[R] Read.table problems

[Steve Murray]

Dear all,

I have a file which I've converted from NetCDF (.nc) to text (.txt) using ncdump in Unix (as I had problems using the ncdf package to do this). The first few rows (as copied and pasted from the Unix console) of the file appear as follows:

 _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, 
    _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, 
    _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, 
    _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, 
    _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, 
    _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, 
    _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, 
    _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, 
    _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, 
    _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,


As you can see, there are a lot of NA values before the actual numeric values start further down the dataset. My problem is that I'm having trouble reading this file into R. I think the problem lies with the sep= argument, although I may be wrong. I tried the following command at first, as the data appear to be comma separated:

> read.table("test86.txt", skip=43, na.strings="-", header=FALSE, sep=",") -> test86  # skip =43 due to meta-data information being held in the initial rows
Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,  : 
  line 29 did not have 25 elements

I then tried sep=" ", followed by sep="" but received a similar-type error message (although line 29 doesn't appear to be especially different from the rest).

I subsequently tried using sep=\t and then sep=\n. These both result in the data being read in without an error message being displayed, although the data are formatted as follows:

> head(test86)
                                                                            V1
1     _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, 
2     _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, 
3     _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, 
4     _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, 
5     _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, 
6     _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, 


> dim(test86)
[1] 179899      1


Instead of one column, I'd expect there to be 720.


I think I'm getting something wrong relating to the sep= argument (or possibly mis-using na.strings?). If anyone has any solutions to this then I'd be very grateful to hear them.

Many thanks for any advice,

Steve