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Johan Jackson

2010-May-26 00:05 UTC

[R] reading in table with different number of elements in each row

HI all,

This is probably simple, but I haven't been able to locate the answer either
in the Import Manual or from searching the listserve.

I have tab-delimited data with different numbers of elements in each row. I
want to read it into R, such that R fills in "NA" in elements that
have no
data. How do I accomplish this?



Example:


DATA on disk:
      1 -0.068191       -0.050729       -0.113982       -0.044363
-0.072445       -0.044516       -0.048597       -0.051866
-0.051563       -0.041576
      2 -0.032645       -0.062389       -0.054491       -0.058061
-0.034690       -0.038044       -0.045332       -0.043785
-0.050639       -0.049617
      3 -0.068191       -0.044207       -0.058061       -0.050729
-0.034991       -0.045360       -0.051563       -0.060290
-0.043785       -0.048757
      4 -0.068191       -0.062389       -0.050729       -0.058579
-0.056481       -0.044363       -0.042347       -0.060290
-0.051563       -0.037216       -0.041576       -0.056476
      5 -0.068191       -0.047649       -0.062389       -0.058061
-0.034227       -0.185829       -0.071855       -0.064096
-0.195645
      6 -0.040208       -0.068191       -0.036475       -0.041268
-0.044207       -0.044363       -0.034991       -0.059810
-0.051619       -0.051563       -0.037216       -0.041576
-0.019762
      7 -0.068191       -0.034227       -0.044363       -0.051563
-0.041576       -0.053823       -0.057023       -0.046083
-0.089374       -0.057436
      8 -0.068191       -0.050731       -0.044207       -0.169714
-0.060025       -0.048597       -0.037827       -0.053823
-0.055154
      9 -0.062389       -0.044207       -0.050729       -0.044363
-0.043785
     10 -0.040208       -0.036716       -0.068191       -0.051466
-0.050731       -0.050729       -0.048095       -0.044363
-0.044817       -0.059810       -0.051563       -0.037827
-0.053985       -0.059573       -0.052893
     11 -0.068191       -0.034227       -0.048597       -0.051563
-0.041576       -0.056512
     12 -0.040208       -0.050731       -0.044207       -0.048095
-0.044363       -0.044817       -0.037827       -0.053985       -0.059573

My attempts:
x <-
read.table("DATA",fill=TRUE,sep="\t",colClasses="numeric")> x          V1        V2        V3        V4        V5        V6
V7        V8        V9       V10       V11       V12       V13
1  -0.068191 -0.050729 -0.113982 -0.044363 -0.072445 -0.044516 -0.048597
-0.051866 -0.051563 -0.041576        NA        NA        NA
2  -0.032645 -0.062389 -0.054491 -0.058061 -0.034690 -0.038044 -0.045332
-0.043785 -0.050639 -0.049617        NA        NA        NA
3  -0.068191 -0.044207 -0.058061 -0.050729 -0.034991 -0.045360 -0.051563
-0.060290 -0.043785 -0.048757        NA        NA        NA
4  -0.068191 -0.062389 -0.050729 -0.058579 -0.056481 -0.044363 -0.042347
-0.060290 -0.051563 -0.037216 -0.041576 -0.056476        NA
5  -0.068191 -0.047649 -0.062389 -0.058061 -0.034227 -0.185829 -0.071855
-0.064096 -0.195645        NA        NA        NA        NA
6  -0.040208 -0.068191 -0.036475 -0.041268 -0.044207 -0.044363 -0.034991
-0.059810 -0.051619 -0.051563 -0.037216 -0.041576 -0.019762
7  -0.068191 -0.034227 -0.044363 -0.051563 -0.041576 -0.053823 -0.057023
-0.046083 -0.089374 -0.057436        NA        NA        NA
8  -0.068191 -0.050731 -0.044207 -0.169714 -0.060025 -0.048597 -0.037827
-0.053823 -0.055154        NA        NA        NA        NA
9  -0.062389 -0.044207 -0.050729 -0.044363 -0.043785        NA
NA        NA        NA        NA        NA        NA        NA
10 -0.040208 -0.036716 -0.068191 -0.051466 -0.050731 -0.050729 -0.048095
-0.044363 -0.044817 -0.059810 -0.051563 -0.037827 -0.053985
11 -0.059573 -0.052893        NA        NA        NA        NA
NA        NA        NA        NA        NA        NA        NA
12 -0.068191 -0.034227 -0.048597 -0.051563 -0.041576 -0.056512
NA        NA        NA        NA        NA        NA        NA
13 -0.040208 -0.050731 -0.044207 -0.048095 -0.044363 -0.044817 -0.037827
-0.053985 -0.059573        NA        NA        NA        NA

The above is almost right, but x has 13 rows instead of 12! WHY? Row 10
(which has 15 elements) was cut off at 13, and then the last two elements
were put in a new row. WHY?
I have tried messing with colClasses to no avail. Any help would be ...
umm... helpful!

JJ

	[[alternative HTML version deleted]]

jim holtman

2010-May-26 00:59 UTC

head link

[R] reading in table with different number of elements in each row

This is in the Detail of the help page:

The number of data columns is determined by looking at the first five
lines of input (or the whole file if it has less than five lines), or
from the length of col.names if it is specified and is longer. This
could conceivably be wrong if fill or blank.lines.skip are true, so
specify col.names if necessary.


try:  read.table(..., col.names=1:30)

This will assume there are 30 columns of data (you only said a max of
15, but lets double it)

On Tue, May 25, 2010 at 8:05 PM, Johan Jackson
<johan.h.jackson at gmail.com> wrote:> HI all,
>
> This is probably simple, but I haven't been able to locate the answer
either
> in the Import Manual or from searching the listserve.
>
> I have tab-delimited data with different numbers of elements in each row. I
> want to read it into R, such that R fills in "NA" in elements
that have no
> data. How do I accomplish this?
>
>
>
> Example:
>
>
> DATA on disk:
> ? ? ?1 -0.068191 ? ? ? -0.050729 ? ? ? -0.113982 ? ? ? -0.044363
> -0.072445 ? ? ? -0.044516 ? ? ? -0.048597 ? ? ? -0.051866
> -0.051563 ? ? ? -0.041576
> ? ? ?2 -0.032645 ? ? ? -0.062389 ? ? ? -0.054491 ? ? ? -0.058061
> -0.034690 ? ? ? -0.038044 ? ? ? -0.045332 ? ? ? -0.043785
> -0.050639 ? ? ? -0.049617
> ? ? ?3 -0.068191 ? ? ? -0.044207 ? ? ? -0.058061 ? ? ? -0.050729
> -0.034991 ? ? ? -0.045360 ? ? ? -0.051563 ? ? ? -0.060290
> -0.043785 ? ? ? -0.048757
> ? ? ?4 -0.068191 ? ? ? -0.062389 ? ? ? -0.050729 ? ? ? -0.058579
> -0.056481 ? ? ? -0.044363 ? ? ? -0.042347 ? ? ? -0.060290
> -0.051563 ? ? ? -0.037216 ? ? ? -0.041576 ? ? ? -0.056476
> ? ? ?5 -0.068191 ? ? ? -0.047649 ? ? ? -0.062389 ? ? ? -0.058061
> -0.034227 ? ? ? -0.185829 ? ? ? -0.071855 ? ? ? -0.064096
> -0.195645
> ? ? ?6 -0.040208 ? ? ? -0.068191 ? ? ? -0.036475 ? ? ? -0.041268
> -0.044207 ? ? ? -0.044363 ? ? ? -0.034991 ? ? ? -0.059810
> -0.051619 ? ? ? -0.051563 ? ? ? -0.037216 ? ? ? -0.041576
> -0.019762
> ? ? ?7 -0.068191 ? ? ? -0.034227 ? ? ? -0.044363 ? ? ? -0.051563
> -0.041576 ? ? ? -0.053823 ? ? ? -0.057023 ? ? ? -0.046083
> -0.089374 ? ? ? -0.057436
> ? ? ?8 -0.068191 ? ? ? -0.050731 ? ? ? -0.044207 ? ? ? -0.169714
> -0.060025 ? ? ? -0.048597 ? ? ? -0.037827 ? ? ? -0.053823
> -0.055154
> ? ? ?9 -0.062389 ? ? ? -0.044207 ? ? ? -0.050729 ? ? ? -0.044363
> -0.043785
> ? ? 10 -0.040208 ? ? ? -0.036716 ? ? ? -0.068191 ? ? ? -0.051466
> -0.050731 ? ? ? -0.050729 ? ? ? -0.048095 ? ? ? -0.044363
> -0.044817 ? ? ? -0.059810 ? ? ? -0.051563 ? ? ? -0.037827
> -0.053985 ? ? ? -0.059573 ? ? ? -0.052893
> ? ? 11 -0.068191 ? ? ? -0.034227 ? ? ? -0.048597 ? ? ? -0.051563
> -0.041576 ? ? ? -0.056512
> ? ? 12 -0.040208 ? ? ? -0.050731 ? ? ? -0.044207 ? ? ? -0.048095
> -0.044363 ? ? ? -0.044817 ? ? ? -0.037827 ? ? ? -0.053985 ? ? ? -0.059573
>
> My attempts:
> x <-
read.table("DATA",fill=TRUE,sep="\t",colClasses="numeric")
>> x
> ? ? ? ? ?V1 ? ? ? ?V2 ? ? ? ?V3 ? ? ? ?V4 ? ? ? ?V5 ? ? ? ?V6
> V7 ? ? ? ?V8 ? ? ? ?V9 ? ? ? V10 ? ? ? V11 ? ? ? V12 ? ? ? V13
> 1 ?-0.068191 -0.050729 -0.113982 -0.044363 -0.072445 -0.044516 -0.048597
> -0.051866 -0.051563 -0.041576 ? ? ? ?NA ? ? ? ?NA ? ? ? ?NA
> 2 ?-0.032645 -0.062389 -0.054491 -0.058061 -0.034690 -0.038044 -0.045332
> -0.043785 -0.050639 -0.049617 ? ? ? ?NA ? ? ? ?NA ? ? ? ?NA
> 3 ?-0.068191 -0.044207 -0.058061 -0.050729 -0.034991 -0.045360 -0.051563
> -0.060290 -0.043785 -0.048757 ? ? ? ?NA ? ? ? ?NA ? ? ? ?NA
> 4 ?-0.068191 -0.062389 -0.050729 -0.058579 -0.056481 -0.044363 -0.042347
> -0.060290 -0.051563 -0.037216 -0.041576 -0.056476 ? ? ? ?NA
> 5 ?-0.068191 -0.047649 -0.062389 -0.058061 -0.034227 -0.185829 -0.071855
> -0.064096 -0.195645 ? ? ? ?NA ? ? ? ?NA ? ? ? ?NA ? ? ? ?NA
> 6 ?-0.040208 -0.068191 -0.036475 -0.041268 -0.044207 -0.044363 -0.034991
> -0.059810 -0.051619 -0.051563 -0.037216 -0.041576 -0.019762
> 7 ?-0.068191 -0.034227 -0.044363 -0.051563 -0.041576 -0.053823 -0.057023
> -0.046083 -0.089374 -0.057436 ? ? ? ?NA ? ? ? ?NA ? ? ? ?NA
> 8 ?-0.068191 -0.050731 -0.044207 -0.169714 -0.060025 -0.048597 -0.037827
> -0.053823 -0.055154 ? ? ? ?NA ? ? ? ?NA ? ? ? ?NA ? ? ? ?NA
> 9 ?-0.062389 -0.044207 -0.050729 -0.044363 -0.043785 ? ? ? ?NA
> NA ? ? ? ?NA ? ? ? ?NA ? ? ? ?NA ? ? ? ?NA ? ? ? ?NA ? ? ? ?NA
> 10 -0.040208 -0.036716 -0.068191 -0.051466 -0.050731 -0.050729 -0.048095
> -0.044363 -0.044817 -0.059810 -0.051563 -0.037827 -0.053985
> 11 -0.059573 -0.052893 ? ? ? ?NA ? ? ? ?NA ? ? ? ?NA ? ? ? ?NA
> NA ? ? ? ?NA ? ? ? ?NA ? ? ? ?NA ? ? ? ?NA ? ? ? ?NA ? ? ? ?NA
> 12 -0.068191 -0.034227 -0.048597 -0.051563 -0.041576 -0.056512
> NA ? ? ? ?NA ? ? ? ?NA ? ? ? ?NA ? ? ? ?NA ? ? ? ?NA ? ? ? ?NA
> 13 -0.040208 -0.050731 -0.044207 -0.048095 -0.044363 -0.044817 -0.037827
> -0.053985 -0.059573 ? ? ? ?NA ? ? ? ?NA ? ? ? ?NA ? ? ? ?NA
>
> The above is almost right, but x has 13 rows instead of 12! WHY? Row 10
> (which has 15 elements) was cut off at 13, and then the last two elements
> were put in a new row. WHY?
> I have tried messing with colClasses to no avail. Any help would be ...
> umm... helpful!
>
> JJ
>
> ? ? ? ?[[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.
>


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

What is the problem that you are trying to solve?

David Winsemius

2010-May-26 01:05 UTC

head link

[R] reading in table with different number of elements in each row

On May 25, 2010, at 8:05 PM, Johan Jackson wrote:
> HI all,
>
> This is probably simple, but I haven't been able to locate the  
> answer either
> in the Import Manual or from searching the listserve.
>
> I have tab-delimited data with different numbers of elements in each  
> row. I
> want to read it into R, such that R fills in "NA" in elements
that
> have no
> data. How do I accomplish this?
Look at the fill argument to read.table.

  read.table(textConnection("     1 -0.068191       -0.050729        
-0.113982       -0.044363\n
  -0.072445       -0.044516       -0.048597       -0.051866\n
  -0.051563       -0.041576\n
       2 -0.032645       -0.062389       -0.054491       -0.058061\n
  -0.034690       -0.038044       -0.045332       -0.043785\n
  -0.050639       -0.049617"), header=FALSE, fill =TRUE,  
colClasses=rep("numeric", 4))


          V1        V2        V3        V4        V5
1  1.000000 -0.068191 -0.050729 -0.113982 -0.044363
2 -0.072445 -0.044516 -0.048597 -0.051866        NA
3 -0.051563 -0.041576        NA        NA        NA
4  2.000000 -0.032645 -0.062389 -0.054491 -0.058061
5 -0.034690 -0.038044 -0.045332 -0.043785        NA
6 -0.050639 -0.049617        NA        NA        NA

In your case you may want to use sep="\t"

-- 
David.>
>
>
> Example:
>
>
> DATA on disk:
>      1 -0.068191       -0.050729       -0.113982       -0.044363
> -0.072445       -0.044516       -0.048597       -0.051866
> -0.051563       -0.041576
>      2 -0.032645       -0.062389       -0.054491       -0.058061
> -0.034690       -0.038044       -0.045332       -0.043785
> -0.050639       -0.049617
>      3 -0.068191       -0.044207       -0.058061       -0.050729
> -0.034991       -0.045360       -0.051563       -0.060290
> -0.043785       -0.048757
>      4 -0.068191       -0.062389       -0.050729       -0.058579
> -0.056481       -0.044363       -0.042347       -0.060290
> -0.051563       -0.037216       -0.041576       -0.056476
>      5 -0.068191       -0.047649       -0.062389       -0.058061
> -0.034227       -0.185829       -0.071855       -0.064096
> -0.195645
>      6 -0.040208       -0.068191       -0.036475       -0.041268
> -0.044207       -0.044363       -0.034991       -0.059810
> -0.051619       -0.051563       -0.037216       -0.041576
> -0.019762
>      7 -0.068191       -0.034227       -0.044363       -0.051563
> -0.041576       -0.053823       -0.057023       -0.046083
> -0.089374       -0.057436
>      8 -0.068191       -0.050731       -0.044207       -0.169714
> -0.060025       -0.048597       -0.037827       -0.053823
> -0.055154
>      9 -0.062389       -0.044207       -0.050729       -0.044363
> -0.043785
>     10 -0.040208       -0.036716       -0.068191       -0.051466
> -0.050731       -0.050729       -0.048095       -0.044363
> -0.044817       -0.059810       -0.051563       -0.037827
> -0.053985       -0.059573       -0.052893
>     11 -0.068191       -0.034227       -0.048597       -0.051563
> -0.041576       -0.056512
>     12 -0.040208       -0.050731       -0.044207       -0.048095
> -0.044363       -0.044817       -0.037827       -0.053985        
> -0.059573
>
> My attempts:
> x <-
read.table("DATA",fill=TRUE,sep="\t",colClasses="numeric")
>> x
>          V1        V2        V3        V4        V5        V6
> V7        V8        V9       V10       V11       V12       V13
> 1  -0.068191 -0.050729 -0.113982 -0.044363 -0.072445 -0.044516  
> -0.048597
> -0.051866 -0.051563 -0.041576        NA        NA        NA
> 2  -0.032645 -0.062389 -0.054491 -0.058061 -0.034690 -0.038044  
> -0.045332
> -0.043785 -0.050639 -0.049617        NA        NA        NA
> 3  -0.068191 -0.044207 -0.058061 -0.050729 -0.034991 -0.045360  
> -0.051563
> -0.060290 -0.043785 -0.048757        NA        NA        NA
> 4  -0.068191 -0.062389 -0.050729 -0.058579 -0.056481 -0.044363  
> -0.042347
> -0.060290 -0.051563 -0.037216 -0.041576 -0.056476        NA
> 5  -0.068191 -0.047649 -0.062389 -0.058061 -0.034227 -0.185829  
> -0.071855
> -0.064096 -0.195645        NA        NA        NA        NA
> 6  -0.040208 -0.068191 -0.036475 -0.041268 -0.044207 -0.044363  
> -0.034991
> -0.059810 -0.051619 -0.051563 -0.037216 -0.041576 -0.019762
> 7  -0.068191 -0.034227 -0.044363 -0.051563 -0.041576 -0.053823  
> -0.057023
> -0.046083 -0.089374 -0.057436        NA        NA        NA
> 8  -0.068191 -0.050731 -0.044207 -0.169714 -0.060025 -0.048597  
> -0.037827
> -0.053823 -0.055154        NA        NA        NA        NA
> 9  -0.062389 -0.044207 -0.050729 -0.044363 -0.043785        NA
> NA        NA        NA        NA        NA        NA        NA
> 10 -0.040208 -0.036716 -0.068191 -0.051466 -0.050731 -0.050729  
> -0.048095
> -0.044363 -0.044817 -0.059810 -0.051563 -0.037827 -0.053985
> 11 -0.059573 -0.052893        NA        NA        NA        NA
> NA        NA        NA        NA        NA        NA        NA
> 12 -0.068191 -0.034227 -0.048597 -0.051563 -0.041576 -0.056512
> NA        NA        NA        NA        NA        NA        NA
> 13 -0.040208 -0.050731 -0.044207 -0.048095 -0.044363 -0.044817  
> -0.037827
> -0.053985 -0.059573        NA        NA        NA        NA
>
> The above is almost right, but x has 13 rows instead of 12! WHY? Row  
> 10
> (which has 15 elements) was cut off at 13, and then the last two  
> elements
> were put in a new row. WHY?
> I have tried messing with colClasses to no avail. Any help would  
> be ...
> umm... helpful!
>
> JJ
>
> 	[[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.
David Winsemius, MD
West Hartford, CT

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