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Identifying the number of subjects who had treatment switch

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Contributor ved
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Posts: 27
Accepted Solution

Identifying the number of subjects who had treatment switch

Hi SAS folks,

 

I am working on some reseach project using hospital visit data. I have to identify the subjects who had switched their treatment. the defination of treatment switch is like:

 

Treatments are grouped by topical, non-biologic systemic, and biologic. A switching event is defined as the withdrawal of a medication that was not dispensed at the time of the last treatment withdrawal. There is a hierarchy, with biologics at the top, then non-bio systemics, then topical.

  • If a patient is first observed withdrawing a topical, any withdrawal of a treatment after that to a bio, non-bio systemic, or new topical is a switch
  • If a patient is first observed withdrawing a non-bio systemic, any withdrawal of a treatment after that to a bio or a new non-bio systemic is a switch
    • A withdrawal of any topical is not a switch
  • If a patient is first observed withdrawing a bio, a switch can only be made to another bio (which is different from the first)
    • A withdrawal of any topical or non-bio systemic is not a switch

 

According to the logic above, once a patient has switched to a higher class of therapy, the lower classes are considered concomitant medication and a withdrawal of a concomitant medication does not indicate a treatment switch.

 

In nutshell, If a patient moves from lower class of treatment to upper or withing the same class(different ATC code) then it will consider as a Switch.

 

Treatment hierarchy

Biologics> Non_Bio_Sys>Topical

 

I am adding sample dataset for the reference, with variable information :

LPNR: unique subjID

EDATUM: prescrition date ( treatment recieved date)

ATC_CODE: codes for each of treament type

'D05AX52' ,
'D05AX02' = PSorasis(Topical)
    
'L01XC02'  ,
'L04AA24',
'L04AB01',
'L04AB02',
'L04AB04',
'L04AB05',
'L04AB06',
'L04AC03',
'L04AC07' =Non_Bio_systemic


'A11CC03'  ,           
'D05BB02',                
'L01BA01',               
'L01BB03' ,               
'L01XX05' ,               
'L04AA21' ,               
'L04AD01' ,               
'L04AX03' =Biologics

 

TYPE: Treatment type

 

It would be great , if you can help me with SAS code to indentify the Subjects with Switches .


Accepted Solutions
Solution
‎05-16-2016 05:40 AM
Contributor
Posts: 27

Re: Identifying the number of subjects who had treatment switch

proc format;
value treatType 1 = "Topical"
2 = "Non-biologic systemics"
3 = "Biologics";
run;

data have;
format pnr 8. tType treatType. tCode $10. date YYMMDDs8.;
informat tType 1. date yymmdd10.;
input pnr tCode tType date;
datalines;
478 L04AX03 2 2010-02-10
478 D05AX52 1 2010-02-23
478 L04AX03 2 2010-03-05
478 L04AX03 2 2010-05-18
478 L04AX03 2 2010-08-02
478 L04AX03 2 2010-11-03
478 L04AX03 2 2011-02-07
478 L04AX03 2 2011-08-16
478 L04AX03 2 2011-11-22
603 D05AX02 1 2005-08-24
603 D05AX02 1 2005-10-13
603 D05AX02 1 2006-06-02
603 D05AX02 1 2006-07-19
603 D05AX02 1 2007-04-03
603 D05AX02 1 2007-12-07
603 D05AX02 1 2008-01-04
603 D05AX02 1 2008-01-04
603 D05AX02 1 2008-10-02
603 D05AX52 1 2009-03-16
603 D05AX52 1 2009-03-16
603 D05AX52 1 2009-05-07
603 D05AX52 1 2009-08-21
603 D05AX52 1 2009-11-09
603 D05AX52 1 2010-03-19
603 D05AX52 1 2010-07-30
603 D05AX52 1 2010-07-30
603 D05AX52 1 2011-01-13
603 D05AX52 1 2011-05-03
603 D05AX52 1 2011-12-12
1103 L04AX03 2 2006-01-17
1103 L04AX03 2 2006-08-23
1103 L04AX03 2 2006-11-09
1103 D05AX52 1 2007-04-19
1103 L04AX03 2 2007-04-19
1103 D05AX52 1 2007-10-26
1103 D05AX52 1 2008-04-01
1103 L04AX03 2 2008-10-20
1103 D05AX52 1 2008-10-20
1103 L04AX03 2 2009-04-07
1103 L04AX03 2 2009-11-20
1103 L04AX03 2 2010-11-12
1103 L04AX03 2 2011-08-12
1103 D05AX52 1 2011-10-22
1103 D05AX52 1 2011-12-29
run;
proc sort data=have;
by pnr date;
run;

data want;
set have;
by pnr;
format switch 1. tCode_prev $10. tType_prev 3.;
retain tCode_prev '' tType_prev .;
format switch 1.;

if first.pnr then do;
switch = 0;
end;

else if tType_prev = 1 then do;
if tType > 1 or tCode ne tCode_prev then switch = 1;
else switch = 0;
end;

else if tType_prev = 2 then do;
if tType > 2 or (tType = 2 and tCode ne tCode_prev) then switch = 1;
else switch = 0;
end;

else if tType_prev = 3 then do;
/* Here's your homework */
end;

output;
tCode_prev = tCode;
tType_prev = tType;

drop tCode_prev tType_prev;
run;

View solution in original post


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Regular Contributor
Posts: 212

Re: Identifying the number of subjects who had treatment switch

[ Edited ]

Hi mate.

 

I couldn't understand what you mean exactly but i think you are looking for something to check where are these dependencies changed.

 

My guess is you can use the LAST. or FIRST. options.

 

Check the code below:

 

FILENAME REFFILE "/PATH/sample_data.xlsx" TERMSTR=CR;

PROC IMPORT DATAFILE=REFFILE
	DBMS=XLSX
	OUT=WORK.IMPORT;
	GETNAMES=YES;
RUN;

PROC SORT DATA=IMPORT;
  BY LPNR ATC_CODE TYPE;
RUN;

DATA NEED;
	LENGTH INFO_CHANGE $ 20; 
	SET IMPORT;
	BY LPNR ATC_CODE TYPE;
	IF LAST.LPNR AND LAST.ATC_CODE AND LAST.TYPE THEN INFO_CHANGE = "CHANGED";
	ELSE INFO_CHANGE = "UNCHANGED";
RUN;

The last data step in this code prints the changed if the dependencies occured in the last time they changed.

And unchanged for the rest.

If you need the first time jus switch to FIRST. and checkout the result.

 

Hope this helps

Contributor ved
Contributor
Posts: 27

Re: Identifying the number of subjects who had treatment switch

Posted in reply to DartibaliRodrigo

@DartibaliRodrigo Hi , Thanks for the quick reply. I am sorry for the unclear explaination, but what i exactly means is:

as you see the data, we have three treatment type in TYPE variable. Now for each Type variable we have different ATC_CODEs. I need to identify the event (SWITCH) , whenever subject changes his treatment type from Lower treatment type( i,e Topical) to Higher treatment group(i,e Non_bio_sys or Biologics) during his treatment period. Same is true for Non_sys_Bio , if Subject changes to Biologics, then it will also consider as Switch.  Event is also to be counted whenever subjects changes his ATC_CODEs within his treatment TYPE , ie in case, when Treatment TYPE is "Psorasis" and if Its' ATC_CODE changes , then we have to identify it as SWITCH.

 same is true for other treatment arm.

 

order of treatment: BIOLOGICS> NON_BIO_SYS> TOPICAL.

 

Hope i am able to clear you doubt. please help. thanks

Contributor
Posts: 27

Re: Identifying the number of subjects who had treatment switch

[ Edited ]

data have;
length TYPE $20.;
input pnr ATC_CODE $ type $ EDATUM $ 10. ;
date=input(edatum,mmddyy10.);
format date mmddyy10.;
cards;
478 L04AX03 Nonbiologic_systemic 2/10/2010
478 D05AX52 Psoriasis 2/23/2010
478 L04AX03 Nonbiologic_systemic 3/5/2010
478 L04AX03 Nonbiologic_systemic 5/18/2010
478 L04AX03 Nonbiologic_systemic 8/2/2010
478 L04AX03 Nonbiologic_systemic 11/3/2010
478 L04AX03 Nonbiologic_systemic 2/7/2011
478 L04AX03 Nonbiologic_systemic 8/16/2011
478 L04AX03 Nonbiologic_systemic 11/22/2011
603 D05AX02 Psoriasis 8/24/2005
603 D05AX02 Psoriasis 10/13/2005
603 D05AX02 Psoriasis 6/2/2006
603 D05AX02 Psoriasis 7/19/2006
603 D05AX02 Psoriasis 4/3/2007
603 D05AX02 Psoriasis 12/7/2007
603 D05AX02 Psoriasis 1/4/2008
603 D05AX02 Psoriasis 1/4/2008
603 D05AX02 Psoriasis 10/2/2008
603 D05AX52 Psoriasis 3/16/2009
603 D05AX52 Psoriasis 3/16/2009
603 D05AX52 Psoriasis 5/7/2009
603 D05AX52 Psoriasis 8/21/2009
603 D05AX52 Psoriasis 11/9/2009
603 D05AX52 Psoriasis 3/19/2010
603 D05AX52 Psoriasis 7/30/2010
603 D05AX52 Psoriasis 7/30/2010
603 D05AX52 Psoriasis 1/13/2011
603 D05AX52 Psoriasis 5/3/2011
603 D05AX52 Psoriasis 12/12/2011
1103 L04AX03 Nonbiologic_systemic 1/17/2006
1103 L04AX03 Nonbiologic_systemic 8/23/2006
1103 L04AX03 Nonbiologic_systemic 11/9/2006
1103 D05AX52 Psoriasis 4/19/2007
1103 L04AX03 Nonbiologic_systemic 4/19/2007
1103 D05AX52 Psoriasis 10/26/2007
1103 D05AX52 Psoriasis 4/1/2008
1103 L04AX03 Nonbiologic_systemic 10/20/2008
1103 D05AX52 Psoriasis 10/20/2008
1103 L04AX03 Nonbiologic_systemic 4/7/2009
1103 L04AX03 Nonbiologic_systemic 11/20/2009
1103 L04AX03 Nonbiologic_systemic 11/12/2010
1103 L04AX03 Nonbiologic_systemic 8/12/2011
1103 D05AX52 Psoriasis 10/22/2011
1103 D05AX52 Psoriasis 12/29/2011
;
run;


/*sort the data to keep the date in increase order to know subject moved to other treatment or not*/


proc sort data=have;
by pnr date;
run;


data need;
set have;
length change $ 10.;
by pnr;
/*create new variable change and keep constant if it is topical for first observation*/
/*compare topical values with next values if it changes to other non bio or bio then switched*/


if first.pnr and atc_code in ( 'D05AX52','D05AX02') then change="";
else if not first.pnr and atc_code not in('D05AX52','D05AX02','L01XC02','L04AA24','L04AB01','L04AB02','L04AB04','L04AB05','L04AB06','L04AC03','L04AC07','A11CC03','D05BB02','L01BA01','L01BB03' ,'L01XX05' ,'L04AA21' ,'L04AD01' ,'L04AX03')
then change='switched';

/*compare non bio values with next values if it changes to other non bio or bio then switched*/
if first.pnr and atc_code in ('L01XC02','L04AA24','L04AB01','L04AB02','L04AB04','L04AB05','L04AB06','L04AC03','L04AC07') then change="";
else if not first.pnr and atc_code not in( 'D05AX52','D05AX02') and atc_code in('L01XC02','L04AA24','L04AB01','L04AB02','L04AB04','L04AB05','L04AB06','L04AC03','L04AC07','A11CC03','D05BB02','L01BA01','L01BB03' ,'L01XX05' ,'L04AA21' ,'L04AD01' ,'L04AX03')
then change='switched';

/*compare bio with next values if it changes to other bio then switched*/

if first.pnr and atc_code in('A11CC03','D05BB02','L01BA01','L01BB03' ,'L01XX05' ,'L04AA21' ,'L04AD01' ,'L04AX03') then change='';
else if not first.pnr and atc_code not in( 'D05AX52','D05AX02') and atc_code in('A11CC03','D05BB02','L01BA01','L01BB03' ,'L01XX05' ,'L04AA21' ,'L04AD01' ,'L04AX03') then change='switched';
if atc_code=lag(atc_code) then change="";

run;

 

Hope this may help you Smiley Happy

Contributor ved
Contributor
Posts: 27

Re: Identifying the number of subjects who had treatment switch

[ Edited ]
Posted in reply to ramchinna24

@ramchinna24 Hi, Thanks for the logic, but what if ATC code withing the psorasis or within other treatment group changes, we also need to identify those changes as switches.

 

i want this :

lpnr ATC_CODE TYPE EDATUM Flag_switch Comment
478 L04AX03 Nonbiologic_systemic 2/10/2010    
478 D05AX52 Psoriasis 2/23/2010    
478 L04AX03 Nonbiologic_systemic 3/5/2010 Y This is switch because subject is changing his treatment from lower(psorais) to higher treatment(non_bio_sys/bio)
478 L04AX03 Nonbiologic_systemic 5/18/2010    
478 L04AX03 Nonbiologic_systemic 8/2/2010    
478 L04AX03 Nonbiologic_systemic 11/3/2010    
478 L04AX03 Nonbiologic_systemic 2/7/2011    
478 L04AX03 Nonbiologic_systemic 8/16/2011    
478 L04AX03 Nonbiologic_systemic 11/22/2011    
603 D05AX02 Psoriasis 8/24/2005    
603 D05AX02 Psoriasis 10/13/2005    
603 D05AX02 Psoriasis 6/2/2006    
603 D05AX02 Psoriasis 7/19/2006    
603 D05AX02 Psoriasis 4/3/2007    
603 D05AX02 Psoriasis 12/7/2007    
603 D05AX02 Psoriasis 1/4/2008    
603 D05AX02 Psoriasis 10/2/2008    
603 D05AX52 Psoriasis 3/16/2009 Y This is switch because subject is changing his ATC code within Psorasis(or any other treatment group)
603 D05AX52 Psoriasis 5/7/2009    
603 D05AX52 Psoriasis 8/21/2009    
603 D05AX52 Psoriasis 11/9/2009    
603 D05AX52 Psoriasis 3/19/2010    
603 D05AX52 Psoriasis 7/30/2010    
603 D05AX52 Psoriasis 1/13/2011    
603 D05AX52 Psoriasis 5/3/2011    
603 D05AX52 Psoriasis 12/12/2011    
1103 L04AX03 Nonbiologic_systemic 1/17/2006    
1103 L04AX03 Nonbiologic_systemic 8/23/2006    
1103 L04AX03 Nonbiologic_systemic 11/9/2006    
1103 L04AX03 Nonbiologic_systemic 4/19/2007    
1103 D05AX52 Psoriasis 10/26/2007    
1103 D05AX52 Psoriasis 4/1/2008    
1103 L04AX03 Nonbiologic_systemic 10/20/2008 Y This is switch because subject is changing his treatment from lower(psorais) to higher treatment(non_bio_sys/bio)
1103 D05AX52 Psoriasis 10/20/2008    
1103 L04AX03 Nonbiologic_systemic 4/7/2009 Y This is switch because subject is changing his treatment from lower(psorais) to higher treatment(non_bio_sys/bio)
1103 L04AX03 Nonbiologic_systemic 11/20/2009    
1103 L04AX03 Nonbiologic_systemic 11/12/2010    
1103 L04AX03 Nonbiologic_systemic 8/12/2011    
1103 D05AX52 Psoriasis 10/22/2011    
1103 D05AX52 Psoriasis 12/29/2011    
Contributor
Posts: 27

Re: Identifying the number of subjects who had treatment switch

[ Edited ]

even if code changes with in the group, it works. Just try it once. hope it works. If it doesnt work, tell me .

Contributor ved
Contributor
Posts: 27

Re: Identifying the number of subjects who had treatment switch

Posted in reply to ramchinna24

@ramchinna24 Hi , code is working on treatment Type level, however whenever atc_codes are changing withing the treatment type, it's not working. I have added the desired output in previous reply, please kindly check.

Many thanks for your's help!!

Contributor
Posts: 27

Re: Identifying the number of subjects who had treatment switch

Did u try last updated solution? I sent updated code and it works for you
Contributor
Posts: 27

Re: Identifying the number of subjects who had treatment switch

proc sort data=have;
by pnr atc_code type date;
run;

data need;
set have;
length change $ 10.;
by pnr atc_code;
/*create new variable change and keep constant if it is topical for first observation*/
/*compare topical values with next values if it changes to other non bio or bio then switched*/

if first.pnr and atc_code in ( 'D05AX52','D05AX02') then change="";
else if not first.pnr and atc_code in('D05AX52','D05AX02','L01XC02','L04AA24','L04AB01','L04AB02','L04AB04','L04AB05','L04AB06','L04AC03','L04AC07','A11CC03','D05BB02','L01BA01','L01BB03' ,'L01XX05' ,'L04AA21' ,'L04AD01' ,'L04AX03')
then change='switched';
/*compare non bio values with next values if it changes to other non bio or bio then switched*/
if first.pnr and atc_code in ('L01XC02','L04AA24','L04AB01','L04AB02','L04AB04','L04AB05','L04AB06','L04AC03','L04AC07') then change="";
else if not first.pnr and atc_code not in( 'D05AX52','D05AX02') and atc_code in('L01XC02','L04AA24','L04AB01','L04AB02','L04AB04','L04AB05','L04AB06','L04AC03','L04AC07','A11CC03','D05BB02','L01BA01','L01BB03' ,'L01XX05' ,'L04AA21' ,'L04AD01' ,'L04AX03')
then change='switched';
/*compare bio with next values if it changes to other bio then switched*/
if first.pnr and atc_code in('A11CC03','D05BB02','L01BA01','L01BB03' ,'L01XX05' ,'L04AA21' ,'L04AD01' ,'L04AX03') then change='';
else if not first.pnr and atc_code not in( 'D05AX52','D05AX02','L01XC02','L04AA24','L04AB01','L04AB02','L04AB04','L04AB05','L04AB06','L04AC03','L04AC07') and atc_code in('A11CC03','D05BB02','L01BA01','L01BB03' ,'L01XX05' ,'L04AA21' ,'L04AD01' ,'L04AX03') then change='switched';
if atc_code=lag(atc_code) then change="";

run;
Contributor ved
Contributor
Posts: 27

Re: Identifying the number of subjects who had treatment switch

Posted in reply to ramchinna24

@ramchinna24 I think, sorting order is conflicting with data, for example on: PNR 478, Switch was recorded at 5th March 2010 ,

Nonbiologic_systemic 2/10/2010
Psoriasis 2/23/2010
Nonbiologic_systemic 3/5/2010

 

but when we are sorting it on atc_code and then type and followed by edatum , switch is recording at 2/10/2010. 

Contributor ved
Contributor
Posts: 27

Re: Identifying the number of subjects who had treatment switch

@ramchinna24  Hi I have tried this:

 

data test;

    set new_have;/*sorted on pnr date*/
    by pnr;
       if lag(type)='Psoriasis' and type in ('Nonbiologic_systemic' 'Biologics')   then f=1;
       if lag(type)='Psoriasis' and type='Psoriasis' and lag(atc_code) ne atc_code then f=1;    
       
       if lag(type)='Nonbiologic_systemic' and type in ('Biologics') then f=1;
       if lag(type)='Nonbiologic_systemic' and type='Nonbiologic_systemic' and lag(atc_code) ne atc_code then f=1;

    if lag(type) in ('Nonbiologic_systemic' 'Psoriasis') and type='Biologics' then f=1;
    if lag(type)='Biologics' and type='Biologics' and lag(atc_code) ne atc_code then f=1;
    
/*     if lag(pnr) =pnr and lag(atc_code) ne atc_code then f=1; */

run;  

 

But it's ignoring the by group and adding flagging  for situations when patient by group is changes.

Solution
‎05-16-2016 05:40 AM
Contributor
Posts: 27

Re: Identifying the number of subjects who had treatment switch

proc format;
value treatType 1 = "Topical"
2 = "Non-biologic systemics"
3 = "Biologics";
run;

data have;
format pnr 8. tType treatType. tCode $10. date YYMMDDs8.;
informat tType 1. date yymmdd10.;
input pnr tCode tType date;
datalines;
478 L04AX03 2 2010-02-10
478 D05AX52 1 2010-02-23
478 L04AX03 2 2010-03-05
478 L04AX03 2 2010-05-18
478 L04AX03 2 2010-08-02
478 L04AX03 2 2010-11-03
478 L04AX03 2 2011-02-07
478 L04AX03 2 2011-08-16
478 L04AX03 2 2011-11-22
603 D05AX02 1 2005-08-24
603 D05AX02 1 2005-10-13
603 D05AX02 1 2006-06-02
603 D05AX02 1 2006-07-19
603 D05AX02 1 2007-04-03
603 D05AX02 1 2007-12-07
603 D05AX02 1 2008-01-04
603 D05AX02 1 2008-01-04
603 D05AX02 1 2008-10-02
603 D05AX52 1 2009-03-16
603 D05AX52 1 2009-03-16
603 D05AX52 1 2009-05-07
603 D05AX52 1 2009-08-21
603 D05AX52 1 2009-11-09
603 D05AX52 1 2010-03-19
603 D05AX52 1 2010-07-30
603 D05AX52 1 2010-07-30
603 D05AX52 1 2011-01-13
603 D05AX52 1 2011-05-03
603 D05AX52 1 2011-12-12
1103 L04AX03 2 2006-01-17
1103 L04AX03 2 2006-08-23
1103 L04AX03 2 2006-11-09
1103 D05AX52 1 2007-04-19
1103 L04AX03 2 2007-04-19
1103 D05AX52 1 2007-10-26
1103 D05AX52 1 2008-04-01
1103 L04AX03 2 2008-10-20
1103 D05AX52 1 2008-10-20
1103 L04AX03 2 2009-04-07
1103 L04AX03 2 2009-11-20
1103 L04AX03 2 2010-11-12
1103 L04AX03 2 2011-08-12
1103 D05AX52 1 2011-10-22
1103 D05AX52 1 2011-12-29
run;
proc sort data=have;
by pnr date;
run;

data want;
set have;
by pnr;
format switch 1. tCode_prev $10. tType_prev 3.;
retain tCode_prev '' tType_prev .;
format switch 1.;

if first.pnr then do;
switch = 0;
end;

else if tType_prev = 1 then do;
if tType > 1 or tCode ne tCode_prev then switch = 1;
else switch = 0;
end;

else if tType_prev = 2 then do;
if tType > 2 or (tType = 2 and tCode ne tCode_prev) then switch = 1;
else switch = 0;
end;

else if tType_prev = 3 then do;
/* Here's your homework */
end;

output;
tCode_prev = tCode;
tType_prev = tType;

drop tCode_prev tType_prev;
run;

Contributor ved
Contributor
Posts: 27

Re: Identifying the number of subjects who had treatment switch

Posted in reply to ramchinna24

@ramchinna24 Many Thanks for the help and time! . It worked 

☑ This topic is solved.

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