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Mike Jones

2005-Nov-15 15:18 UTC

[R] Reading in a table with unequal columns

Hi, 

Wasn't sure how to explain this problem succinctly in a title.  I am
trying to read in a text file that looks like:

0   1000  175  1  2  3
1   1000  58   0  2  9
2   1000  35   0  1  3 10
3   1000  300  0  2  4  5  10  11  18
4   1000  150  3  5  6
5   1000  100 3  4  6  7  18
6   1000   50  4  5  7  8
7   1000  155  5  6  8  19
8   1000  255  6  7 19
9   1000  200  1 10 12
10  1000  52   2  3  9  11  12  13
11  1000  70  3  10 14 15  16  17  18  19
12  1000  250 9  10 13
13  1000  40 10 12 14
14  1000  235 11 13 15
15  1000  127 11 14 16 17
16  1000  177 11 15 17
17  1000  358 11 15 16
18  1000  296 3  5  11  19
19  1000  120 7  8  11  18

The problem with this is that the 12th row (row with 11 in the first
column) doesn't get read in correctly.  To read into R, I'm using a
command like:

matrix(unlist(read.table(datafile, sep="",fill=T)),
             ncol=max(count.fields(datafile, sep="")),byrow=F)

but that gives

      [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11]
 [1,]    0   19 1000  358   11   14   15   NA   NA    NA    18
 [2,]    1 1000 1000  296   11   15   16   NA   NA    NA    NA
 [3,]    2 1000  175  120    3   15   17   17   NA    NA    NA
 [4,]    3 1000   58    1    7    5   16   NA   NA    NA    NA
 [5,]    4 1000   35    0    2    8   11   NA   NA    NA    NA
 [6,]    5 1000  300    0    2    3   11   19   NA    NA    NA
 [7,]    6 1000  150    0    1    9   NA   18   NA    NA    NA
 [8,]    7 1000  100    3    2    3   NA   NA   NA    NA    NA
 [9,]    8 1000   50    3    5    4   10   NA   NA    NA    NA
[10,]    9 1000  155    4    4    6    5   NA   NA    NA    NA
[11,]   10 1000  255    5    5    6   NA   10   NA    NA     0
[12,]   11 1000  200    6    6    7    7   NA   11    NA     1
[13,]   19 1000   52    1    7    8    8   18   NA    18     2
[14,]   12   NA   70    2   10   19   19   NA   NA    NA     3
[15,]   13 1000   NA    3    3   12   NA   NA   NA    NA     4
[16,]   14 1000  250   NA   10    9   NA   NA   NA    NA     5
[17,]   15 1000   40    9   NA   14   11   NA   NA    NA     6
[18,]   16 1000  235   10   10   NA   15   12   NA    NA     7
[19,]   17 1000  127   11   12   13   NA   16   13    NA     8
[20,]   18 1000  177   11   13   14   NA   NA   17    NA     9

I've tried other things, but this is as close as I've been able to get
and I'm at a loss at this point.  Any input would be
helpful...thanks...mj

Sundar Dorai-Raj

2005-Nov-15 15:44 UTC

head link

[R] Reading in a table with unequal columns

Mike Jones wrote:> Hi, 
> 
> Wasn't sure how to explain this problem succinctly in a title.  I am
> trying to read in a text file that looks like:
> 
> 0   1000  175  1  2  3
> 1   1000  58   0  2  9
> 2   1000  35   0  1  3 10
> 3   1000  300  0  2  4  5  10  11  18
> 4   1000  150  3  5  6
> 5   1000  100 3  4  6  7  18
> 6   1000   50  4  5  7  8
> 7   1000  155  5  6  8  19
> 8   1000  255  6  7 19
> 9   1000  200  1 10 12
> 10  1000  52   2  3  9  11  12  13
> 11  1000  70  3  10 14 15  16  17  18  19
> 12  1000  250 9  10 13
> 13  1000  40 10 12 14
> 14  1000  235 11 13 15
> 15  1000  127 11 14 16 17
> 16  1000  177 11 15 17
> 17  1000  358 11 15 16
> 18  1000  296 3  5  11  19
> 19  1000  120 7  8  11  18
> 
> The problem with this is that the 12th row (row with 11 in the first
> column) doesn't get read in correctly.  To read into R, I'm using a
> command like:
> 
> matrix(unlist(read.table(datafile, sep="",fill=T)),
>              ncol=max(count.fields(datafile, sep="")),byrow=F)
> 
> but that gives
> 
>       [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11]
>  [1,]    0   19 1000  358   11   14   15   NA   NA    NA    18
>  [2,]    1 1000 1000  296   11   15   16   NA   NA    NA    NA
>  [3,]    2 1000  175  120    3   15   17   17   NA    NA    NA
>  [4,]    3 1000   58    1    7    5   16   NA   NA    NA    NA
>  [5,]    4 1000   35    0    2    8   11   NA   NA    NA    NA
>  [6,]    5 1000  300    0    2    3   11   19   NA    NA    NA
>  [7,]    6 1000  150    0    1    9   NA   18   NA    NA    NA
>  [8,]    7 1000  100    3    2    3   NA   NA   NA    NA    NA
>  [9,]    8 1000   50    3    5    4   10   NA   NA    NA    NA
> [10,]    9 1000  155    4    4    6    5   NA   NA    NA    NA
> [11,]   10 1000  255    5    5    6   NA   10   NA    NA     0
> [12,]   11 1000  200    6    6    7    7   NA   11    NA     1
> [13,]   19 1000   52    1    7    8    8   18   NA    18     2
> [14,]   12   NA   70    2   10   19   19   NA   NA    NA     3
> [15,]   13 1000   NA    3    3   12   NA   NA   NA    NA     4
> [16,]   14 1000  250   NA   10    9   NA   NA   NA    NA     5
> [17,]   15 1000   40    9   NA   14   11   NA   NA    NA     6
> [18,]   16 1000  235   10   10   NA   15   12   NA    NA     7
> [19,]   17 1000  127   11   12   13   NA   16   13    NA     8
> [20,]   18 1000  177   11   13   14   NA   NA   17    NA     9
> 
> I've tried other things, but this is as close as I've been able to
get
> and I'm at a loss at this point.  Any input would be
> helpful...thanks...mj
> 

There are two ways that I know of to get around this. I'm sure there are 
others:

## read in the file to determine the max number of columns
x <- scan("file.txt", what = "", sep = "\n")
x <- strsplit(x, "[ \t]+") # split string by white space
max.col <- max(sapply(x, length))

## option 1
## specify col.names as ?read.table suggests
cn <- paste("V", 1:max.col, sep = "")
z1 <- read.table("file.txt", fill = TRUE, col.names = cn)

## option 2
## parse `x' yourself and construct a matrix
z2 <- t(sapply(x, function(i) {
   n <- length(i)
   y <- rep(NA, max.col)
   y[1:n] <- as.numeric(i)
   y
}))

Gabor Grothendieck

2005-Nov-15 15:54 UTC

head link

[R] Reading in a table with unequal columns

On 11/15/05, Mike Jones <MikeJones at westat.com>
wrote:> Hi,
>
> Wasn't sure how to explain this problem succinctly in a title.  I am
> trying to read in a text file that looks like:
>
> 0   1000  175  1  2  3
> 1   1000  58   0  2  9
> 2   1000  35   0  1  3 10
> 3   1000  300  0  2  4  5  10  11  18
> 4   1000  150  3  5  6
> 5   1000  100 3  4  6  7  18
> 6   1000   50  4  5  7  8
> 7   1000  155  5  6  8  19
> 8   1000  255  6  7 19
> 9   1000  200  1 10 12
> 10  1000  52   2  3  9  11  12  13
> 11  1000  70  3  10 14 15  16  17  18  19
> 12  1000  250 9  10 13
> 13  1000  40 10 12 14
> 14  1000  235 11 13 15
> 15  1000  127 11 14 16 17
> 16  1000  177 11 15 17
> 17  1000  358 11 15 16
> 18  1000  296 3  5  11  19
> 19  1000  120 7  8  11  18
>
> The problem with this is that the 12th row (row with 11 in the first
> column) doesn't get read in correctly.  To read into R, I'm using a
> command like:
>
> matrix(unlist(read.table(datafile, sep="",fill=T)),
>             ncol=max(count.fields(datafile, sep="")),byrow=F)
>
> but that gives
>
>      [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11]
>  [1,]    0   19 1000  358   11   14   15   NA   NA    NA    18
>  [2,]    1 1000 1000  296   11   15   16   NA   NA    NA    NA
>  [3,]    2 1000  175  120    3   15   17   17   NA    NA    NA
>  [4,]    3 1000   58    1    7    5   16   NA   NA    NA    NA
>  [5,]    4 1000   35    0    2    8   11   NA   NA    NA    NA
>  [6,]    5 1000  300    0    2    3   11   19   NA    NA    NA
>  [7,]    6 1000  150    0    1    9   NA   18   NA    NA    NA
>  [8,]    7 1000  100    3    2    3   NA   NA   NA    NA    NA
>  [9,]    8 1000   50    3    5    4   10   NA   NA    NA    NA
> [10,]    9 1000  155    4    4    6    5   NA   NA    NA    NA
> [11,]   10 1000  255    5    5    6   NA   10   NA    NA     0
> [12,]   11 1000  200    6    6    7    7   NA   11    NA     1
> [13,]   19 1000   52    1    7    8    8   18   NA    18     2
> [14,]   12   NA   70    2   10   19   19   NA   NA    NA     3
> [15,]   13 1000   NA    3    3   12   NA   NA   NA    NA     4
> [16,]   14 1000  250   NA   10    9   NA   NA   NA    NA     5
> [17,]   15 1000   40    9   NA   14   11   NA   NA    NA     6
> [18,]   16 1000  235   10   10   NA   15   12   NA    NA     7
> [19,]   17 1000  127   11   12   13   NA   16   13    NA     8
> [20,]   18 1000  177   11   13   14   NA   NA   17    NA     9
>
Try this:

nf <- max(count.fields(datafile))
read.table(datafile, fill = TRUE, col.names = 1:nf)

ronggui

2005-Nov-15 16:56 UTC

head link

[R] Reading in a table with unequal columns

======= 2005-11-15 23:18:05 伳侜佋佢伬伌佇伵佒佇佇伌伒伬仯伜======>Hi, 
>
>Wasn't sure how to explain this problem succinctly in a title.  I am
>trying to read in a text file that looks like:
>
>0   1000  175  1  2  3
>1   1000  58   0  2  9
>2   1000  35   0  1  3 10
>3   1000  300  0  2  4  5  10  11  18
>4   1000  150  3  5  6
>5   1000  100 3  4  6  7  18
>6   1000   50  4  5  7  8
>7   1000  155  5  6  8  19
>8   1000  255  6  7 19
>9   1000  200  1 10 12
>10  1000  52   2  3  9  11  12  13
>11  1000  70  3  10 14 15  16  17  18  19
>12  1000  250 9  10 13
>13  1000  40 10 12 14
>14  1000  235 11 13 15
>15  1000  127 11 14 16 17
>16  1000  177 11 15 17
>17  1000  358 11 15 16
>18  1000  296 3  5  11  19
>19  1000  120 7  8  11  18
>
>The problem with this is that the 12th row (row with 11 in the first
>column) doesn't get read in correctly.  To read into R, I'm using a
>command like:
>
>matrix(unlist(read.table(datafile, sep="",fill=T)),
>             ncol=max(count.fields(datafile, sep="")),byrow=F)?read.table will find
   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.
So try:
nc<-max(count.fields(datafile, sep="")
x<-read.table(datafile,sep="",col.names=paste("v",1:nc,sep="."),fill=T)
matrix(unlist(x),ncol=nc)
>but that gives
>
>      [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11]
> [1,]    0   19 1000  358   11   14   15   NA   NA    NA    18
> [2,]    1 1000 1000  296   11   15   16   NA   NA    NA    NA
> [3,]    2 1000  175  120    3   15   17   17   NA    NA    NA
> [4,]    3 1000   58    1    7    5   16   NA   NA    NA    NA
> [5,]    4 1000   35    0    2    8   11   NA   NA    NA    NA
> [6,]    5 1000  300    0    2    3   11   19   NA    NA    NA
> [7,]    6 1000  150    0    1    9   NA   18   NA    NA    NA
> [8,]    7 1000  100    3    2    3   NA   NA   NA    NA    NA
> [9,]    8 1000   50    3    5    4   10   NA   NA    NA    NA
>[10,]    9 1000  155    4    4    6    5   NA   NA    NA    NA
>[11,]   10 1000  255    5    5    6   NA   10   NA    NA     0
>[12,]   11 1000  200    6    6    7    7   NA   11    NA     1
>[13,]   19 1000   52    1    7    8    8   18   NA    18     2
>[14,]   12   NA   70    2   10   19   19   NA   NA    NA     3
>[15,]   13 1000   NA    3    3   12   NA   NA   NA    NA     4
>[16,]   14 1000  250   NA   10    9   NA   NA   NA    NA     5
>[17,]   15 1000   40    9   NA   14   11   NA   NA    NA     6
>[18,]   16 1000  235   10   10   NA   15   12   NA    NA     7
>[19,]   17 1000  127   11   12   13   NA   16   13    NA     8
>[20,]   18 1000  177   11   13   14   NA   NA   17    NA     9
>
>I've tried other things, but this is as close as I've been able to
get
>and I'm at a loss at this point.  Any input would be
>helpful...thanks...mj
>
>______________________________________________
>R-help at 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
= = = = = = = = = = = = = = = = = = = 			


 

2005-11-16

------
Deparment of Sociology
Fudan University

My new mail addres is ronggui.huang at gmail.com
Blog:http://sociology.yculblog.com

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