[R] read file problem
R-help, I have the following file I want to import to R (some lines removed) Calibrated CTD data for station:00280001 Calibrated:23/8 2001, Salinity Unsmoothed, Fluorescence Uncalibrated Maximum observed depth:36 m QUAL has one digit for each of pressure, temp., sal. and fluor. QUAL=1:Uncal., QUAL=2:OK, QUAL=6:Interp., QUAL=9:No data DEPTH CTDPRS CTDTMP CTDSAL RAWFLU NUMB. QUAL MDBAR IPTS-68 PSS-78 OBS. *** *** *** *** 1 1.0 2999 2 2.0 5.9793 35.1629.10717 2221 3 3.0 5.9797 35.1631.10117 2221 4 4.0 5.9809 35.1631.11812 2221 5 5.1 5.9811 35.1629.11542 2221 6 6.1 5.9810 35.1631.11618 2221 7 7.1 5.9797 35.1631.11615 2221 8 8.1 5.9798 35.1630.10213 2221 9 9.1 5.9792 35.1629.11311 2221 ... . If I use : read.table(file, skip = 10) it works fine but sometimes the missing data are not only in line number 1 ( 1 1.0 2999) but in lines 1,2,3,,, and therefore R fails to import the data file How can I fix it? I have tried with the arguments strip.white = TRUE , fill = TRUE , blank.lines.skip = TRUE but still not get what I want Thanks in advance version _ platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major 2 minor 4.0 year 2006 month 10 day03 svn rev39566 language R version.string R version 2.4.0 (2006-10-03) __ 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 file problem
Hi If the file is tab delimited you could try something like this: a-read.delim(file, skip = 9, header=F, na.strings=NA) Are you sure you want to skip 10 lines? (Is there a blank line somewhere?) J --- -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Luis Ridao Cruz Sent: 03 November 2006 14:03 To: r-help@stat.math.ethz.ch Subject: [R] read file problem R-help, I have the following file I want to import to R (some lines removed) Calibrated CTD data for station:00280001 Calibrated:23/8 2001, Salinity Unsmoothed, Fluorescence Uncalibrated Maximum observed depth:36 m QUAL has one digit for each of pressure, temp., sal. and fluor. QUAL=1:Uncal., QUAL=2:OK, QUAL=6:Interp., QUAL=9:No data DEPTH CTDPRS CTDTMP CTDSAL RAWFLU NUMB. QUAL MDBAR IPTS-68 PSS-78 OBS. *** *** *** *** 1 1.0 2999 2 2.0 5.9793 35.1629.10717 2221 3 3.0 5.9797 35.1631.10117 2221 4 4.0 5.9809 35.1631.11812 2221 5 5.1 5.9811 35.1629.11542 2221 6 6.1 5.9810 35.1631.11618 2221 7 7.1 5.9797 35.1631.11615 2221 8 8.1 5.9798 35.1630.10213 2221 9 9.1 5.9792 35.1629.11311 2221 ... . If I use : read.table(file, skip = 10) it works fine but sometimes the missing data are not only in line number 1 ( 1 1.0 2999) but in lines 1,2,3,,, and therefore R fails to import the data file How can I fix it? I have tried with the arguments strip.white = TRUE , fill = TRUE , blank.lines.skip = TRUE but still not get what I want Thanks in advance version _ platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major 2 minor 4.0 year 2006 month 10 day03 svn rev39566 language R version.string R version 2.4.0 (2006-10-03) __ 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 file problem
You should pay attention to the argument na.string. na.strings: a character vector of strings which are to be interpreted as 'NA' values. Blank fields are also considered to be missing values in logical, integer, numeric and complex fields. On 11/3/06, Luis Ridao Cruz [EMAIL PROTECTED] wrote: R-help, I have the following file I want to import to R (some lines removed) Calibrated CTD data for station:00280001 Calibrated:23/8 2001, Salinity Unsmoothed, Fluorescence Uncalibrated Maximum observed depth:36 m QUAL has one digit for each of pressure, temp., sal. and fluor. QUAL=1:Uncal., QUAL=2:OK, QUAL=6:Interp., QUAL=9:No data DEPTH CTDPRS CTDTMP CTDSAL RAWFLU NUMB. QUAL MDBAR IPTS-68 PSS-78 OBS. *** *** *** *** 1 1.0 2999 2 2.0 5.9793 35.1629.10717 2221 3 3.0 5.9797 35.1631.10117 2221 4 4.0 5.9809 35.1631.11812 2221 5 5.1 5.9811 35.1629.11542 2221 6 6.1 5.9810 35.1631.11618 2221 7 7.1 5.9797 35.1631.11615 2221 8 8.1 5.9798 35.1630.10213 2221 9 9.1 5.9792 35.1629.11311 2221 ... . If I use : read.table(file, skip = 10) it works fine but sometimes the missing data are not only in line number 1 ( 1 1.0 2999) but in lines 1,2,3,,, and therefore R fails to import the data file How can I fix it? I have tried with the arguments strip.white = TRUE , fill = TRUE , blank.lines.skip = TRUE but still not get what I want Thanks in advance version _ platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major 2 minor 4.0 year 2006 month 10 day03 svn rev39566 language R version.string R version 2.4.0 (2006-10-03) __ 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. -- Ronggui Huang Department of Sociology Fudan University, Shanghai, China 黄荣贵 复旦大学社会学系 __ 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 file problem
On Fri, Nov 03, 2006 at 02:02:35PM +, Luis Ridao Cruz wrote: DEPTH CTDPRS CTDTMP CTDSAL RAWFLU NUMB. QUAL MDBAR IPTS-68 PSS-78 OBS. *** *** *** *** 1 1.0 2999 2 2.0 5.9793 35.1629.10717 2221 3 3.0 5.9797 35.1631.10117 2221 4 4.0 5.9809 35.1631.11812 2221 5 5.1 5.9811 35.1629.11542 2221 6 6.1 5.9810 35.1631.11618 2221 7 7.1 5.9797 35.1631.11615 2221 8 8.1 5.9798 35.1630.10213 2221 9 9.1 5.9792 35.1629.11311 2221 read.table(file, skip = 10) To me it looks like your data is in a fixed-width format. If that is the case you should use read.fwf() instead of read.table(). cu Philipp -- Dr. Philipp PagelTel. +49-8161-71 2131 Dept. of Genome Oriented Bioinformatics Fax. +49-8161-71 2186 Technical University of Munich Science Center Weihenstephan 85350 Freising, Germany http://mips.gsf.de/staff/pagel __ 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 file problem
Luis Ridao Cruz wrote: R-help, I have the following file I want to import to R (some lines removed) Calibrated CTD data for station:00280001 Calibrated:23/8 2001, Salinity Unsmoothed, Fluorescence Uncalibrated Maximum observed depth:36 m QUAL has one digit for each of pressure, temp., sal. and fluor. QUAL=1:Uncal., QUAL=2:OK, QUAL=6:Interp., QUAL=9:No data DEPTH CTDPRS CTDTMP CTDSAL RAWFLU NUMB. QUAL MDBAR IPTS-68 PSS-78 OBS. *** *** *** *** 1 1.0 2999 2 2.0 5.9793 35.1629.10717 2221 3 3.0 5.9797 35.1631.10117 2221 4 4.0 5.9809 35.1631.11812 2221 5 5.1 5.9811 35.1629.11542 2221 6 6.1 5.9810 35.1631.11618 2221 7 7.1 5.9797 35.1631.11615 2221 8 8.1 5.9798 35.1630.10213 2221 9 9.1 5.9792 35.1629.11311 2221 ... . If I use : read.table(file, skip = 10) it works fine but sometimes the missing data are not only in line number 1 ( 1 1.0 2999) but in lines 1,2,3,,, and therefore R fails to import the data file How can I fix it? I have tried with the arguments strip.white = TRUE , fill = TRUE , blank.lines.skip = TRUE but still not get what I want This looks like a job for read.fwf... ?read.fwf -- --- Jeff NewmillerThe . . Go Live... DCN:[EMAIL PROTECTED]Basics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/BatteriesO.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k __ 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.
