R help - May 2008 - Importing data in text file into R

Dear all,
I am quite new to R; facing certain problems:
Say, I have a text file( named as "try"):
Year	C1	C2	C3	C4	C5	C6
Y1	3.5	13.8	9.5	6.8	0.4	24.2
Y2	3.8	13.9	9.9	7.6	0.7	12.8
Y3	4.5	14.5	14.2	9.2	0.6	14.5
Y4	5.9	16.2	24.6	12.7	0.2	24.3
Y5	7.2	20.4	40.6	18.2	0.8	28.2
Y6	5.9	18.6	37.4	14.5	0.3	36.9
Y7	8.0	16.1	88.6	24.1	0.1	34.6
Y8	13.6	21.1	56.3	19.0	0.7	33.3

I wish to import the file into R and make certain
computations, like intercorrelation matrix. I tried
the following syntax:

# Inputting the data file (saved in text format)
df="trial.txt"
idt=read.table(df,header=T, sep="\t")
idt
# To generate intercorrelatio matrix
r = cor(idt)
r=round(r, 4)
r

The seems to have been read, but further computations
not made, with the following output:
> # Inputting the data file (saved in text format)
> df="trial.txt"
> idt=read.table(df,header=T, sep="\t")
> idt
  Year   C1   C2   C3   C4  C5   C6
1   Y1  3.5 13.8  9.5  6.8 0.4 24.2
2   Y2  3.8 13.9  9.9  7.6 0.7 12.8
3   Y3  4.5 14.5 14.2  9.2 0.6 14.5
4   Y4  5.9 16.2 24.6 12.7 0.2 24.3
5   Y5  7.2 20.4 40.6 18.2 0.8 28.2
6   Y6  5.9 18.6 37.4 14.5 0.3 36.9
7   Y7  8.0 16.1 88.6 24.1 0.1 34.6
8   Y8 13.6 21.1 56.3 19.0 0.7 33.3
> # To generate intercorrelatio matrix
> r = cor(idt)
Error in cor(idt) : missing observations in cov/cor
In addition: Warning message:
In cor(idt) : NAs introduced by coercion
> r=round(r, 4)
Error: object "r" not found
> r
Error: object "r" not found

Kindly advise me as to how to get rid of the error
message.

AJSS

Dear AJSS,

The problem is that the way you've read the data, the first column of  
the data frame is a factor, not a numerical variable, and thus is not  
suitable for computing correlations.

You could use the command cor(idt[,-1]) to compute correlations on all  
but the first column, but your intention was probably to use the first  
column of the input file for row names, not as a variable. One way to  
do this is simply to omit the variable name "Year" in the first row of
the input data file.

I hope this helps,
  John

On 23-May-08, at 11:40 PM, amarjit singh sethi wrote:
> Dear all,
> I am quite new to R; facing certain problems:
> Say, I have a text file( named as "try"):
> Year	C1	C2	C3	C4	C5	C6
> Y1	3.5	13.8	9.5	6.8	0.4	24.2
> Y2	3.8	13.9	9.9	7.6	0.7	12.8
> Y3	4.5	14.5	14.2	9.2	0.6	14.5
> Y4	5.9	16.2	24.6	12.7	0.2	24.3
> Y5	7.2	20.4	40.6	18.2	0.8	28.2
> Y6	5.9	18.6	37.4	14.5	0.3	36.9
> Y7	8.0	16.1	88.6	24.1	0.1	34.6
> Y8	13.6	21.1	56.3	19.0	0.7	33.3
>
> I wish to import the file into R and make certain
> computations, like intercorrelation matrix. I tried
> the following syntax:
>
> # Inputting the data file (saved in text format)
> df="trial.txt"
> idt=read.table(df,header=T, sep="\t")
> idt
> # To generate intercorrelatio matrix
> r = cor(idt)
> r=round(r, 4)
> r
>
> The seems to have been read, but further computations
> not made, with the following output:
>
>> # Inputting the data file (saved in text format)
>> df="trial.txt"
>> idt=read.table(df,header=T, sep="\t")
>> idt
>  Year   C1   C2   C3   C4  C5   C6
> 1   Y1  3.5 13.8  9.5  6.8 0.4 24.2
> 2   Y2  3.8 13.9  9.9  7.6 0.7 12.8
> 3   Y3  4.5 14.5 14.2  9.2 0.6 14.5
> 4   Y4  5.9 16.2 24.6 12.7 0.2 24.3
> 5   Y5  7.2 20.4 40.6 18.2 0.8 28.2
> 6   Y6  5.9 18.6 37.4 14.5 0.3 36.9
> 7   Y7  8.0 16.1 88.6 24.1 0.1 34.6
> 8   Y8 13.6 21.1 56.3 19.0 0.7 33.3
>> # To generate intercorrelatio matrix
>> r = cor(idt)
> Error in cor(idt) : missing observations in cov/cor
> In addition: Warning message:
> In cor(idt) : NAs introduced by coercion
>> r=round(r, 4)
> Error: object "r" not found
>> r
> Error: object "r" not found
>
> Kindly advise me as to how to get rid of the error
> message.
>
> AJSS
>
> ______________________________________________
> 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.

On Fri, 23-May-2008 at 08:40PM -0700, amarjit singh sethi wrote:

|> Dear all,
|> I am quite new to R; facing certain problems:
|> Say, I have a text file( named as "try"):


|> > idt=read.table(df,header=T, sep="\t")
|> > idt
|>   Year   C1   C2   C3   C4  C5   C6
|> 1   Y1  3.5 13.8  9.5  6.8 0.4 24.2
|> 2   Y2  3.8 13.9  9.9  7.6 0.7 12.8
|> 3   Y3  4.5 14.5 14.2  9.2 0.6 14.5
|> 4   Y4  5.9 16.2 24.6 12.7 0.2 24.3
|> 5   Y5  7.2 20.4 40.6 18.2 0.8 28.2
|> 6   Y6  5.9 18.6 37.4 14.5 0.3 36.9
|> 7   Y7  8.0 16.1 88.6 24.1 0.1 34.6
|> 8   Y8 13.6 21.1 56.3 19.0 0.7 33.3
|> > # To generate intercorrelatio matrix
|> > r = cor(idt)
|> Error in cor(idt) : missing observations in cov/cor
|> In addition: Warning message:
|> In cor(idt) : NAs introduced by coercion


The help file for cor says this about x and y:

       x: a numeric vector, matrix or data frame.

       y: 'NULL' (default) or a vector, matrix or data frame with
          compatible dimensions to 'x'.  The default is equivalent to
          'y = x' (but more efficient).

Your x isn't a numeric vector, matrix or data frame.

x[,-1] is, and that might give what you want, but read the rest of the
help file to determine if that's what you want it to do.  Having
rownames on your dataframe might help seeing what is happening.  The
easiest way I can see to get row names is in your read.table line.
Add row.names = 1.

HTH

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