Here is one way of doing it; it reads the file and create a 'long' version.
##########
input <- file("/temp/ClinicalReports.txt", 'r')
outFile <- '/temp/output.txt' # tempfile()
output <- file(outFile, 'w')
writeLines("ID, Date, variable, value", output)
ID <- NULL
dataSw <- NULL
repeat{
line <- readLines(input, n = 1)
if (length(line) == 0) break
if (!is.null(dataSw)){
if (line == ''){ # end of data
ID <- NULL
dataSw <- NULL
next
}
# now write CSV output file
cat(ID
, ','
, Date
, ','
, substring(line, 1, 31)
, ','
, substring(line, 32, 43)
, '\n'
, sep = ''
, file = output
)
next
}
if (grepl("Acc.ne", line)){
ID <- (substring(line, 29,35))
Date <- (substring(line, 52,61))
next
}
if (!is.null(ID)){ # looking for Esame
if (grepl("Esame", line)){
# skip two lines
readLines(input, n = 2)
dataSw <- 1
next
}
}
}
# now read in the data in a long format
close(output)
result <- read.csv(outFile, as.is = TRUE)
the results from your test data is:
> str(result)
'data.frame': 43 obs. of 4 variables:
$ ID : int 185 185 185 185 185 185 185 185 185 185 ...
$ Date : chr "05/12/2011" "05/12/2011" "05/12/2011" "05/12/2011" ...
$ variable: chr "AZOTEMIA " "CREATININEMIA
" "SODIEMIA " "POTASSIEMIA
" ...
$ value : num 33.6 0.99 136 4.22 94.2 8.68 1.87 1.79 189 118 ...
> head(result)
ID Date variable value
1 185 05/12/2011 AZOTEMIA 33.60
2 185 05/12/2011 CREATININEMIA 0.99
3 185 05/12/2011 SODIEMIA 136.00
4 185 05/12/2011 POTASSIEMIA 4.22
5 185 05/12/2011 CLOREMIA 94.20
6 185 05/12/2011 CALCEMIA 8.68
>
On Thu, Mar 8, 2012 at 8:24 AM, ginger <bi...@igm.cnr.it> wrote:
> Ooops,
> I forgot to specify that for each raw, containing records of the clinical
> reports , the values of the 22 parameter measurement have to be reported.
> For example, first raw, first 5 columns:
> ID DATE GLICEMIA AZOTEMIA
> CREATININEMIA SODIEMIA ... ... ...
> 0000185 05/12/2011 115 33.6 0.99
> 136 ... ... ...
>
> --
> View this message in context:
> http://r.789695.n4.nabble.com/parsing-text-files-tp4456355p4456389.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> R-help@r-project.org mailing list
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
--
Jim Holtman
Data Munger Guru
What is the problem that you are trying to solve?
Tell me what you want to do, not how you want to do it.
______________________________________________
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and provide commented, minimal, self-contained, reproducible code.
