[R] extracting information from txt file

[David Winsemius]

On Oct 31, 2012, at 9:46 AM, chuck.01 wrote:

> Hello,
> 
> Here is a link to some data:
> http://www.epa.gov/emap/html/data/surfwatr/data/mastreams/9396/wchem/chmval.txt
> 
> I am trying to read this in, and want to use: 
> chmval <-
> read.table("http://www.epa.gov/emap/html/data/surfwatr/data/mastreams/9396/wchem/chmval.txt",
> sep=",", skip= 84, header=T)
> 
> the # 84, for 84 lines skipped needs to be derived from the 5th line of the
> txt file  
> # Header Records:  85 
> 
> so, I need that # (-1) for input into the read.table statement above

That "# (-1)" is fairly cryptic to my reading, but it appears you are seeing the behavior of the "3" character in terminating input for comments. Changing the comment character in the call to read.table will allow input from that line.

?read.table

You will need to read only the first 5 or 6 lines first, then execute a separate read.table while skipping input from those lines as well as the variable list that forms a secondary header.

> headfrm <- read.table( file=url( "http://www.epa.gov/emap/html/data/surfwatr/data/mastreams/9396/wchem/chmval.txt"), nrows=6, sep=":", comment.char="")
> headfrm
                V1                                       V2
1          Dataset               EMAP Stream Chemistry Data
2        File Name                                   chmval
3     Date Created                                 02/22/99
4      # Variables                                       75
5 # Header Records                                       85
6   # Data Records                                      711



> 
> I've tried grep but that didn't work: 
> (for this I downloaded the txt file and manually removed that hash mark!)
> 
> grep("Header Records:", read.table("chmval.txt", header=T))
> Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, 
> : 
>  line 1 did not have 5 elements
> 
> Any ideas?
> Can I just extract the 5th line?
> 
> 
> 
> 
> --
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David Winsemius, MD
Alameda, CA, USA