Hi
First of all you should not use HTML formated posts, it is big chance that it
gets scrambled.
You should compare your ld2 after for cycle and result of
clinicVdate[Id2, 'VisitDate'], sep=':')
Most probably ld2 after for cycle does not conform to row names of clinicVdate.
Cheers
Petr
> -----Original Message-----
> From: R-help <r-help-boun...@r-project.org> On Behalf Of Nicola Cecchino
> Sent: Wednesday, September 12, 2018 3:50 AM
> To: R-help@r-project.org
> Subject: [R] Correcting dates in research / medical record using R
>
> Hi,
>
> I'm not that well versed with R - I'm trying to correct the dates of
> service in a de-identified research medical record of several subjects.
> The correct dates come from a csv file, in the VisitDate column, that
> looks like this in Excel. The empty cells have other data in them that
> I don't need and the file name is DateR.csv:
>
>
> Id1 Id2
>
>
>
>
> VisitDate
> 12345 12345
>
>
>
>
> 4/3/2018
>
>
> The research medical record is a text file and the "DATE OF SERVICE" in
> the top matter is in error in all of the subjects and needs to be
> replaced with the "VisitDate" in the csv file. The file name for the
> medical records is test3.NEW. Here is a screen grab of the top matter
> of the research medical record; below this data excerpt is other
> gathered data for that subject:
>
>
> ===================================================================
> =============
>
> PATIENT NAME: CONFIDENTIAL,#12345
> PATIENT ID #: 12345
> DATE OF SERVICE: 04/10/2018
> ACCESSION NUMBER: RR1234567
>
> TEST PROCEDURE HIGH/LOW TEST RESULTS UNITS NORMAL VALUES
>
>
> As described above, I need to update the text file DATE OF SERVICE:
> date with the VisitDate in the csv file.
>
> I made several attempts at this to failure and so now I turn to you.
> Here is the code that exhibits my attempts:
>
>
> clinicVdate <- read.csv("DateR.csv")
>
> rownames(clinicVdate) <- as.character(clinicVdate[,'Id2'])
>
> Id2 <- NA
>
> input_data <- readLines("D:/test/test3.NEW")
> output_data <- c()
>
> for(input_line in input_data){
> output_line = input_line
> if(length(grep('PATIENT ID #:', input_line))>0) {
> Id2 = as.character(strsplit(input_line, ':')[[1]][2])
> }
>
> if (length(grep( 'DATE OF SERVICE: ', input_line))){
>
> output_line = paste('DATE OF SERVICE', clinicVdate[Id2,
> 'VisitDate'], sep=':')
>
> }
> output_data = paste(output_data, output_line, sep='\n')
> }
>
> cat(output_data)
>
>
> The results of the above remove the erroneous date and replace it with
> NA. Here is an example of the results:
>
>
> ===================================================================
> =============
>
> PATIENT NAME: CONFIDENTIAL,#12345
> PATIENT ID #: 12345
> DATE OF SERVICE: NA
> ACCESSION NUMBER: RR1234567
>
> TEST PROCEDURE HIGH/LOW TEST RESULTS UNITS NORMAL VALUES
>
>
> Where am I going wrong? If I didn't pose my question appropriately,
> please let me know too!! Any help with this would be greatly appreciated!!
>
> Kind regards,
>
> Nic Cecchino
>
>
>
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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