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how can I import op.gz files with read.csv or otherwise
4 messages · Bernd Dittmann, arun, John Kane +1 more
HI, May be this link helps you: http://stackoverflow.com/questions/5764499/decompress-gz-file-using-r A.K. ----- Original Message ----- From: herr dittmann <herrdittmann at yahoo.co.uk> To: "r-help at r-project.org" <r-help at r-project.org> Cc: Sent: Friday, December 21, 2012 9:51 AM Subject: [R] how can I import op.gz files with read.csv or otherwise Dear R-users, I am struggling to directly read an "op.gz" file into R. NOAA kindly provides daily weather data on their FTP server for download.
sessionInfo()
R version 2.15.1 (2012-06-22) Platform: x86_64-pc-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United Kingdom.1252? LC_CTYPE=English_United Kingdom.1252??? LC_MONETARY=English_United Kingdom.1252 [4] LC_NUMERIC=C??????????????????????????? LC_TIME=English_United Kingdom.1252?? ? attached base packages: [1] stats???? graphics? grDevices utils???? datasets? methods?? base??? ? loaded via a namespace (and not attached): [1] tools_2.15.1 Here is the data set in question: x <- read.csv(file="ftp://ftp.ncdc.noaa.gov/pub/data/gsod/2012/285880-99999-2012.op.gz", skip = 1, sep = "") and "structure" returns some incomprehensible gibberish:
str(x)
'data.frame':?? 70 obs. of? 6 variables:
?$ X4?tYd...??8.?WD...??.??.X.QT?VP..????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? : Factor w/ 70 levels "\005~4?d???E\031y\020???\035J???I???\021?B??R{?Ykv\035`???a\017Z\021?sP?e?h??""| __truncated__,..: 44 13 56 64 28 23 67 3 2 33 ...
?$ X.?oM??T..??_...??g?7.?..T?.??.?...5?J...???j.Q?..?.e???Gm????g..a...??.J..?.?s?.??.?.?klsUD?.?..?U...u1.z?.W?..x...3._..E.?.?ZD.?o??.dv?....?k.C.y...8h: Factor w/ 41 levels "","\025?\016\v??i;?4??\002\001P??\0025????{????=??4&?w\\\\Q??????\"hn???I???b*??\035b\b>6??$W!??R=?\022?Pq?[?j\004$T??3?*??%??N??\"| __truncated__,..: 1 1 1 39 1 1 1 8 1 5 ...
?$ X.i?.y??..?2.h..??7.?J.3k..jLm...Q..uY?J?.K.zkU.8.??..Y.7.3...???A.?.3??..Z..5...??.??????????????????????????????????????????????????????????????????? : Factor w/ 29 levels "","\001q?^+n?1",..: 1 1 1 4 1 1 1 14 1 6 ...
?$ X.?Fd.m.?..v.?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? : Factor w/ 17 levels "","??SL\a????\035d)??$?Z??????J?????B6?\006%5l[???\025a\024??+gT+3",..: 1 1 1 16 1 1 1 1 1 1 ...
?$ ?A..E.?JkEZ.??.?.?.......?.z..?.z..?..??.???g.????????????????????????????????????????????????????????????????????????????????????????????????????????? : Factor w/ 8 levels "","\001S\177?\017iS??i??#\017\"Ug?:i??\016p?\031U??D""| __truncated__,..: 1 1 1 1 1 1 1 1 1 1 ...
?$ X..o??nP?o?W?j.??..B..???.Q??...????? ?
While I can manually open and read the op.gz file in a text editor, read.csv() or read.table() the imported file is simply unreadable.
How can I best get the job done? Any pointers, suggestions, ideas most welcome!!
Thanks in advance!
Bernd
??? [[alternative HTML version deleted]]
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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.
Try downloading it and decompress it: url <- "ftp://ftp.ncdc.noaa.gov/pub/data/gsod/2012/285880-99999-2012.op.gz" dest <- "/home/john/rdata/weather.op.gz" download.file(url, dest) However it does not look like a nicely formatted file and you may have to do some cleanup in a text editior or perhaps load it into a spreadsheet before you read it into R. I tried the method from the link arun provided and it did not work. It looks like the headers and data are not consistant John Kane Kingston ON Canada
-----Original Message----- From: herrdittmann at yahoo.co.uk Sent: Fri, 21 Dec 2012 14:51:05 +0000 (GMT) To: r-help at r-project.org Subject: [R] how can I import op.gz files with read.csv or otherwise Dear R-users, I am struggling to directly read an "op.gz" file into R. NOAA kindly provides daily weather data on their FTP server for download.
sessionInfo()
R version 2.15.1 (2012-06-22) Platform: x86_64-pc-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United Kingdom.1252B LC_CTYPE=English_United Kingdom.1252B B B LC_MONETARY=English_United Kingdom.1252 [4] LC_NUMERIC=CB B B B B B B B B B B B B B B B B B B B B B B B B B B LC_TIME=English_United Kingdom.1252B B B attached base packages: [1] statsB B B B graphicsB grDevices utilsB B B B datasetsB methodsB B baseB B B B loaded via a namespace (and not attached): [1] tools_2.15.1 Here is the data set in question: x <-
read.csv(file="ftp://ftp.ncdc.noaa.gov/pub/data/gsod/2012/285880-99999-2012.op.gz",
skip = 1, sep = "") and "structure" returns some incomprehensible gibberish:
str(x)
'data.frame':B B 70 obs. ofB 6 variables:
B $ X4C tYd...C?C?8.C%WD...C+C<.C/C?.X.QTC1VP..B B B B B B B B B B B B B
B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B
B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B
B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B : Factor w/
70 levels "\005~4C(dE?C?C-E\031y\020C?C-B:\035JC+C/C?IK?C?C-\021b?
BC?C?R{E>Ykv\035`b??C,B0a\017Z\021C?sPb??eC?hC?C?""| __truncated__,..: 44
13 56 64 28 23 67 3 2 33 ...
B $ X.C6oMC=C?T..C?B:_...C?C-gC?7.C"..TC>.C<C?.B*...5C?J...E>C-C?j.QC
..C#.eC?F?C?GmC2C=C'B:g..a...C?C&.J..C?.C#sC'.C*E .C;.C
klsUDC?.E ..C"U...u1.zC?.WC?..x...3._..E.C2.C
ZD.C/oC?C?.dvC&....C2k.C.y...8h: Factor w/ 41 levels
"","\025C'\016\vC?B2i;B'4F?C1\002\001Pb??C!\0025B6b?"C"C?{C?C?b?"B9=C?B$4&C0w\\\\QB-B4b?:B-C?B4\"hnC?b?"b?0IB(C?E
b*B*E!\035b\b>6C?C?$W!C?C?R=B(\022b??PqK?[B;j\004$TC?b?"3B2*C?B1%C B-Nb??b?:\"| __truncated__,..: 1 1 1 39 1 1 1 8 1 5 ... B $ X.iE?.yC?C;..C=2.h..C;C 7.C#J.3k..jLm...Q..uYC?JC$.K.zkU.8.C6C?..Y.7.3...C<C C.A.C .3C;C?..Z..5...C"E!.B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B : Factor w/ 29 levels "","\001qC?^+nC*1",..: 1 1 1 4 1 1 1 14 1 6 ... B $ X.C.Fd.m.E ..v.B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B : Factor w/ 17 levels "","B B4SL\aE!C?C?B0\035d)b??B<$C-ZC?B<C2B6C.C?JC b??C$C>b? B6C%\006%5l[b??B<E!\025a\024C1C/+gT+3",..: 1 1 1 16 1 1 1 1 1 1 ... B $ C?A..E.E8JkEZ.C?C .C!.C+.......E?.z..C?.z..E?..C2C?.C?C?C#g.C6B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B : Factor w/ 8 levels "","\001S\177B?\017iSC?C?iC?C?#\017\"UgC?:iB4C-\016pC?\031UC?C)D""| __truncated__,..: 1 1 1 1 1 1 1 1 1 1 ... B $ X..oC0C'nPC?oC?WC5j.C)C?..B..C?C?C+.QC*C9...C8B B B B B While I can manually open and read the op.gz file in a text editor, read.csv() or read.table() the imported file is simply unreadable. How can I best get the job done? Any pointers, suggestions, ideas most welcome!! Thanks in advance! Bernd [[alternative HTML version deleted]]
______________________________________________ R-help at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
____________________________________________________________ FREE 3D EARTH SCREENSAVER - Watch the Earth right on your desktop!
Hello, It can be read using readLines. I've changed url to URL because there's a function of that name. I've also changed dest. URL <- "ftp://ftp.ncdc.noaa.gov/pub/data/gsod/2012/285880-99999-2012.op.gz" dest <- "weather.op.gz" download.file(URL, dest) gz <- gzfile(dest, open = "rt") x <- readLines(gz) close(gz) x Like you say, headers and data are not consistent, it seems some column headers are missing. Hope this helps, Rui Barradas Em 21-12-2012 17:44, John Kane escreveu:
Try downloading it and decompress it: url <- "ftp://ftp.ncdc.noaa.gov/pub/data/gsod/2012/285880-99999-2012.op.gz" dest <- "/home/john/rdata/weather.op.gz" download.file(url, dest) However it does not look like a nicely formatted file and you may have to do some cleanup in a text editior or perhaps load it into a spreadsheet before you read it into R. I tried the method from the link arun provided and it did not work. It looks like the headers and data are not consistant John Kane Kingston ON Canada
-----Original Message----- From: herrdittmann at yahoo.co.uk Sent: Fri, 21 Dec 2012 14:51:05 +0000 (GMT) To: r-help at r-project.org Subject: [R] how can I import op.gz files with read.csv or otherwise Dear R-users, I am struggling to directly read an "op.gz" file into R. NOAA kindly provides daily weather data on their FTP server for download.
sessionInfo()
R version 2.15.1 (2012-06-22) Platform: x86_64-pc-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United Kingdom.1252B LC_CTYPE=English_United Kingdom.1252B B B LC_MONETARY=English_United Kingdom.1252 [4] LC_NUMERIC=CB B B B B B B B B B B B B B B B B B B B B B B B B B B LC_TIME=English_United Kingdom.1252B B B attached base packages: [1] statsB B B B graphicsB grDevices utilsB B B B datasetsB methodsB B baseB B B B loaded via a namespace (and not attached): [1] tools_2.15.1 Here is the data set in question: x <-
read.csv(file="ftp://ftp.ncdc.noaa.gov/pub/data/gsod/2012/285880-99999-2012.op.gz",
skip = 1, sep = "") and "structure" returns some incomprehensible gibberish:
str(x)
'data.frame':B B 70 obs. ofB 6 variables:
B $ X4C tYd...C?C?8.C%WD...C+C<.C/C?.X.QTC1VP..B B B B B B B B B B B B B
B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B
B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B
B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B : Factor w/
70 levels "\005~4C(dE?C?C-E\031y\020C?C-B:\035JC+C/C?IK?C?C-\021b?
BC?C?R{E>Ykv\035`b??C,B0a\017Z\021C?sPb??eC?hC?C?""| __truncated__,..: 44
13 56 64 28 23 67 3 2 33 ...
B $ X.C6oMC=C?T..C?B:_...C?C-gC?7.C"..TC>.C<C?.B*...5C?J...E>C-C?j.QC
..C#.eC?F?C?GmC2C=C'B:g..a...C?C&.J..C?.C#sC'.C*E .C;.C
klsUDC?.E ..C"U...u1.zC?.WC?..x...3._..E.C2.C
ZD.C/oC?C?.dvC&....C2k.C.y...8h: Factor w/ 41 levels
"","\025C'\016\vC?B2i;B'4F?C1\002\001Pb??C!\0025B6b?"C"C?{C?C?b?"B9=C?B$4&C0w\\\\QB-B4b?:B-C?B4\"hnC?b?"b?0IB(C?E
b*B*E!\035b\b>6C?C?$W!C?C?R=B(\022b??PqK?[B;j\004$TC?b?"3B2*C?B1%C B-Nb??b?:\"| __truncated__,..: 1 1 1 39 1 1 1 8 1 5 ... B $ X.iE?.yC?C;..C=2.h..C;C 7.C#J.3k..jLm...Q..uYC?JC$.K.zkU.8.C6C?..Y.7.3...C<C C.A.C .3C;C?..Z..5...C"E!.B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B : Factor w/ 29 levels "","\001qC?^+nC*1",..: 1 1 1 4 1 1 1 14 1 6 ... B $ X.C.Fd.m.E ..v.B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B : Factor w/ 17 levels "","B B4SL\aE!C?C?B0\035d)b??B<$C-ZC?B<C2B6C.C?JC b??C$C>b? B6C%\006%5l[b??B<E!\025a\024C1C/+gT+3",..: 1 1 1 16 1 1 1 1 1 1 ... B $ C?A..E.E8JkEZ.C?C .C!.C+.......E?.z..C?.z..E?..C2C?.C?C?C#g.C6B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B : Factor w/ 8 levels "","\001S\177B?\017iSC?C?iC?C?#\017\"UgC?:iB4C-\016pC?\031UC?C)D""| __truncated__,..: 1 1 1 1 1 1 1 1 1 1 ... B $ X..oC0C'nPC?oC?WC5j.C)C?..B..C?C?C+.QC*C9...C8B B B B B While I can manually open and read the op.gz file in a text editor, read.csv() or read.table() the imported file is simply unreadable. How can I best get the job done? Any pointers, suggestions, ideas most welcome!! Thanks in advance! Bernd [[alternative HTML version deleted]]
______________________________________________ R-help at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
____________________________________________________________ FREE 3D EARTH SCREENSAVER - Watch the Earth right on your desktop! ______________________________________________ R-help at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.