CODEWITHSUNDEEP
rfileinput
pritamps
pritamps

Reputation: 121

Reading from a file in R

I am trying to read text header files in R. I have been pretty successful except for the following:

One part of the file contains:

.  
.    
. (Other stuff)  
spectra names = {  
 Endmember  1, Endmember  2, Endmember  3, Endmember  4, Endmember  5,   
 Endmember  6, Endmember  7, Endmember  8, Endmember  9, Endmember  10,   
 Endmember  11, Endmember  12, Endmember  13, Endmember  14, Endmember  15,   
 Endmember  16, Endmember  17, Endmember  18, Endmember  19, Endmember  20,   
 Endmember  21, Endmember  22, Endmember  23, Endmember  24, Endmember  25,   
 Endmember  26, Endmember  27, Endmember  28, Endmember  29, Endmember  30}  
.  
.  
.

I want the output to be a list containing the names of the spectra, i.e. ["Endmember 1" "Endmember 2" and so on...

I tried read.csv(), read.table(), but nothing seems to work. I am stumped by the ends of the lines and the '{', '}' characters

What I want to do is: start reading at "spectra names" and then store everything between the {} as an array of strings as I mentioned above.

Upvotes: 1

Views: 144

Answers (2)

agstudy
agstudy

Reputation: 121568

using scan and gsub as suggested in the comment , you can get easily this.

tt <- scan(text = "spectra names = {  
  Endmember  1, Endmember  2, Endmember  3, Endmember  4, Endmember  5,   
  Endmember  6, Endmember  7, Endmember  8, Endmember  9, Endmember  10,   
  Endmember  11, Endmember  12, Endmember  13, Endmember  14, Endmember  15,   
  Endmember  16, Endmember  17, Endmember  18, Endmember  19, Endmember  20,   
  Endmember  21, Endmember  22, Endmember  23, Endmember  24, Endmember  25,   
  Endmember  26, Endmember  27, Endmember  28, Endmember  29, Endmember  30}" ,what = 'character' ,sep =',')

gsub('[{|}]','',tt) ## not really clever but it is a good begining
[1] "spectra names =   " "  Endmember  1"     " Endmember  2"      " Endmember  3"      " Endmember  4"      " Endmember  5"     
[7] "   "                "  Endmember  6"     " Endmember  7"      " Endmember  8"      " Endmember  9"      " Endmember  10"    
[13] "   "                "  Endmember  11"    " Endmember  12"     " Endmember  13"     " Endmember  14"     " Endmember  15"    
[19] "   "                "  Endmember  16"    " Endmember  17"     " Endmember  18"     " Endmember  19"     " Endmember  20"    
[25] "   "                "  Endmember  21"    " Endmember  22"     " Endmember  23"     " Endmember  24"     " Endmember  25"    
[31] "   "                "  Endmember  26"    " Endmember  27"     " Endmember  28"     " Endmember  29"     " Endmember  30"

Upvotes: 1

Mark Miller
Mark Miller

Reputation: 13103

This is an example of how to implement Justin's suggestion. Suppose the data file looked like this:

4 5 6
2 3 4
1 2 3 
spectra names = {Endmember  1, Endmember  2, Endmember  3}
1 1 1
1 1 2
1 2 1
1 2 2
2 1 1
2 1 2
2 2 1
2 2 2

You could read it like so:

aa <- readLines('c:/users/Mark W Miller/simple R programs/odd data file with headers in the middle.txt', 
     n = 4)

bb <- gsub("spectra names = {","", aa[4], fixed=TRUE)
bb <- gsub("}","", bb, fixed=TRUE)
bb <- gsub("  "," ", bb, fixed=TRUE)
bb <- gsub(", ",",", bb, fixed=TRUE)
cc <- unlist(strsplit(bb, ","))
cc

dd <- read.table('c:/users/Mark W Miller/simple R programs/odd data file with headers in the middle.txt', 
     skip = 4, header=F)
dd

colnames(dd) <- cc
dd

I am sure there are ways to condense all my gsub statements into one line. If this does not do exactly what you want maybe you can use it as a start.

I was not sure I understood the part of creating a list for column names.

Upvotes: 1

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