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

[PIKAL Petr]

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-bounces using r-project.org> On Behalf Of Nicola Cecchino
> Sent: Wednesday, September 12, 2018 3:50 AM
> To: R-help using 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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