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Nicola Cecchino

2018-Sep-12 01:49 UTC

[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]]

PIKAL Petr

2018-Sep-12 06:26 UTC

head link

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

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 at r-project.org> On Behalf Of Nicola
Cecchino
> Sent: Wednesday, September 12, 2018 3:50 AM
> To: R-help at 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]]
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.Osobn? ?daje: Informace o zpracov?n? a ochran? osobn?ch ?daj? obchodn?ch
partner? PRECHEZA a.s. jsou zve?ejn?ny na:
https://www.precheza.cz/zasady-ochrany-osobnich-udaju/ | Information about
processing and protection of business partner?s personal data are available on
website: https://www.precheza.cz/en/personal-data-protection-principles/
D?v?rnost: Tento e-mail a jak?koliv k n?mu p?ipojen? dokumenty jsou d?v?rn? a
podl?haj? tomuto pr?vn? z?vazn?mu prohl??en? o vylou?en? odpov?dnosti:
https://www.precheza.cz/01-dovetek/ | This email and any documents attached to
it may be confidential and are subject to the legally binding disclaimer:
https://www.precheza.cz/en/01-disclaimer/

PIKAL Petr

2018-Sep-13 07:53 UTC

head link

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

Hi

You should send your responses to R helplist, others could offer
better/different solutions.

I myself am not an expert for regex so if all your files are formated in the
same way I would use strsplit.

# I read header to test object
test<-readLines("clipboard")
str(test)
 chr [1:4] "PATIENT NAME: CONFIDENTIAL,#12345" "PATIENT ID #:
12345" ...

# here is something similar to your csv file
test2<-read.table("clipboard")
test2
    Id1   Id2 VisitDate
1 12345 12345  4/3/2018
2 11111 11111  5/4/2018

# here I split second line of patient record, select 4th item and compare with
Id2 value from csv file.

sel<-which(test2$Id2 == as.numeric(unlist(strsplit(test[2], "
"))[4]))

# I take third line of patient record and split it
out<-unlist(strsplit(test[3], split=" "))

# and change 4th item with selected value from csv VisitDate
out[4] <- as.character(test2$VisitDate[sel])

# here you should be aware of difference between factors and characters
# and finally make collapsed line, which could be used to change third line in
patient record
paste(out, collapse=" ")
[1] "DATE OF SERVICE: 4/3/2018"

But what you want to do with it? It actually manipulates objects in your R
session and not original files. I believe that there are other tools more
suitable for such tasks.

Cheers
Petr
> -----Original Message-----
> From: Nicola Cecchino <ncecchino at gmail.com>
> Sent: Thursday, September 13, 2018 5:04 AM
> To: PIKAL Petr <petr.pikal at precheza.cz>
> Subject: Re: [R] Correcting dates in research / medical record using R
>
> Hi Petr,
>
> Thank you for your help but I'm not sure what that code is supposed to
do?  I'm
> really new to regular expressions and am having difficulties with this
whole
> thing.
>
> Nic
>
>
>
>
> On 9/12/2018 2:26 AM, PIKAL Petr wrote:
> > 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 at r-project.org> On Behalf Of
Nicola
> >> Cecchino
> >> Sent: Wednesday, September 12, 2018 3:50 AM
> >> To: R-help at 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]]
> >>
> >> ______________________________________________
> >> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more,
see
> >> https://stat.ethz.ch/mailman/listinfo/r-help
> >> PLEASE do read the posting guide
> >> http://www.R-project.org/posting-guide.html
> >> and provide commented, minimal, self-contained, reproducible code.
> > Osobn? ?daje: Informace o zpracov?n? a ochran? osobn?ch ?daj?
> > obchodn?ch partner? PRECHEZA a.s. jsou zve?ejn?ny na:
> > https://www.precheza.cz/zasady-ochrany-osobnich-udaju/ | Information
> > about processing and protection of business partner?s personal data
> > are available on website:
> > https://www.precheza.cz/en/personal-data-protection-principles/
> > D?v?rnost: Tento e-mail a jak?koliv k n?mu p?ipojen? dokumenty jsou
> > d?v?rn? a podl?haj? tomuto pr?vn? z?vazn?mu prohl??en? o vylou?en?
> > odpov?dnosti: https://www.precheza.cz/01-dovetek/ | This email and any
> > documents attached to it may be confidential and are subject to the
> > legally binding disclaimer: https://www.precheza.cz/en/01-disclaimer/
> >
Osobn? ?daje: Informace o zpracov?n? a ochran? osobn?ch ?daj? obchodn?ch
partner? PRECHEZA a.s. jsou zve?ejn?ny na:
https://www.precheza.cz/zasady-ochrany-osobnich-udaju/ | Information about
processing and protection of business partner?s personal data are available on
website: https://www.precheza.cz/en/personal-data-protection-principles/
D?v?rnost: Tento e-mail a jak?koliv k n?mu p?ipojen? dokumenty jsou d?v?rn? a
podl?haj? tomuto pr?vn? z?vazn?mu prohl??en? o vylou?en? odpov?dnosti:
https://www.precheza.cz/01-dovetek/ | This email and any documents attached to
it may be confidential and are subject to the legally binding disclaimer:
https://www.precheza.cz/en/01-disclaimer/

R help - Sep 2018 - Correcting dates in research / medical record using R

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

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

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