topic Re: lines of treatment in SAS Procedures

lines of treatment

saipriya92 — Mon, 02 Dec 2019 22:11:50 GMT

Hi all,

I have this dataset ;

sasuser.sample1_drugs

Obs PTID DRUG_DT DRUG123456789101112131415161718192021222324252627282930313233343536373839404142434445464748495051525354555657585960616263646566676869707172737475767778798081828384858687888990919293949596979899100101102103104105106107108109110111112113114115116117118119120121122123124125126127128129130131132133

PT078375333	31DEC2014	ETOPOSIDE
PT078375333	01JAN2015	CISPLATIN
PT078375333	01JAN2015	ETOPOSIDE
PT078375333	02JAN2015	ETOPOSIDE
PT078375333	21JAN2015	CISPLATIN
PT078375333	21JAN2015	ETOPOSIDE
PT078375333	22JAN2015	ETOPOSIDE
PT078375333	23JAN2015	ETOPOSIDE
PT078375333	11FEB2015	CISPLATIN
PT078375333	11FEB2015	ETOPOSIDE
PT078375333	12FEB2015	ETOPOSIDE
PT078375333	13FEB2015	ETOPOSIDE
PT078375333	04MAR2015	CISPLATIN
PT078375333	05MAR2015	ETOPOSIDE
PT078375333	06MAR2015	ETOPOSIDE
PT078837214	13NOV2013	CARBOPLATIN
PT078837214	13NOV2013	ETOPOSIDE
PT078837214	11DEC2013	CARBOPLATIN
PT078837214	11DEC2013	ETOPOSIDE
PT078837214	12DEC2013	ETOPOSIDE
PT082388044	18MAR2013	CARBOPLATIN
PT082388044	18MAR2013	ETOPOSIDE
PT082388044	19MAR2013	ETOPOSIDE
PT082388044	20MAR2013	ETOPOSIDE
PT082388044	08APR2013	CARBOPLATIN
PT082388044	08APR2013	ETOPOSIDE
PT082388044	09APR2013	ETOPOSIDE
PT082388044	10APR2013	ETOPOSIDE
PT082388044	01MAY2013	CARBOPLATIN
PT082388044	01MAY2013	ETOPOSIDE
PT082388044	02MAY2013	ETOPOSIDE
PT082388044	03MAY2013	ETOPOSIDE
PT082388044	22MAY2013	CARBOPLATIN
PT082388044	22MAY2013	ETOPOSIDE
PT082388044	23MAY2013	ETOPOSIDE
PT082388044	24MAY2013	ETOPOSIDE
PT082388044	19JAN2015	CARBOPLATIN
PT082388044	19JAN2015	ETOPOSIDE
PT082388044	20JAN2015	ETOPOSIDE
PT082388044	21JAN2015	ETOPOSIDE
PT082388044	09FEB2015	CARBOPLATIN
PT082388044	09FEB2015	ETOPOSIDE
PT082388044	10FEB2015	ETOPOSIDE
PT082388044	11FEB2015	ETOPOSIDE
PT082388044	03MAR2015	CARBOPLATIN
PT082388044	03MAR2015	ETOPOSIDE
PT082388044	04MAR2015	ETOPOSIDE
PT082388044	05MAR2015	ETOPOSIDE
PT082388044	24MAR2015	CARBOPLATIN
PT082388044	24MAR2015	ETOPOSIDE
PT082388044	25MAR2015	ETOPOSIDE
PT082388044	26MAR2015	ETOPOSIDE
PT082388044	02FEB2016	CARBOPLATIN
PT082388044	02FEB2016	ETOPOSIDE
PT082388044	03FEB2016	ETOPOSIDE
PT082388044	04FEB2016	ETOPOSIDE
PT082388044	23FEB2016	CARBOPLATIN
PT082388044	23FEB2016	ETOPOSIDE
PT082388044	24FEB2016	ETOPOSIDE
PT082388044	25FEB2016	ETOPOSIDE
PT082388044	15MAR2016	CARBOPLATIN
PT082388044	15MAR2016	ETOPOSIDE
PT082388044	16MAR2016	ETOPOSIDE
PT082388044	17MAR2016	ETOPOSIDE
PT083585377	17APR2012	CARBOPLATIN
PT083585377	17APR2012	ETOPOSIDE
PT083585377	18APR2012	ETOPOSIDE
PT083585377	19APR2012	ETOPOSIDE
PT083585377	09MAY2012	CARBOPLATIN
PT083585377	09MAY2012	ETOPOSIDE
PT083585377	10MAY2012	ETOPOSIDE
PT083585377	11MAY2012	ETOPOSIDE
PT083585377	30MAY2012	CARBOPLATIN
PT083585377	30MAY2012	ETOPOSIDE
PT083585377	31MAY2012	ETOPOSIDE
PT083585377	01JUN2012	ETOPOSIDE
PT083585377	20JUN2012	CARBOPLATIN
PT083585377	20JUN2012	ETOPOSIDE
PT083585377	21JUN2012	ETOPOSIDE
PT083585377	22JUN2012	ETOPOSIDE
PT083585377	25JUL2012	CARBOPLATIN
PT083585377	25JUL2012	ETOPOSIDE
PT083585377	26JUL2012	ETOPOSIDE
PT083585377	27JUL2012	ETOPOSIDE
PT083585377	15AUG2012	CARBOPLATIN
PT083585377	15AUG2012	ETOPOSIDE
PT083585377	16AUG2012	ETOPOSIDE
PT083585377	17AUG2012	ETOPOSIDE
PT083585377	03JAN2013	CARBOPLATIN
PT083585377	03JAN2013	ETOPOSIDE
PT083585377	22JAN2013	CARBOPLATIN
PT083585377	22JAN2013	IRINOTECAN
PT083585377	18FEB2013	CARBOPLATIN
PT083585377	18FEB2013	IRINOTECAN
PT083585377	25FEB2013	CARBOPLATIN
PT083585377	25FEB2013	IRINOTECAN
PT083585377	04MAR2013	CARBOPLATIN
PT083585377	04MAR2013	IRINOTECAN
PT083585377	16APR2013	CARBOPLATIN
PT083585377	16APR2013	IRINOTECAN
PT083585377	23APR2013	CARBOPLATIN
PT083585377	23APR2013	IRINOTECAN
PT083585377	30APR2013	CARBOPLATIN
PT083585377	30APR2013	IRINOTECAN
PT083585377	31MAY2013	CARBOPLATIN
PT083585377	31MAY2013	IRINOTECAN
PT083585377	07JUN2013	CARBOPLATIN
PT083585377	07JUN2013	IRINOTECAN
PT083585377	24JUN2013	TOPOTECAN
PT083585377	25JUN2013	TOPOTECAN
PT083585377	26JUN2013	TOPOTECAN
PT083585377	27JUN2013	TOPOTECAN
PT083585377	28JUN2013	TOPOTECAN
PT083585377	22JUL2013	CARBOPLATIN
PT083585377	22JUL2013	IRINOTECAN
PT083585377	22JUL2013	TOPOTECAN
PT083585377	29JUL2013	TOPOTECAN
PT083585377	30JUL2013	TOPOTECAN
PT083585377	31JUL2013	TOPOTECAN
PT083585377	01AUG2013	TOPOTECAN
PT083585377	02AUG2013	TOPOTECAN
PT083585377	26AUG2013	TOPOTECAN
PT083585377	27AUG2013	TOPOTECAN
PT083585377	28AUG2013	TOPOTECAN
PT083585377	29AUG2013	TOPOTECAN
PT083585377	16SEP2013	DOCETAXEL
PT083585377	08OCT2013	DOCETAXEL
PT083585377	11NOV2013	GEMCITABINE
PT083585377	18NOV2013	GEMCITABINE
PT083585377	09DEC2013	GEMCITABINE
PT083585377	23DEC2013	GEMCITABINE
PT083585377	30DEC2013	GEMCITABINE
PT083585377	06JAN2014	GEMCITABINE

I have made this intermediate step ;

sasuser.sample1_step1

Obs PTID DRUG STDT ENDDT12345678910111213141516

PT078375333	Etoposide	31DEC2014	06MAR2015
PT078375333	Cisplatin	01JAN2015	04MAR2015
PT078837214	Carboplatin	13NOV2013	11DEC2013
PT078837214	Etoposide	13NOV2013	12DEC2013
PT082388044	Carboplatin	18MAR2013	22MAY2013
PT082388044	Etoposide	18MAR2013	24MAY2013
PT082388044	Carboplatin	19JAN2015	24MAR2015
PT082388044	Etoposide	19JAN2015	26MAR2015
PT083585377	Carboplatin	17APR2012	15AUG2012
PT083585377	Etoposide	17APR2012	17AUG2012
PT083585377	Etoposide	03JAN2013	03JAN2013
PT083585377	Carboplatin	03JAN2013	22JUL2013
PT083585377	Irinotecan	22JAN2013	22JUL2013
PT083585377	Topotecan	24JUN2013	29AUG2013
PT083585377	Docetaxel	16SEP2013	08OCT2013
PT083585377	Gemcitabine	11NOV2013	06JAN2014

The code for the intermediate step is:

proc sort data=sasuser.sample1_drugs out=sample1_sorted;
	by ptid drug ;
run ;

data step1_1 ;
	set sample1_sorted ;
	by ptid drug ;
	if first.drug then gap=0;
	format lag_date date9. ;
	lag_date= lag(drug_dt);
	if drug_dt-lag_date >=60 /*and first.ptid=0*/ then gap + 1;
run ;

proc sql;
	create table step1_final as 
	select ptid, drug, min(drug_dt) as stdt format=date9. ,max(drug_dt) as enddt format=date9. 	
	from step1_1 
	group by ptid, drug, gap ;
quit ;

I want to create this final dataset ;

sasuser.sample1_step2

Obs PTID REGIMEN SDATE EDATE12345678910111213141516171819202122

PT078375333	Etoposide	31DEC2014	31DEC2014
PT078375333	Cisplatin+Etoposide	01JAN2015	04MAR2015
PT078375333	Etoposide	05MAR2015	06MAR2015
PT078837214	Carboplatin+Etoposide	13NOV2013	11DEC2013
PT078837214	Etoposide	12DEC2013	12DEC2013
PT082388044	Carboplatin+Etoposide	18MAR2013	22MAY2013
PT082388044	Etoposide	23MAY2013	24MAY2013
PT082388044	Blank	25MAY2013	18JAN2015
PT082388044	Carboplatin+Etoposide	19JAN2015	24MAR2015
PT082388044	Etoposide	25MAR2015	26MAR2015
PT083585377	Carboplatin+Etoposide	17APR2012	15AUG2012
PT083585377	Etoposide	16AUG2012	17AUG2012
PT083585377	Blank	18AUG2012	02JAN2013
PT083585377	Carboplatin+Etoposide	03JAN2013	03JAN2013
PT083585377	Carboplatin	04JAN2013	21JAN2013
PT083585377	Carboplatin+Irinotecan	22JAN2013	23JUN2013
PT083585377	Carboplatin+Irinotecan+Topotecan	24JUN2013	22JUL2013
PT083585377	Topotecan	23JUL2013	29AUG2013
PT083585377	Blank	30AUG2013	15SEP2013
PT083585377	Docetaxel	16SEP2013	08OCT2013
PT083585377	Blank	09OCT2013	10NOV2013
PT083585377	Gemcitabine	11NOV2013	06JAN2014

How to code for this ?

Re: lines of treatment

PaigeMiller — Mon, 02 Dec 2019 22:58:22 GMT

Please explain the logic that enables you to get the final data set from the original data set.

Re: lines of treatment

saipriya92 — Tue, 03 Dec 2019 04:51:06 GMT

Step 1: Find the treatment periods of each individual drug for each patient. Use the drug encounter data to create periods of continuous treatment for each individual chemotherapy. A period of continuous chemo administration starts on the first date of use and ends when there is a gap of greater than 60 days between 2 consecutive chemotherapy (of the same drug) administrations.

Step 2: Line up treatments and create the patient's treatment journey from start of first treatment to the end of the last treatment. Identify treatments that are being given concurrently. If there are no treatments given during a certain period, that period will be labeled as a blank regimen.

Re: lines of treatment

s_lassen — Wed, 04 Dec 2019 10:32:23 GMT

Here is a "brute force" method, which simply generates one obs per date per regimen, and then sums that up:

data all_days;
  set step1_final;
  do date=stdt to enddt;
    output;
    end;
  drop stdt enddt;
run;

proc sort;
  by ptid date;
run;

data all_days2;
  do until(last.date);
    set all_days;
    by ptid date;
    length regimen $200;
    call catx('+',regimen,drug);
    end;
run;

data all_days3;
  set all_days2;
  by ptid date; 
  diff=dif(date);
  output;
  if not first.ptid and diff>1 then do;
    regimen='BLANK';
    do date=date-diff+1 to date-1;
      output;
      end;
    end;
run;

proc sort;
  by ptid date;
run;

data want;
  do until(last.regimen);
    set all_days3;
    by ptid regimen notsorted;
    if first.regimen then
      stdt=date;
    end;
  enddt=date;
  format stdt enddt date9.;
  keep ptid regimen stdt enddt;
run;

I realized that my first suggestion might create to many "BLANK" records if one patient was followed by another whose regimen started after the first patient's regimen ended. So I edited my response a bit to account for that (the datastep ALL_DAYS2 is split into two steps).

Re: lines of treatment

ed_sas_member — Wed, 04 Dec 2019 01:21:26 GMT

Hi @saipriya92 ,

You can try this. Hope this help!

/* Expand dataset: create one row per day for each drug */

data sample1_step1_exp;
	set sample1_step1;
	format DAY date9.;
	do DAY=STDT to ENDDT;
		output;
	end;
run;

proc sort data=sample1_step1_exp;
	by PTID DAY;
run;

/* Transpose drugs to create combination regimens */

proc transpose data=sample1_step1_exp out=sample1_step1_tr (drop=_name_);
	var DRUG;
	by PTID DAY;
run;

data sample1_step1_regimen1;
	set sample1_step1_tr;
	
	REGIMEN = catx(" + ",of col:);
	
	keep PTID DAY REGIMEN;
run;

/* Creation of the variable COUNTER, which is incremented each time a new regimen is given */
data sample1_step1_regimen2;
	set sample1_step1_regimen1;
	
	by PTID REGIMEN notsorted;
	if first.PTID then COUNTER=0;

	if first.REGIMEN then COUNTER + 1;
run;

/* Creation of the final table without "blank" periods of time */
proc sql;
	create table sample1_step1_regimen3 as
	select PTID,
	min(DAY) as STDT format=date9.,
	max(DAY) as ENDDT format=date9.,
	REGIMEN
	from sample1_step1_regimen2 group by PTID, REGIMEN, COUNTER order by PTID, STDT ;
quit;

/* Identification of "blank" periods of time */
data sample1_step1_blank (keep= PTID REGIMEN _STDT_blank _ENDDT_blank );
	set sample1_step1_regimen3;
	format _STDT_blank _ENDDT_blank date9.;
	by PTID;
	_STDT_blank = lag(ENDDT) +1 ;
	if first.PTID or _STDT_blank = STDT then _STDT_blank=.;
	if _STDT_blank ne . then do;
			_ENDDT_blank = STDT - 1;
			REGIMEN = "Blank";
			output;
		end;
run;

/* Creation of the final table (retrieve "blank" periods of time) */
data sample1_step2;
	set sample1_step1_regimen3 sample1_step1_blank (rename=(_STDT_blank= STDT _ENDDT_blank=ENDDT));
run;

proc sort data=sample1_step2;
	by PTID STDT;
run;

Output: