[R] Correcting dates in research / medical record using R

[Nicola Cecchino]

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




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