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arthurbeer01

2009-Dec-24 01:31 UTC

[R] Column naming issues using read.table

Hi, this is my first post so please be gentle.
I quite new to R and using it for my biology degree.

My problem is. Im trying to import data from a .csv file using the
read.table command. The .csv file header starts on row 2 but is contained in
column 1, i have 600 data files and for future ease would rather not edit
each file seperatly. The data starts on row three and I only need the first
381 data points.

The R error message using the code iv got so far is

Error in read.table(file("s1-2c83.csv"), header = FALSE, sep =
",", quote "",  :
  more columns than column names

The code I have so far is

framename<-read.table(file ("s1-2c83.csv"),
header = FALSE, # FLASE indicates headers are not included in input file
sep = ",",    # must have "," otherwise errors in table
quote = "",
dec = ".",
row.names = 1, # must = 1 or extra column of row numbering is entered
col.names = ("Nr2sec,Cnt1X,Cnt1Y,Cnt2X,Cnt2Y,sec100,hour"),
as.is = FALSE,
na.strings = "NA",
colClasses = NULL,
nrows = 381, # rows to stop data.table recording (not input file row
number!)
skip = 2,    # number of rows to skp before reading data from input file
strip.white = FALSE,
comment.char = "")

write.csv(framename, file = "s1-2c83-ok.csv")

If I delete the line col.names, Iv manged to get the data read and saved to
a new .csv file but cannot work out how to get the column headers renamed.
The read.table (framename) displays the headers as v1,v2,v3 etc, this is
what i cant change. Also it has the first column without a header (i think
its the row number) which I dont want in the output file

The read data file example s1-2c83.csv

1:Samplerate = 2 samps/sec						
2:      Nr   Cnt1X   Cnt1Y   Cnt2X   Cnt2Y  sec100  hour						
3: 1	53	84	43	2	22	12
4: 2	90	155	74	0	72	12
5: 3	90	155	74	0	121	12

Any help will be greatly appreciated after the 5hrs Iv spent already on this
problem.

Many thanks in advance

 Adam



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jim holtman

2009-Dec-24 01:55 UTC

head link

[R] Column naming issues using read.table

This reads in your posted data:
> x <- read.table(textConnection("Samplerate = 2 samps/sec+       Nr   Cnt1X   Cnt1Y   Cnt2X   Cnt2Y  sec100  hour
+  1    53      84      43      2       22      12
+  2    90      155     74      0       72      12
+  3    90      155     74      0       121     12"), skip=1,
header=TRUE)> closeAllConnections()
>
> x  Nr Cnt1X Cnt1Y Cnt2X Cnt2Y sec100 hour
1  1    53    84    43     2     22   12
2  2    90   155    74     0     72   12
3  3    90   155    74     0    121   12


On Wed, Dec 23, 2009 at 8:31 PM, arthurbeer01
<arthur_beer@hotmail.com>wrote:
>
> Hi, this is my first post so please be gentle.
> I quite new to R and using it for my biology degree.
>
> My problem is. Im trying to import data from a .csv file using the
> read.table command. The .csv file header starts on row 2 but is contained
> in
> column 1, i have 600 data files and for future ease would rather not edit
> each file seperatly. The data starts on row three and I only need the first
> 381 data points.
>
> The R error message using the code iv got so far is
>
> Error in read.table(file("s1-2c83.csv"), header = FALSE, sep =
",", quote > "",  :
>  more columns than column names
>
> The code I have so far is
>
> framename<-read.table(file ("s1-2c83.csv"),
> header = FALSE, # FLASE indicates headers are not included in input file
> sep = ",",    # must have "," otherwise errors in table
> quote = "",
> dec = ".",
> row.names = 1, # must = 1 or extra column of row numbering is entered
> col.names = ("Nr2sec,Cnt1X,Cnt1Y,Cnt2X,Cnt2Y,sec100,hour"),
> as.is = FALSE,
> na.strings = "NA",
> colClasses = NULL,
> nrows = 381, # rows to stop data.table recording (not input file row
> number!)
> skip = 2,    # number of rows to skp before reading data from input file
> strip.white = FALSE,
> comment.char = "")
>
> write.csv(framename, file = "s1-2c83-ok.csv")
>
> If I delete the line col.names, Iv manged to get the data read and saved to
> a new .csv file but cannot work out how to get the column headers renamed.
> The read.table (framename) displays the headers as v1,v2,v3 etc, this is
> what i cant change. Also it has the first column without a header (i think
> its the row number) which I dont want in the output file
>
> The read data file example s1-2c83.csv
>
> 1:Samplerate = 2 samps/sec
> 2:      Nr   Cnt1X   Cnt1Y   Cnt2X   Cnt2Y  sec100  hour
> 3: 1    53      84      43      2       22      12
> 4: 2    90      155     74      0       72      12
> 5: 3    90      155     74      0       121     12
>
> Any help will be greatly appreciated after the 5hrs Iv spent already on
> this
> problem.
>
> Many thanks in advance
>
>  Adam
>
>
>
> --
> View this message in context:
>
http://n4.nabble.com/Column-naming-issues-using-read-table-tp978241p978241.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
>
http://www.R-project.org/posting-guide.html<http://www.r-project.org/posting-guide.html>
> and provide commented, minimal, self-contained, reproducible code.
>


-- 
Jim Holtman
Cincinnati, OH
+1 513 646 9390

What is the problem that you are trying to solve?

	[[alternative HTML version deleted]]

John Kane

2009-Dec-24 15:22 UTC

head link

[R] Column naming issues using read.table

I'm not exactly an expert so this is not likely a good way to do it but if
the actual variable names are constant across the files why not just read in the
data and assign the names later?

see skip in ?read.table.

x  <- read.table("d:/junk1.txt", skip=2)

should read in the data.  


You can clean up the file(s) for length, etc once you have read it/them in. 
Using your sample data I drop column one and only keep 2 of the three lines of
data.

xx <- xx[1:2, -1]

names(xx)  <-c("A",
"B","C","D","E", "F")




--- On Wed, 12/23/09, arthurbeer01 <arthur_beer at hotmail.com> wrote:
> From: arthurbeer01 <arthur_beer at hotmail.com>
> Subject: [R]  Column naming issues using read.table
> To: r-help at r-project.org
> Received: Wednesday, December 23, 2009, 8:31 PM
> 
> Hi, this is my first post so please be gentle.
> I quite new to R and using it for my biology degree.
> 
> My problem is. Im trying to import data from a .csv file
> using the
> read.table command. The .csv file header starts on row 2
> but is contained in
> column 1, i have 600 data files and for future ease would
> rather not edit
> each file seperatly. The data starts on row three and I
> only need the first
> 381 data points.
> 
> The R error message using the code iv got so far is
> 
> Error in read.table(file("s1-2c83.csv"), header = FALSE,
> sep = ",", quote > "",? : 
> ? more columns than column names
> 
> The code I have so far is
> 
> framename<-read.table(file ("s1-2c83.csv"),
> header = FALSE, # FLASE indicates headers are not included
> in input file
> sep = ",",? ? # must have "," otherwise errors in
> table
> quote = "",
> dec = ".",
> row.names = 1, # must = 1 or extra column of row numbering
> is entered
> col.names > ("Nr2sec,Cnt1X,Cnt1Y,Cnt2X,Cnt2Y,sec100,hour"),
> as.is = FALSE,
> na.strings = "NA",
> colClasses = NULL,
> nrows = 381, # rows to stop data.table recording (not input
> file row
> number!)
> skip = 2,? ? # number of rows to skp before
> reading data from input file
> strip.white = FALSE,
> comment.char = "")
> 
> write.csv(framename, file = "s1-2c83-ok.csv")
> 
> If I delete the line col.names, Iv manged to get the data
> read and saved to
> a new .csv file but cannot work out how to get the column
> headers renamed.
> The read.table (framename) displays the headers as v1,v2,v3
> etc, this is
> what i cant change. Also it has the first column without a
> header (i think
> its the row number) which I dont want in the output file
> 
> The read data file example s1-2c83.csv
> 
> 1:Samplerate = 2 samps/sec???
> ??? ??? ???
> ??? ??? 
> 2:? ? ?
> Nr???Cnt1X???Cnt1Y???Cnt2X???Cnt2Y?
> sec100? hour??? ???
> ??? ??? ???
> ??? 
> 3: 1??? 53???
> 84??? 43???
> 2??? 22??? 12
> 4: 2??? 90???
> 155??? 74???
> 0??? 72??? 12
> 5: 3??? 90???
> 155??? 74???
> 0??? 121??? 12
> 
> Any help will be greatly appreciated after the 5hrs Iv
> spent already on this
> problem.
> 
> Many thanks in advance
> 
>  Adam
> 
> 
> 
> -- 
> View this message in context:
http://n4.nabble.com/Column-naming-issues-using-read-table-tp978241p978241.html
> Sent from the R help mailing list archive at Nabble.com.
> 
> ______________________________________________
> 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.
> 

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