX-5_at 36.369.892.052.057.364.9
AFFX-DapX-M_at 133.4 75.176.2108.9 74.0100.2
AFFX-DapX-3_at 10.011.184.09.6 9.3 9.6
AFFX-LysX-5_at 40.431.18.3 6.6 8.6 50.0
AFFX-LysX-M_at 12.816.565.267.813.739.1
AFFX-LysX-3_at 66.18.6 83.59.4 43.928.7
AFFX-PheX-5_at 14.817.69.7 14.715.219.3
AFFX-PheX-M_at 70.612.422.888.08.0 18.5
AFFX-PheX-3_at 33.297.431.631.7129.5 11.1
AFFX-ThrX-5_at 26.431.314.523.428.124.2
AFFX-ThrX-M_at 87.443.989.433.052.452.8
AFFX-ThrX-3_at 19.918.913.926.124.017.0
AFFX-TrpnX-5_at 32.613.526.511.460.318.4
AFFX-TrpnX-M_at 14.97.5 12.110.111.312.8
AFFX-TrpnX-3_at 17.34.3 7.0 26.02.3 8.6
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Re: [R] read.table without sep
Vasu,
You have a lot of problems here.
1. How was your file generated? Excel? You have trailing tabs on
all but row 1 which is why your read.table call with sep=\t
gives you columns that don't seem to agree with what you expect.
See the argument row.names in ?read.table.
2. It's never a good idea to use colnames that begin with a digit.
3. read.table creates a _data frame_ for which data[i] would be
a data frame; your function does not accept data frames as input.
You probably want data[,i].
4. One-line 158-character function definitions with no spaces
are not exactly easy to read.
5. It's not clear whether you want the first column to be rownames
or data. R can handle both, but you need to tell it what to do.
6. * Best not to send such questions to R-devel. They have
nothing to do with the development of R.
Peter
Vasundhara Akkineni wrote:
Hello all,
I have a data file table.txt which i have attached. I am trying to pass the
columns as arguments to a function totnorm where i am displaying a total
normalization plot. The function is given below:
totnorm-function(x,y){scale-sum(x)/sum(y);xlab-colnames(x);ylab-colnames(y);x1-x[[1]];y1-scale*y[[1]];plot(x1,y1,xlab=xlab,ylab=ylab,col=6,
col.lab=4);}
i tried doing this:
data-read.table(alldata.txt,header=TRUE,sep=\t)
a-data[1]
b-data[2]
totnorm(a,b)
The problem i am facing is- xlab and ylab contain the column names of
data[1] and data[2], but data[1][[1]] which is assigned to x1 has different
data which does not correspond to the colname(data[1]). Stating more
clearly, the colnames and the coldata don't match. I tried usind
read.tablewithout sep attribute, as given below:
data1-read.table(alldata.txt,header=TRUE)
But this statement is not getting executed using Rserve when i make a
connection to R and try to execute it from a java servlet. I don't know why
it was doing so, so thought it would be better to fix this on R side, i.e,
try to use the sep attribue in read.table and still make the colnames and
coldata point to the same col#.
Please suggest a solution.
Thanks,
Vasu.
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[R] read.table error with R 2.2.0
Dear all, I just upgraded version of R to R 2.2.0, and I have a problem with a script that did not happen with my previous version. Here is the error : - param-read.table(file=param.dat,sep =\t,header=TRUE,fill=TRUE, na.strings=NA) Erreur dans read.table.default(file = param.dat, sep = \t, header = TRUE, : 5 arguments passed to 'readTableHead' which requires 6 - whereas all was OK before. I cannot understand what's happening. Has someone already encountered this ?? Any help greatly appreciated, Thanks a lot, Florence. [[alternative HTML version deleted]] __ R-help@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
Re: [R] read.table error with R 2.2.0
On 11/9/2005 10:07 AM, Florence Combes wrote: Dear all, I just upgraded version of R to R 2.2.0, and I have a problem with a script that did not happen with my previous version. Here is the error : - param-read.table(file=param.dat,sep =\t,header=TRUE,fill=TRUE, na.strings=NA) Erreur dans read.table.default(file = param.dat, sep = \t, header = TRUE, : 5 arguments passed to 'readTableHead' which requires 6 - whereas all was OK before. I cannot understand what's happening. Has someone already encountered this ?? Any help greatly appreciated, There is no read.table.default in standard R 2.2.0, so it appears that you have installed a replacement for read.table, and it no longer works. If you type getAnywhere(read.table)$where and getAnywhere(read.table.default)$where you are likely to see where those functions came from. (I see getAnywhere(read.table)$where [1] package:base namespace:base getAnywhere(read.table.default)$where character(0) indicating that read.table comes from the base package, and read.table.default doesn't exist. Duncan Murdoch __ R-help@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
Re: [R] read.table error with R 2.2.0
Thanks a lot for your answer. In fact I found the solution, it's seems strange to me so I put it here if it could bu useful for other people ... I have the same as you getAnywhere(read.table)$where [1] package:base namespace:base getAnywhere(read.table.default)$where character(0) when I run it in a native R console, and the line : param-read.table(file=param.dat,sep =\t,header=TRUE,fill=TRUE, na.strings=NA) works very well. (I didn't test this before). BUT when I load the aroma package (which I need for what I want to do), then I have : getAnywhere(read.table)$where [1] package:aroma [2] package:base [3] registered S3 method for read from namespace base [4] namespace:base getAnywhere(read.table.default)$where [1] package:aroma registered S3 method for read and the read.table didn't work. So I reinstall the aroma package (even if I had the latest version) and it works well now). best regards, Florence. On 11/9/05, Duncan Murdoch [EMAIL PROTECTED] wrote: On 11/9/2005 10:07 AM, Florence Combes wrote: Dear all, I just upgraded version of R to R 2.2.0, and I have a problem with a script that did not happen with my previous version. Here is the error : - param-read.table(file=param.dat,sep =\t,header=TRUE,fill=TRUE, na.strings=NA) Erreur dans read.table.default(file = param.dat, sep = \t, header = TRUE, : 5 arguments passed to 'readTableHead' which requires 6 - whereas all was OK before. I cannot understand what's happening. Has someone already encountered this ?? Any help greatly appreciated, There is no read.table.default in standard R 2.2.0, so it appears that you have installed a replacement for read.table, and it no longer works. If you type getAnywhere(read.table)$where and getAnywhere(read.table.default)$where you are likely to see where those functions came from. (I see getAnywhere(read.table)$where [1] package:base namespace:base getAnywhere(read.table.default)$where character(0) indicating that read.table comes from the base package, and read.table.default doesn't exist. Duncan Murdoch [[alternative HTML version deleted]] __ R-help@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
Re: [R] read.table error with R 2.2.0
Florence Combes [EMAIL PROTECTED] writes: Dear all, I just upgraded version of R to R 2.2.0, and I have a problem with a script that did not happen with my previous version. Here is the error : - param-read.table(file=param.dat,sep =\t,header=TRUE,fill=TRUE, na.strings=NA) Erreur dans read.table.default(file = param.dat, sep = \t, header = TRUE, : 5 arguments passed to 'readTableHead' which requires 6 - whereas all was OK before. I cannot understand what's happening. read.table is not generic in 2.2.0 and it calls .Internal(readTableHead(file, nlines, comment.char, blank.lines.skip, quote, sep)) So where did read.table.default() come into play? Is it picking up a version that you yourself have modified perhaps? Or are you using some package which redefines read.table and needs to be updated for 2.2.0? -p Has someone already encountered this ?? Any help greatly appreciated, Thanks a lot, Florence. [[alternative HTML version deleted]] __ R-help@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 -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-help@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
Re: [R] read.table error with R 2.2.0
Florence Combes wrote: Thanks a lot for your answer. In fact I found the solution, it's seems strange to me so I put it here if it could bu useful for other people ... I have the same as you getAnywhere(read.table)$where [1] package:base namespace:base getAnywhere(read.table.default)$where character(0) when I run it in a native R console, and the line : param-read.table(file=param.dat,sep =\t,header=TRUE,fill=TRUE, na.strings=NA) works very well. (I didn't test this before). BUT when I load the aroma package (which I need for what I want to do), then I have : getAnywhere(read.table)$where [1] package:aroma [2] package:base [3] registered S3 method for read from namespace base [4] namespace:base getAnywhere(read.table.default)$where [1] package:aroma registered S3 method for read and the read.table didn't work. So I reinstall the aroma package (even if I had the latest version) and it works well now). best regards, Florence. Hi, author of aroma here. This was fixed a few months ago. From showHistory(aroma): Version: 0.84 [2005-07-01] ... o BUG FIX: GenePixData$read() would give Error in read.table.default(... ...): 5 arguments passed to 'readTableHead' which requires 6. What I have done/did is that I created a read.table.QuantArrayData() function, rename base::read.table() to read.table.default() and made read.table() generic. This should make things rather backward compatible. When I looked at my source code history, the reason for this was: # 2002-08-18 # o Since the 'Measurements' section in QuantArray files seems to contain # rows with tailing TAB's (that just should be ignored) read.table() fails # to read them. read.table() is making use of scan() and scan() has the # argument 'flush' which flushes such trailing cells, but it is not used # by read.table(). For this reason I created the static read.table() # method of QuantArrrayData which has the 'flush' argument. I other words, I just added the argument 'flush=FALSE' to read.table[.QuantArrayData]() and passes 'flush=flush' to its internal calls to scan(). I'll send R-devel a note and see if it is possible to add this argument to the default read.table(). However, everything should work correctly as it is now. Cheers Henrik On 11/9/05, Duncan Murdoch [EMAIL PROTECTED] wrote: On 11/9/2005 10:07 AM, Florence Combes wrote: Dear all, I just upgraded version of R to R 2.2.0, and I have a problem with a script that did not happen with my previous version. Here is the error : - param-read.table(file=param.dat,sep =\t,header=TRUE,fill=TRUE, na.strings=NA) Erreur dans read.table.default(file = param.dat, sep = \t, header = TRUE, : 5 arguments passed to 'readTableHead' which requires 6 - whereas all was OK before. I cannot understand what's happening. Has someone already encountered this ?? Any help greatly appreciated, There is no read.table.default in standard R 2.2.0, so it appears that you have installed a replacement for read.table, and it no longer works. If you type getAnywhere(read.table)$where and getAnywhere(read.table.default)$where you are likely to see where those functions came from. (I see getAnywhere(read.table)$where [1] package:base namespace:base getAnywhere(read.table.default)$where character(0) indicating that read.table comes from the base package, and read.table.default doesn't exist. Duncan Murdoch [[alternative HTML version deleted]] __ R-help@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 __ R-help@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
[R] read.table
Hi,
I have a question on read.table.
I have a dataset with 273,000 lines and 195 columns. I used the
read.table to load the data into R:
trn-read.table('train1.dat', header=F, sep='|', na.strings='.')
I found it takes forever.
then I run 1/10 of the data (test) using read.table again. And this
time it finished quickly. So, there might be something wrong in my
data format causing that problem.
then, my question is, is there a way in R to track at which line,
something wrong occurs?
Thanks,
Weiwei
--
Weiwei Shi, Ph.D
Did you always know?
No, I did not. But I believed...
---Matrix III
__
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Re: [R] read.table
add:
I used
trn-matrix(scan('train1.dat', sep='|', na.string='.'), nrow=273529, ncol=195)
it is done.
so it seems that I just have no patience to wait for half an hour :)
but i still have that question:
is there a way to track the process if it takes too long. Could we
stop in the middle to see at which line it hesitates to move on?
regards,
weiwei
On 7/13/05, Weiwei Shi [EMAIL PROTECTED] wrote:
Hi,
I have a question on read.table.
I have a dataset with 273,000 lines and 195 columns. I used the
read.table to load the data into R:
trn-read.table('train1.dat', header=F, sep='|', na.strings='.')
I found it takes forever.
then I run 1/10 of the data (test) using read.table again. And this
time it finished quickly. So, there might be something wrong in my
data format causing that problem.
then, my question is, is there a way in R to track at which line,
something wrong occurs?
Thanks,
Weiwei
--
Weiwei Shi, Ph.D
Did you always know?
No, I did not. But I believed...
---Matrix III
--
Weiwei Shi, Ph.D
Did you always know?
No, I did not. But I believed...
---Matrix III
__
R-help@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
Re: [R] read.table
You could use the nlines= argument to scan to read in a
portion at a time.
On 7/13/05, Weiwei Shi [EMAIL PROTECTED] wrote:
add:
I used
trn-matrix(scan('train1.dat', sep='|', na.string='.'), nrow=273529,
ncol=195)
it is done.
so it seems that I just have no patience to wait for half an hour :)
but i still have that question:
is there a way to track the process if it takes too long. Could we
stop in the middle to see at which line it hesitates to move on?
regards,
weiwei
On 7/13/05, Weiwei Shi [EMAIL PROTECTED] wrote:
Hi,
I have a question on read.table.
I have a dataset with 273,000 lines and 195 columns. I used the
read.table to load the data into R:
trn-read.table('train1.dat', header=F, sep='|', na.strings='.')
I found it takes forever.
then I run 1/10 of the data (test) using read.table again. And this
time it finished quickly. So, there might be something wrong in my
data format causing that problem.
then, my question is, is there a way in R to track at which line,
something wrong occurs?
Thanks,
Weiwei
--
Weiwei Shi, Ph.D
Did you always know?
No, I did not. But I believed...
---Matrix III
--
Weiwei Shi, Ph.D
Did you always know?
No, I did not. But I believed...
---Matrix III
__
R-help@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
[[alternative HTML version deleted]]
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Re: [R] read.table
[I had some email problems and am sending this again. Sorry
if you get it twice.]
You could use the nlines= argument to scan to read in a
portion at a time.
On 7/13/05, Weiwei Shi [EMAIL PROTECTED] wrote:
add:
I used
trn-matrix(scan('train1.dat', sep='|', na.string='.'), nrow=273529,
ncol=195)
it is done.
so it seems that I just have no patience to wait for half an hour :)
but i still have that question:
is there a way to track the process if it takes too long. Could we
stop in the middle to see at which line it hesitates to move on?
regards,
weiwei
On 7/13/05, Weiwei Shi [EMAIL PROTECTED] wrote:
Hi,
I have a question on read.table.
I have a dataset with 273,000 lines and 195 columns. I used the
read.table to load the data into R:
trn-read.table('train1.dat', header=F, sep='|', na.strings='.')
I found it takes forever.
then I run 1/10 of the data (test) using read.table again. And this
time it finished quickly. So, there might be something wrong in my
data format causing that problem.
then, my question is, is there a way in R to track at which line,
something wrong occurs?
Thanks,
Weiwei
--
Weiwei Shi, Ph.D
Did you always know?
No, I did not. But I believed...
---Matrix III
--
Weiwei Shi, Ph.D
Did you always know?
No, I did not. But I believed...
---Matrix III
__
R-help@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
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PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] read.table
that sort of works for my purpose.
btw, is there a bettter way to get data.frame by passing around
matrix(). Since I could not find data.frame() with nrow or ncol
arguments. so i have to use matrix first and then as.data.frame to
convert it.
is there any other (better) way?
weiwei
On 7/13/05, Gabor Grothendieck [EMAIL PROTECTED] wrote:
You could use the nlines= argument to scan to read in a
portion at a time.
On 7/13/05, Weiwei Shi [EMAIL PROTECTED] wrote:
add:
I used
trn-matrix(scan('train1.dat', sep='|', na.string='.'), nrow=273529,
ncol=195)
it is done.
so it seems that I just have no patience to wait for half an hour :)
but i still have that question:
is there a way to track the process if it takes too long. Could we
stop in the middle to see at which line it hesitates to move on?
regards,
weiwei
On 7/13/05, Weiwei Shi [EMAIL PROTECTED] wrote:
Hi,
I have a question on read.table.
I have a dataset with 273,000 lines and 195 columns. I used the
read.table to load the data into R:
trn-read.table('train1.dat', header=F, sep='|', na.strings='.')
I found it takes forever.
then I run 1/10 of the data (test) using read.table again. And this
time it finished quickly. So, there might be something wrong in my
data format causing that problem.
then, my question is, is there a way in R to track at which line,
something wrong occurs?
Thanks,
Weiwei
--
Weiwei Shi, Ph.D
Did you always know?
No, I did not. But I believed...
---Matrix III
--
Weiwei Shi, Ph.D
Did you always know?
No, I did not. But I believed...
---Matrix III
__
R-help@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
--
Weiwei Shi, Ph.D
Did you always know?
No, I did not. But I believed...
---Matrix III
__
R-help@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
Re: [R] read.table
Maybe you don't really need a data frame in the first place?
You were concerned with speed and matrices tend to
have higher performance than data frames.
On 7/13/05, Weiwei Shi [EMAIL PROTECTED] wrote:
that sort of works for my purpose.
btw, is there a bettter way to get data.frame by passing around
matrix(). Since I could not find data.frame() with nrow or ncol
arguments. so i have to use matrix first and then as.data.frame to
convert it.
is there any other (better) way?
weiwei
On 7/13/05, Gabor Grothendieck [EMAIL PROTECTED] wrote:
You could use the nlines= argument to scan to read in a
portion at a time.
On 7/13/05, Weiwei Shi [EMAIL PROTECTED] wrote:
add:
I used
trn-matrix(scan('train1.dat', sep='|', na.string='.'), nrow=273529,
ncol=195)
it is done.
so it seems that I just have no patience to wait for half an hour :)
but i still have that question:
is there a way to track the process if it takes too long. Could we
stop in the middle to see at which line it hesitates to move on?
regards,
weiwei
On 7/13/05, Weiwei Shi [EMAIL PROTECTED] wrote:
Hi,
I have a question on read.table.
I have a dataset with 273,000 lines and 195 columns. I used the
read.table to load the data into R:
trn-read.table('train1.dat', header=F, sep='|', na.strings='.')
I found it takes forever.
then I run 1/10 of the data (test) using read.table again. And this
time it finished quickly. So, there might be something wrong in my
data format causing that problem.
then, my question is, is there a way in R to track at which line,
something wrong occurs?
Thanks,
Weiwei
--
Weiwei Shi, Ph.D
Did you always know?
No, I did not. But I believed...
---Matrix III
--
Weiwei Shi, Ph.D
Did you always know?
No, I did not. But I believed...
---Matrix III
__
R-help@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
--
Weiwei Shi, Ph.D
Did you always know?
No, I did not. But I believed...
---Matrix III
__
R-help@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
Re: [R] read.table
there is another problem since last time i forgot byrow :(
trn-matrix(scan('train1.dat', sep='|', na.string='.'), nrow=273529,
ncol=195, byrow=T)
Read 53338155 items
Error: cannot allocate vector of size 416704 Kb
please help with this 'simple' reading task.
weiwei
On 7/13/05, Weiwei Shi [EMAIL PROTECTED] wrote:
that sort of works for my purpose.
btw, is there a bettter way to get data.frame by passing around
matrix(). Since I could not find data.frame() with nrow or ncol
arguments. so i have to use matrix first and then as.data.frame to
convert it.
is there any other (better) way?
weiwei
On 7/13/05, Gabor Grothendieck [EMAIL PROTECTED] wrote:
You could use the nlines= argument to scan to read in a
portion at a time.
On 7/13/05, Weiwei Shi [EMAIL PROTECTED] wrote:
add:
I used
trn-matrix(scan('train1.dat', sep='|', na.string='.'), nrow=273529,
ncol=195)
it is done.
so it seems that I just have no patience to wait for half an hour :)
but i still have that question:
is there a way to track the process if it takes too long. Could we
stop in the middle to see at which line it hesitates to move on?
regards,
weiwei
On 7/13/05, Weiwei Shi [EMAIL PROTECTED] wrote:
Hi,
I have a question on read.table.
I have a dataset with 273,000 lines and 195 columns. I used the
read.table to load the data into R:
trn-read.table('train1.dat', header=F, sep='|', na.strings='.')
I found it takes forever.
then I run 1/10 of the data (test) using read.table again. And this
time it finished quickly. So, there might be something wrong in my
data format causing that problem.
then, my question is, is there a way in R to track at which line,
something wrong occurs?
Thanks,
Weiwei
--
Weiwei Shi, Ph.D
Did you always know?
No, I did not. But I believed...
---Matrix III
--
Weiwei Shi, Ph.D
Did you always know?
No, I did not. But I believed...
---Matrix III
__
R-help@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
--
Weiwei Shi, Ph.D
Did you always know?
No, I did not. But I believed...
---Matrix III
--
Weiwei Shi, Ph.D
Did you always know?
No, I did not. But I believed...
---Matrix III
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
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Re: [R] read.table
Try reading it into and transposing the matrix afterwards. Don't know if
that would work but its worth a try. Actually if you
are having problems read it into a vector, check that its of the required
size, just in case, and then turn it into a matrix and transpose it.
On 7/13/05, Weiwei Shi [EMAIL PROTECTED] wrote:
there is another problem since last time i forgot byrow :(
trn-matrix(scan('train1.dat', sep='|', na.string='.'), nrow=273529,
ncol=195, byrow=T)
Read 53338155 items
Error: cannot allocate vector of size 416704 Kb
please help with this 'simple' reading task.
weiwei
On 7/13/05, Weiwei Shi [EMAIL PROTECTED] wrote:
that sort of works for my purpose.
btw, is there a bettter way to get data.frame by passing around
matrix(). Since I could not find data.frame() with nrow or ncol
arguments. so i have to use matrix first and then as.data.frame to
convert it.
is there any other (better) way?
weiwei
On 7/13/05, Gabor Grothendieck [EMAIL PROTECTED] wrote:
You could use the nlines= argument to scan to read in a
portion at a time.
On 7/13/05, Weiwei Shi [EMAIL PROTECTED] wrote:
add:
I used
trn-matrix(scan('train1.dat', sep='|', na.string='.'), nrow=273529,
ncol=195)
it is done.
so it seems that I just have no patience to wait for half an hour :)
but i still have that question:
is there a way to track the process if it takes too long. Could we
stop in the middle to see at which line it hesitates to move on?
regards,
weiwei
On 7/13/05, Weiwei Shi [EMAIL PROTECTED] wrote:
Hi,
I have a question on read.table.
I have a dataset with 273,000 lines and 195 columns. I used the
read.table to load the data into R:
trn-read.table('train1.dat', header=F, sep='|', na.strings='.')
I found it takes forever.
then I run 1/10 of the data (test) using read.table again. And this
time it finished quickly. So, there might be something wrong in my
data format causing that problem.
then, my question is, is there a way in R to track at which line,
something wrong occurs?
Thanks,
Weiwei
--
Weiwei Shi, Ph.D
Did you always know?
No, I did not. But I believed...
---Matrix III
--
Weiwei Shi, Ph.D
Did you always know?
No, I did not. But I believed...
---Matrix III
__
R-help@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
--
Weiwei Shi, Ph.D
Did you always know?
No, I did not. But I believed...
---Matrix III
--
Weiwei Shi, Ph.D
Did you always know?
No, I did not. But I believed...
---Matrix III
__
R-help@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
Re: [R] read.table
i think what you meant is
trn-matrix(scan('train1.dat', sep='|', na.string='.'), nrow=195,
ncol=273529)
and then transpose it. However:
Error: cannot allocate vector of size 512000 Kb
the answer is no :(
I think i am going to write my own function to split the result from
scan but not sure if it can be made into matrix or not even if I
succeed.
On 7/13/05, Gabor Grothendieck [EMAIL PROTECTED] wrote:
Try reading it into and transposing the matrix afterwards. Don't know if
that would work but its worth a try. Actually if you
are having problems read it into a vector, check that its of the required
size, just in case, and then turn it into a matrix and transpose it.
On 7/13/05, Weiwei Shi [EMAIL PROTECTED] wrote:
there is another problem since last time i forgot byrow :(
trn-matrix(scan('train1.dat', sep='|', na.string='.'), nrow=273529,
ncol=195, byrow=T)
Read 53338155 items
Error: cannot allocate vector of size 416704 Kb
please help with this 'simple' reading task.
weiwei
On 7/13/05, Weiwei Shi [EMAIL PROTECTED] wrote:
that sort of works for my purpose.
btw, is there a bettter way to get data.frame by passing around
matrix(). Since I could not find data.frame() with nrow or ncol
arguments. so i have to use matrix first and then as.data.frame to
convert it.
is there any other (better) way?
weiwei
On 7/13/05, Gabor Grothendieck [EMAIL PROTECTED] wrote:
You could use the nlines= argument to scan to read in a
portion at a time.
On 7/13/05, Weiwei Shi [EMAIL PROTECTED] wrote:
add:
I used
trn-matrix(scan('train1.dat', sep='|', na.string='.'), nrow=273529,
ncol=195)
it is done.
so it seems that I just have no patience to wait for half an hour :)
but i still have that question:
is there a way to track the process if it takes too long. Could we
stop in the middle to see at which line it hesitates to move on?
regards,
weiwei
On 7/13/05, Weiwei Shi [EMAIL PROTECTED] wrote:
Hi,
I have a question on read.table.
I have a dataset with 273,000 lines and 195 columns. I used the
read.table to load the data into R:
trn-read.table('train1.dat', header=F, sep='|', na.strings='.')
I found it takes forever.
then I run 1/10 of the data (test) using read.table again. And this
time it finished quickly. So, there might be something wrong in my
data format causing that problem.
then, my question is, is there a way in R to track at which line,
something wrong occurs?
Thanks,
Weiwei
--
Weiwei Shi, Ph.D
Did you always know?
No, I did not. But I believed...
---Matrix III
--
Weiwei Shi, Ph.D
Did you always know?
No, I did not. But I believed...
---Matrix III
__
R-help@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
--
Weiwei Shi, Ph.D
Did you always know?
No, I did not. But I believed...
---Matrix III
--
Weiwei Shi, Ph.D
Did you always know?
No, I did not. But I believed...
---Matrix III
--
Weiwei Shi, Ph.D
Did you always know?
No, I did not. But I believed...
---Matrix III
__
R-help@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
Re: [R] read.table
Sorry for last post.
I don't know why i got the error message last time.
but if i did in the following way:
t-scan('train1.dat', sep='|', na.string='.')
t2-matrix(t, nrow=195, ncol=273529)
t3-t(t2)
t4-as.data.frame(t3)
now I got what i needed.
Thanks a lot for Gabor's prompt help.
weiwei
On 7/13/05, Weiwei Shi [EMAIL PROTECTED] wrote:
i think what you meant is
trn-matrix(scan('train1.dat', sep='|', na.string='.'), nrow=195,
ncol=273529)
and then transpose it. However:
Error: cannot allocate vector of size 512000 Kb
the answer is no :(
I think i am going to write my own function to split the result from
scan but not sure if it can be made into matrix or not even if I
succeed.
On 7/13/05, Gabor Grothendieck [EMAIL PROTECTED] wrote:
Try reading it into and transposing the matrix afterwards. Don't know if
that would work but its worth a try. Actually if you
are having problems read it into a vector, check that its of the required
size, just in case, and then turn it into a matrix and transpose it.
On 7/13/05, Weiwei Shi [EMAIL PROTECTED] wrote:
there is another problem since last time i forgot byrow :(
trn-matrix(scan('train1.dat', sep='|', na.string='.'), nrow=273529,
ncol=195, byrow=T)
Read 53338155 items
Error: cannot allocate vector of size 416704 Kb
please help with this 'simple' reading task.
weiwei
On 7/13/05, Weiwei Shi [EMAIL PROTECTED] wrote:
that sort of works for my purpose.
btw, is there a bettter way to get data.frame by passing around
matrix(). Since I could not find data.frame() with nrow or ncol
arguments. so i have to use matrix first and then as.data.frame to
convert it.
is there any other (better) way?
weiwei
On 7/13/05, Gabor Grothendieck [EMAIL PROTECTED] wrote:
You could use the nlines= argument to scan to read in a
portion at a time.
On 7/13/05, Weiwei Shi [EMAIL PROTECTED] wrote:
add:
I used
trn-matrix(scan('train1.dat', sep='|', na.string='.'),
nrow=273529,
ncol=195)
it is done.
so it seems that I just have no patience to wait for half an hour :)
but i still have that question:
is there a way to track the process if it takes too long. Could we
stop in the middle to see at which line it hesitates to move on?
regards,
weiwei
On 7/13/05, Weiwei Shi [EMAIL PROTECTED] wrote:
Hi,
I have a question on read.table.
I have a dataset with 273,000 lines and 195 columns. I used the
read.table to load the data into R:
trn-read.table('train1.dat', header=F, sep='|', na.strings='.')
I found it takes forever.
then I run 1/10 of the data (test) using read.table again. And
this
time it finished quickly. So, there might be something wrong in my
data format causing that problem.
then, my question is, is there a way in R to track at which line,
something wrong occurs?
Thanks,
Weiwei
--
Weiwei Shi, Ph.D
Did you always know?
No, I did not. But I believed...
---Matrix III
--
Weiwei Shi, Ph.D
Did you always know?
No, I did not. But I believed...
---Matrix III
__
R-help@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
--
Weiwei Shi, Ph.D
Did you always know?
No, I did not. But I believed...
---Matrix III
--
Weiwei Shi, Ph.D
Did you always know?
No, I did not. But I believed...
---Matrix III
--
Weiwei Shi, Ph.D
Did you always know?
No, I did not. But I believed...
---Matrix III
--
Weiwei Shi, Ph.D
Did you always know?
No, I did not. But I believed...
---Matrix III
__
R-help@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
[R] read.table with header and text data
Hi R! I am reading in a text file which has one column of alpha data and 5 columns of numeric data. There is a header row. I would like the alpha data column to just be character rather than factor. Is there a way to do this, please? I'm thinking that it might be I() but can't figure out exactly how. Thanks, Laura mailto: [EMAIL PROTECTED] R 2.0.1 Windows __ R-help@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
Re: [R] read.table with header and text data
See ?read.table, especially the argument as.is. Cheers, Rich On Apr 7, 2005 9:55 AM, Laura Holt [EMAIL PROTECTED] wrote: Hi R! I am reading in a text file which has one column of alpha data and 5 columns of numeric data. There is a header row. I would like the alpha data column to just be character rather than factor. Is there a way to do this, please? I'm thinking that it might be I() but can't figure out exactly how. Thanks, Laura mailto: [EMAIL PROTECTED] R 2.0.1 Windows __ R-help@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 -- Rich FitzJohn rich.fitzjohn at gmail.com |http://homepages.paradise.net.nz/richa183 You are in a maze of twisty little functions, all alike __ R-help@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
[R] read.table
Maybe argument 'fill' of read.table is the solution.
The default value is FALSE in read.table and, therefore, any line not
having the same number of fields as the first line (not skipped) will
make problems. If set to TRUE, as in read.delim and read.csv, lines
with less number of fields get blank fields added at the end.
If exporting tab delimited text files from Excel lines with empty
fields at the end in the Excel file often have less fields than the
header line in the text file. Reading them with read.delim fixes that.
If the problem is more complicated you probably need to find the lines
with count.fields and correct them manually.
You can find them (actually the line number) with something like
which(count.fields('data.txt') != count.fields('data.txt')[1])
assuming that the first line has the correct number of fields.
Tilo
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Re: [R] read.table
Tilo Blenk wrote:
Maybe argument 'fill' of read.table is the solution.
The default value is FALSE in read.table and, therefore, any line not
having the same number of fields as the first line (not skipped) will
make problems. If set to TRUE, as in read.delim and read.csv, lines with
less number of fields get blank fields added at the end.
If exporting tab delimited text files from Excel lines with empty fields
at the end in the Excel file often have less fields than the header line
in the text file. Reading them with read.delim fixes that.
If the problem is more complicated you probably need to find the lines
with count.fields and correct them manually.
You can find them (actually the line number) with something like
which(count.fields('data.txt') != count.fields('data.txt')[1])
assuming that the first line has the correct number of fields.
Tilo
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Tilo,
is this an answer to a R-help question?
If so, I'd like to suggest to cite the original post and reply also to
the original poster who might not be a subscribed member of this list...
Uwe Ligges
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[R] read.table
In addition to other suggestions made, note also count.fields().
cat(10 9 17 # First of 7 lines, 11 13 1 6, 9 14 16,
+ 12 15 14, 8 15 15, 9 13 12, 7 14 18,
+ file=oneBadRow.txt, sep=\n)
nfields - count.fields(oneBadRow.txt)
nfields
[1] 3 4 3 3 3 3 3
table(nfields) ## Use with many records
nfields
3 4
6 1
tab - table(nfields)
(1:length(nfields))[nfields == 4]
[1] 2
readLines(oneBadRow.txt, n=-1)[2]
[1] 11 13 1 6
Note the various option settings for count.fields()
John Maindonald email: [EMAIL PROTECTED]
phone : +61 2 (6125)3473fax : +61 2(6125)5549
Centre for Bioinformation Science, Room 1194,
John Dedman Mathematical Sciences Building (Building 27)
Australian National University, Canberra ACT 0200.
On 26 Feb 2005, at 10:03 PM, [EMAIL PROTECTED] wrote:
From: Sean Davis [EMAIL PROTECTED]
Date: 26 February 2005 7:11:48 AM
To: r-help r-help@stat.math.ethz.ch
Subject: [R] read.table
I have a commonly recurring problem and wondered if folks would share
tips. I routinely get tab-delimited text files that I need to read
in. In very many cases, I get:
a - read.table('junk.txt.txt',header=T,skip=10,sep=\t)
Error in scan(file = file, what = what, sep = sep, quote = quote, dec
= dec, :
line 67 did not have 88 elements
I am typically able to go through the file and find a single quote or
something like that causing the problem, but with a recent set of
files, I haven't been able to find such an issue. What can I do to
get around this problem? I can use perl, also
Thanks,
Sean
__
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PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] read.table
I have a commonly recurring problem and wondered if folks would share
tips. I routinely get tab-delimited text files that I need to read in.
In very many cases, I get:
a - read.table('junk.txt.txt',header=T,skip=10,sep=\t)
Error in scan(file = file, what = what, sep = sep, quote = quote, dec =
dec, :
line 67 did not have 88 elements
I am typically able to go through the file and find a single quote or
something like that causing the problem, but with a recent set of
files, I haven't been able to find such an issue. What can I do to get
around this problem? I can use perl, also
Thanks,
Sean
__
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PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] read.table
?readLines
I'm sure Perl will do nicely, but you can also use readLines and grep() or
regexpr() the result in R as you would in Perl to find where the problem
lies. ?nchar can also help to find a non-printing character that may be
messing you up. It's no fun, I know. Excel files can be a particular pain,
especially in their handling of missings.
-- Bert Gunter
Genentech Non-Clinical Statistics
South San Francisco, CA
The business of the statistician is to catalyze the scientific learning
process. - George E. P. Box
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Sean Davis
Sent: Friday, February 25, 2005 12:12 PM
To: r-help
Subject: [R] read.table
I have a commonly recurring problem and wondered if folks would share
tips. I routinely get tab-delimited text files that I need
to read in.
In very many cases, I get:
a - read.table('junk.txt.txt',header=T,skip=10,sep=\t)
Error in scan(file = file, what = what, sep = sep, quote =
quote, dec =
dec, :
line 67 did not have 88 elements
I am typically able to go through the file and find a single quote or
something like that causing the problem, but with a recent set of
files, I haven't been able to find such an issue. What can I
do to get
around this problem? I can use perl, also
Thanks,
Sean
__
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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
On 25-Feb-05 Sean Davis wrote:
I have a commonly recurring problem and wondered if folks
would share tips. I routinely get tab-delimited text files
that I need to read in.
In very many cases, I get:
a - read.table('junk.txt.txt',header=T,skip=10,sep=\t)
Error in scan(file = file, what = what, sep = sep, quote = quote,
dec = dec, :
line 67 did not have 88 elements
I am typically able to go through the file and find a single
quote or something like that causing the problem, but with a
recent set of files, I haven't been able to find such an issue.
What can I do to get around this problem? I can use perl, also
Hi Sean,
This is only a shot in the dark, but your description has reminded
me of similar messes in files which have been exported from Excel.
What I have often done in such cases, to check (e.g.) the numbers
of fields in records (using 'awk' on Linux) is on the following
lines:
cat filename | awk 'BEGIN{FS=\t} {print NF}' | unique
In that case, if there are varying numbers of fields then
two or more different numbers will be printed instead of
the single value which it should be.
If you know how many fields to expect (e.g. 88), then you can
find the line numbers of offending records by something like
cat filename | awk 'BEGIN{FS=\t} {if(NF!=88){print NR}}'
In data files with a lot of records per line, doing it in
this kind of way is vastly superior to trying to spot the
problem by eye -- it's extemely difficult to count 88
tab-separated fields on screen!
Hoping this helps! If not, supply further details and we'll
see what we can think up.
Best wishes,
Ted.
E-Mail: (Ted Harding) [EMAIL PROTECTED]
Fax-to-email: +44 (0)870 094 0861
Date: 25-Feb-05 Time: 20:54:43
-- XFMail --
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RE: [R] read.table
On 25-Feb-05 Ted Harding wrote:
On 25-Feb-05 Sean Davis wrote:
I have a commonly recurring problem and wondered if folks
would share tips. I routinely get tab-delimited text files
that I need to read in.
In very many cases, I get:
a - read.table('junk.txt.txt',header=T,skip=10,sep=\t)
Error in scan(file = file, what = what, sep = sep, quote = quote,
dec = dec, :
line 67 did not have 88 elements
I am typically able to go through the file and find a single
quote or something like that causing the problem, but with a
recent set of files, I haven't been able to find such an issue.
What can I do to get around this problem? I can use perl, also
Hi Sean,
This is only a shot in the dark, but your description has reminded
me of similar messes in files which have been exported from Excel.
What I have often done in such cases, to check (e.g.) the numbers
of fields in records (using 'awk' on Linux) is on the following
lines:
cat filename | awk 'BEGIN{FS=\t} {print NF}' | unique
OOPS!!!
cat filename | awk 'BEGIN{FS=\t} {print NF}' | uniq
Ted.
E-Mail: (Ted Harding) [EMAIL PROTECTED]
Fax-to-email: +44 (0)870 094 0861
Date: 25-Feb-05 Time: 21:14:55
-- XFMail --
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Re: [R] read.table
Berton Gunter [EMAIL PROTECTED] writes: ?readLines I'm sure Perl will do nicely, but you can also use readLines and grep() or regexpr() the result in R as you would in Perl to find where the problem lies. ?nchar can also help to find a non-printing character that may be messing you up. It's no fun, I know. Excel files can be a particular pain, especially in their handling of missings. You might also try read.delim() which has options set specifically to be able to read Excel-generated CSV files. Also check out count.fields(). -- O__ Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-help@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
Re: [R] read.table
Peter Dalgaard [EMAIL PROTECTED] writes: You might also try read.delim() which has options set specifically to be able to read Excel-generated CSV files. Blah. *TAB-delimited* files of course. read.csv() for the other ones. -- O__ Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-help@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
[R] read.table from a list of filenames
I am wondering if it is possible to read.table repeatedly from a list
of file names into a new list of table names.
For example:
filenames - list.files()
then with a function like
rf - function(i) {
word??(filename[i]) - read.table(filenames[i]) }
I can't seem to find a function like word?? that will be the object of
another operation. If this worked, then I could repeat it for the
length of filenames.
Also, even the following function seems to give me an error, but I
don't yet know why.
rf - function(nam, i) { nam - read.table(filenames[i]) }
Any help would be very much appreciated.
Thanks,
Thomas
[[alternative text/enriched version deleted]]
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RE: [R] read.table from a list of filenames
The solution is in section 7.21 of the R FAQ. BTW, `rf' is a built-in R
function for generating random numbers from an F distribution, so better use
some other name.
Andy
From: thomas hills
I am wondering if it is possible to read.table repeatedly from a list
of file names into a new list of table names.
For example:
filenames - list.files()
then with a function like
rf - function(i) {
word??(filename[i]) - read.table(filenames[i]) }
I can't seem to find a function like word?? that will be the
object of
another operation. If this worked, then I could repeat it for the
length of filenames.
Also, even the following function seems to give me an error, but I
don't yet know why.
rf - function(nam, i) { nam - read.table(filenames[i]) }
Any help would be very much appreciated.
Thanks,
Thomas
[[alternative text/enriched version deleted]]
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Re: [R] read.table from a list of filenames
On Tue, 28 Dec 2004, thomas hills wrote:
I am wondering if it is possible to read.table repeatedly from a list
of file names into a new list of table names.
For example:
filenames - list.files()
then with a function like
rf - function(i) {
word??(filename[i]) - read.table(filenames[i]) }
lapply(filenames, read.table)
will do what I think you want to do.
[It is possible to assign each file to a variable whose name is given by
another variable, and FAQ 7.21 tells you how, but that probably isn't a
good idea.]
-thomas
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Re: [R] read.table from a list of filenames
thomas hills [EMAIL PROTECTED] writes:
I am wondering if it is possible to read.table repeatedly from a list
of file names into a new list of table names.
For example:
filenames - list.files()
then with a function like
rf - function(i) {
word??(filename[i]) - read.table(filenames[i]) }
I can't seem to find a function like word?? that will be the object of
another operation. If this worked, then I could repeat it for the
length of filenames.
Also, even the following function seems to give me an error, but I
don't yet know why.
rf - function(nam, i) { nam - read.table(filenames[i]) }
Any help would be very much appreciated.
Something like
listoftables - lapply(filenames, read.table)
names(listoftables) - filenames
might be what you are looking for.
--
O__ Peter Dalgaard Blegdamsvej 3
c/ /'_ --- Dept. of Biostatistics 2200 Cph. N
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907
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[R] read.table in MacOSX
I'm running R version 1.9.0 on Mac OS 10.3.5. I have created text files with data that I need to access from R. When I use the read.table command, I get the warning message: cannot open file These text files DO work on a Mac with a previous version of R. I have tried pasting the data into a new text file, but I just can't make a file that the current version of R will open (I have tried this both with Word and with the native OSX text edit program). Am I doing something wrong or is there some incompatibility here? -- = = = = = = = = Matthew L Forister Section of Evolution and Ecology 2320 Storer Hall University of California One Shields Ave. Davis, CA 95616 lab phone:(530) 752-2225 = = = = = = = = __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Read.Table Reading a Text file
On 7 Oct 2004 at 20:18, Kunal Shetty wrote: Dear R users and Helpers I am beginner with using R and interested in carrying out certain task for my statistical research. I am reading data for a text file, which could contain data in following pattern x y 8 10 1114 1616 1815 6 20 4 4 2018 As per the example I have two columns and 7 rows of data in each. However is real life data situation I may not know how many columns are present and how rows are present and also with the certain data is missing. Yes I am assuming the data is delimited my Tab. My question or rather problem is I want read data from each colum say col x (8,11,16,18?.20) and store it into a variable so that I could perform some operations on them. Hi Better to read by appropriate read.whatever() function to data frame, see eg. ?read.table I hope you have already read some intro documents in which there is stated how you could read your data and organize them. I also recommend to go through Paul Johnsons Rtips. You can find it by e.g. Google. Cheers Petr I have also looked into certain R-help for Read.table and data.frame but still struggling on my requirement. They are http://tolstoy.newcastle.edu.au/R/help/04/07/2040.html http://tolstoy.newcastle.edu.au/R/help/04/07/3152.html Regards Kunal __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Petr Pikal [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Read.Table Reading a Text file
Hi
you really should spend some time to go through introductory
documentation and do some examples provided.
snip
On 8 Oct 2004 at 3:15, Kunal Shetty wrote:
you probably read it by read.table without saying/specifying
header=TRUE so your X and y is included to your data not as
names but as values. Therefore V1 and V2 are factors.
Please consult especially R-intro manual in doc directory. It helps
you to save a lot of frustration and misunderstanding, especially at
the begging of your work with R.
And consider help list as a last source of help as what you have
learned yourself you remember better and you understand better.
Cheers
Petr
V1 V2
1 Xy
2 810
3 11 1 4
4 16 16
5 18 15
6 620
7 4 4
8 20 18
9 2522
and I want to access V1 values.
thank you
regards
Kunal
[EMAIL PROTECTED] wrote:
If you have an unequal number of columns, then use 'fill=T'
onread.table
It putsNAs.
Is this what youwant?
Here is what happens on the input file which is your data and
someextra
columns:
8 10
11 14
16 16
18 15 12
6 20
44 12
20 18
x.1 - read.table('/tempxx.txt',fill=T)
x.1
X8X10
11 14 NA
16 16 NA
18 15 12
6 20 NA
4 4 12
20 18 NA
__
James HoltmanWhat is the problem you are trying tosolve?
Executive Technical Consultant -- Office of Technology,Convergys
[EMAIL PROTECTED]
+1 (513)723-2929
KunalShetty
[EMAIL PROTECTED] To:[EMAIL PROTECTED]
.educc:
Sent by: Subject: [R] Read.Table Reading a Textfile
[EMAIL PROTECTED]
ath.ethz.ch
10/07/200416:18
Dear R users andHelpers
I am beginner with using R and interested in carrying out
certaintask
for
my statisticalresearch.
I am reading data for a text file, which could contain data
infollowing
pattern
x y
8 10
11 14
16 16
18 15
6 20
4 4
20 18
As per the example I have two columns and 7 rows of data ineach.
However is real life data situation I may not know how many
columnsare present and how rows are present and also with the
certain datais missing. Yes I am assuming the data is delimited
myTab.
My question or rather problem is I want read data from each colum
saycol
x
(8,11,16,18EUR.20) and store it into a variable so that I
couldperform
some
operations onthem.
I have also looked into certain R-help for Read.table and
data.framebut still struggling on my requirement. Theyare
http://tolstoy.newcastle.edu.au/R/help/04/07/2040.html
http://tolstoy.newcastle.edu.au/R/help/04/07/3152.html
Regards
Kunal
__
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Petr Pikal
[EMAIL PROTECTED]
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[R] Read.Table Reading a Text file
Dear R users and Helpers I am beginner with using R and interested in carrying out certain task for my statistical research. I am reading data for a text file, which could contain data in following pattern x y 8 10 11 14 16 16 18 15 6 20 4 4 20 18 As per the example I have two columns and 7 rows of data in each. However is real life data situation I may not know how many columns are present and how rows are present and also with the certain data is missing. Yes I am assuming the data is delimited my Tab. My question or rather problem is I want read data from each colum say col x (8,11,16,18 .20) and store it into a variable so that I could perform some operations on them. I have also looked into certain R-help for Read.table and data.frame but still struggling on my requirement. They are http://tolstoy.newcastle.edu.au/R/help/04/07/2040.html http://tolstoy.newcastle.edu.au/R/help/04/07/3152.html Regards Kunal __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Read.Table Reading a Text file
James
Thank you for response. I am working on treatment for missing data for both
bivariate and multivariate normal data. Coming back to example. My problem was that
once we do execute this command
x.1 - read.table('/tempxx.txt', fill=T)
How can access the particular column say X8 and all its values so that I could assign
some other operations on them.
Because if I say
print.default(x.1)
the result..
V1 V2
1 Xy
2 810
3 11 1 4
4 16 16
5 18 15
6 620
7 4 4
8 20 18
9 2522
and I want to access V1 values
..
thank you
regards
Kunal
[EMAIL PROTECTED] wrote:
If you have an unequal number of columns, then use 'fill=T' on read.table
It puts NAs.
Is this what you want?
Here is what happens on the input file which is your data and some extra
columns:
810
11 14
16 16
18 15 12
620
44 12
20 18
x.1 - read.table('/tempxx.txt', fill=T)
x.1
X8 X10
11 14 NA
16 16 NA
18 15 12
6 20 NA
4 4 12
20 18 NA
__
James HoltmanWhat is the problem you are trying to solve?
Executive Technical Consultant -- Office of Technology, Convergys
[EMAIL PROTECTED]
+1 (513) 723-2929
Kunal Shetty
[EMAIL PROTECTED] To: [EMAIL PROTECTED]
.edu cc:
Sent by: Subject: [R] Read.Table Reading a Text file
[EMAIL PROTECTED]
ath.ethz.ch
10/07/2004 16:18
Dear R users and Helpers
I am beginner with using R and interested in carrying out certain task
for
my statistical research.
I am reading data for a text file, which could contain data in following
pattern
xy
810
11 14
16 16
18 15
620
44
20 18
As per the example I have two columns and 7 rows of data in each.
However is real life data situation I may not know how many columns are
present and how rows are present and also with the certain data is
missing. Yes I am assuming the data is delimited my Tab.
My question or rather problem is I want read data from each colum say col
x
(8,11,16,18â¦.20) and store it into a variable so that I could perform
some
operations on them.
I have also looked into certain R-help for Read.table and data.frame but
still struggling on my requirement. They are
http://tolstoy.newcastle.edu.au/R/help/04/07/2040.html
http://tolstoy.newcastle.edu.au/R/help/04/07/3152.html
Regards
Kunal
__
[EMAIL PROTECTED] mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html
__
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RE: [R] Read.Table Reading a Text file
thanks austin, it worked..it was exactly what I was looking for
regards
Kunal
Austin, Matt [EMAIL PROTECTED] wrote:
x.1$V1
or
x.1[,1]
or
x.1['V1']
and you shouldn't need to call print.default() directly, just call
print().
--Matt
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] Behalf Of Kunal Shetty
Sent: Thursday, October 07, 2004 18:44 PM
To: [EMAIL PROTECTED]
Cc: R-help
Subject: Re: [R] Read.Table Reading a Text file
James
Thank you for response. I am working on treatment for missing
data for both bivariate and multivariate normal data. Coming back to
example. My problem was that once we do execute this command
x.1 - read.table('/tempxx.txt', fill=T)
How can access the particular column say X8 and all it's values so that I
could assign some other operations on them.
Because if I say
print.default(x.1)
the result..
V1 V2
1 Xy
2 810
3 11 1 4
4 16 16
5 18 15
6 620
7 4 4
8 20 18
9 2522
and I want to access V1 values.
thank you
regards
Kunal
[EMAIL PROTECTED] wrote:
If you have an unequal number of columns, then use 'fill=T' onread.table
It putsNAs.
Is this what youwant?
Here is what happens on the input file which is your data and someextra
columns:
8 10
11 14
16 16
18 15 12
6 20
44 12
20 18
x.1 - read.table('/tempxx.txt',fill=T)
x.1
X8X10
11 14 NA
16 16 NA
18 15 12
6 20 NA
4 4 12
20 18 NA
__
James HoltmanWhat is the problem you are trying tosolve?
Executive Technical Consultant -- Office of Technology,Convergys
[EMAIL PROTECTED]
+1 (513)723-2929
KunalShetty
[EMAIL PROTECTED] To:[EMAIL PROTECTED]
.educc:
Sent by: Subject: [R] Read.Table Reading a Textfile
[EMAIL PROTECTED]
ath.ethz.ch
10/07/200416:18
Dear R users andHelpers
I am beginner with using R and interested in carrying out certaintask
for
my statisticalresearch.
I am reading data for a text file, which could contain data infollowing
pattern
x y
8 10
11 14
16 16
18 15
6 20
4 4
20 18
As per the example I have two columns and 7 rows of data ineach.
However is real life data situation I may not know how many columnsare
present and how rows are present and also with the certain datais
missing. Yes I am assuming the data is delimited myTab.
My question or rather problem is I want read data from each colum saycol
x
(8,11,16,18âEUR¦.20) and store it into a variable so that I couldperform
some
operations onthem.
I have also looked into certain R-help for Read.table and data.framebut
still struggling on my requirement. Theyare
http://tolstoy.newcastle.edu.au/R/help/04/07/2040.html
http://tolstoy.newcastle.edu.au/R/help/04/07/3152.html
Regards
Kunal
__
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Re: [R] read.table() question
I don't know read.data function, it is a function that you have defined? A.S. Alessandro Semeria Models and Simulations Laboratory Montecatini Environmental Research Center (Edison Group), Via Ciro Menotti 48, 48023 Marina di Ravenna (RA), Italy Tel. +39 544 536811 Fax. +39 544 538663 E-mail: [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] read.table() question
Hi,
In the following code, I got an error meesage if an
input file is empty, and the program stopped running.
Could someone to tell me how to handle this problem. I
want the program to keep running. Thanks.
for i in [1:3]
{
file=paste(file, i, .dat)
x - read.data(file)
x(11)
plot(x);
dev.off()
}
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[R] read.table with spaces
DeaR useRs: Excuses for my english. I am trying to read a file with my dats and the format is a number, 3 spaces, other number, etc... When I use: a-read.table(file=c:/datos2.dat,sep=) R sais: Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, : line 3 did not have 34 elements And I see my dats and in line 3 the first number is an space (missing value) SOS help me Thanks. -- ==oOo= Visit my website in: http://users.servicios.retecal.es/aperez2 Maybe you can find something interesting == -- __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] read.table with spaces
You should make your missing value indicator something other than your separator indicator: 1. Use a text editor to indicate all missing values as NA or 2. Use a text editor to replace the 3 separator spaces with, for example, a comma or semicolon and use the argument sep=, or sep=; which won't trigger on ANY whitespace. HTH, Rob - Original Message - From: AGUSTIN PEREZ MARTIN [EMAIL PROTECTED] To: [EMAIL PROTECTED] Sent: Friday, February 20, 2004 8:01 AM Subject: [R] read.table with spaces DeaR useRs: Excuses for my english. I am trying to read a file with my dats and the format is a number, 3 spaces, other number, etc... When I use: a-read.table(file=c:/datos2.dat,sep=) R sais: Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, : line 3 did not have 34 elements And I see my dats and in line 3 the first number is an space (missing value) SOS help me Thanks. -- ==oOo= Visit my website in: http://users.servicios.retecal.es/aperez2 Maybe you can find something interesting == -- __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] read.table(..)..Help?
Hallo, can someone please help me. I have a proplem reading a file with more that one rows. e.g I used the function: p-read.table(file=FILENAME , header=TRUE,sep=;) and later used the data.Frame() function. It functions when the file has only a row of variables. When I insert the second row I get an error message. How do I do this = = Sylvie B. Forkusam Eppelheimer Str.52/A2-5-2 69115 Heidelberg, Germany Tel: (0049)-06221/346913 Mobile: 0179-6816276 === __ Free Pop-Up Blocker - Get it now __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
