*************************************************************************************************;
* 
*           CLIENT:  ModernaTX, Inc.
*         PROTOCOL:  mRNA-1273-P301
*
*          PURPOSE: Create analysis dataset adttre
*      
*      INPUT FILES: SDTM domains
*     OUTPUT FILES: ADTTRE.sas7bdat
*
*      USAGE NOTES: 
*      
*************************************************************************************************;
*  Copyright 2020 Pharmaceutical Product Development, Inc.
*  All Rights Reserved. 
*************************************************************************************************;

options noquotelenmax;
%include "madam.sas";

**Assign global macro variable DSETNAME to reflect the name of the final ADaM dataset**;
%global DSETNAME;
%let dsetname = ADTTRE;
%let adslvar= USUBJID SUBJID  DTHDT EOSDT CUTOFFDT;


/*proc sort data=adb.adeff2;by usubjid subjid;run;*/
proc sort data=adb.adsl out=adsl(keep=&adslvar.);by usubjid subjid;run;

data ADDadsl(WHERE=(ANL01FL='Y' and FASFL='Y'));
	merge adb.adeff2(in=b) adsl(in=a);
	by usubjid subjid;
	if b;
run;


data adeff2;
	set ADDadsl;

	** PARAM AND PARAMCD********;
	param = tranwrd(param,' in 7 Days','');
	param = tranwrd(param,' in 28 Days','');
	if param="Burden of Disease Score" then paramcd="BOD";
	else if param="Burden of Infection Score" then paramcd="BOI";
	** EVENTSEQ;
	IF PARAMCD="BOD" AND (AVAL=0 OR AVAL=1) THEN DO;
		EVENTSEQ=1;
		IF AVAL=0 THEN CNSR=1;
		ELSE CNSR=0;
		OUTPUT;
	END;
	IF PARAMCD="BOD" AND AVAL=2 THEN DO;
		EVENTSEQ=1;
		CNSR=0;
		OUTPUT;
	END;
	IF PARAMCD="BOD" AND AVAL=2 THEN DO;
		EVENTSEQ=2;
		CNSR=0;
		OUTPUT;
	END;
	IF PARAMCD="BOD" AND AVAL=3 THEN DO;
		EVENTSEQ=1;
		CNSR=0;
		OUTPUT;
	END;
	IF PARAMCD="BOD" AND AVAL=3 THEN DO;
		EVENTSEQ=2;
		CNSR=0;
		OUTPUT;
	END;
	IF PARAMCD="BOD" AND AVAL=3 THEN DO;
		EVENTSEQ=3;
		CNSR=0;
		OUTPUT;
	END;
	IF PARAMCD="BOI" AND (AVAL=0 OR AVAL=0.5) THEN DO;
		EVENTSEQ=1;
		IF AVAL=0 THEN CNSR=1;
		ELSE CNSR=0;
		OUTPUT;
	END;
	
	IF PARAMCD="BOI" AND AVAL=1 THEN DO;
		EVENTSEQ=1;
		CNSR=0;
		OUTPUT;
	END;
	IF PARAMCD="BOI" AND AVAL=1 THEN DO;
		EVENTSEQ=2;
		CNSR=0;
		OUTPUT;
	END;
	IF PARAMCD="BOI" AND AVAL=2 THEN DO;
		EVENTSEQ=1;
		CNSR=0;
		OUTPUT;
	END;
	IF PARAMCD="BOI" AND AVAL=2 THEN DO;
		EVENTSEQ=2;
		CNSR=0;
		OUTPUT;
	END;
	IF PARAMCD="BOI" AND AVAL=2 THEN DO;
		EVENTSEQ=3;
		CNSR=0;
		OUTPUT;
	END;
	IF PARAMCD="BOI" AND AVAL=2 THEN DO;
		EVENTSEQ=4;
		CNSR=0;
		OUTPUT;
	END;
	IF PARAMCD="BOI" AND AVAL=3 THEN DO;
		EVENTSEQ=1;
		CNSR=0;
		OUTPUT;
	END;
	IF PARAMCD="BOI" AND AVAL=3 THEN DO;
		EVENTSEQ=2;
		CNSR=0;
		OUTPUT;
	END;
	IF PARAMCD="BOI" AND AVAL=3 THEN DO;
		EVENTSEQ=3;
		CNSR=0;
		OUTPUT;
	END;
	IF PARAMCD="BOI" AND AVAL=3 THEN DO;
		EVENTSEQ=4;
		CNSR=0;
		OUTPUT;
	END;
	IF PARAMCD="BOI" AND AVAL=3 THEN DO;
		EVENTSEQ=5;
		CNSR=0;
		OUTPUT;
	END;
	IF PARAMCD="BOI" AND AVAL=3 THEN DO;
		EVENTSEQ=6;
		CNSR=0;
		OUTPUT;
	END;
run;
/*PROC FREQ DATA=ADEFF2;TABLE PARAMCD*AVAL;RUN;*/
DATA FINAL;
	SET ADEFF2;
	LENGTH EVNTDESC $100 ; 
	IF PARAMCD = "BOD" THEN DO;
		IF AVAL=0 THEN EVNTDESC = "Without COVID-19";
		ELSE IF AVAL=1 THEN EVNTDESC = "COVID-19 without hospitalization";
		ELSE IF AVAL=2 THEN EVNTDESC = "COVID-19 with hospitalization";
		ELSE IF AVAL=3 THEN EVNTDESC = "Death";
		IF EVENTSEQ=1 THEN STARTVAL=0;
		ELSE IF EVENTSEQ=2 and cmiss(adt,randdt)=0 THEN STARTVAL=(adt-randdt);
		ELSE IF EVENTSEQ=3 and cmiss(adt,randdt)=0 THEN STARTVAL=(adt-randdt)+1*10**(-10);
	END;
	IF PARAMCD = "BOI" THEN DO;
		IF AVAL=0 THEN EVNTDESC = "No infection";
		ELSE IF AVAL=0.5 THEN EVNTDESC = "Asymptomatic infection";
		ELSE IF AVAL=1 THEN EVNTDESC = "COVID-19 without hospitalization";
		ELSE IF AVAL=2 THEN EVNTDESC = "COVID-19 with hospitalization";
		ELSE IF AVAL=3 THEN EVNTDESC = "Death";
		IF EVENTSEQ=1 THEN STARTVAL=0;
		ELSE IF EVENTSEQ=2 and cmiss(adt,tr01sdt)=0 THEN STARTVAL=(adt-tr01sdt);
		ELSE IF EVENTSEQ=3 and cmiss(adt,tr01sdt)=0 THEN STARTVAL=(adt-tr01sdt)+1*10**(-10);
		ELSE IF EVENTSEQ=4 and cmiss(adt,tr01sdt)=0 THEN STARTVAL=(adt-tr01sdt)+2*10**(-10);
		ELSE IF EVENTSEQ=5 and cmiss(adt,tr01sdt)=0 THEN STARTVAL=(adt-tr01sdt)+3*10**(-10);
		ELSE IF EVENTSEQ=6 and cmiss(adt,tr01sdt)=0 THEN STARTVAL=(adt-tr01sdt)+4*10**(-10);
	END;
	minvalue = min(DTHDT,EOSDT,CUTOFFDT,EFFCODT,AP01EDT);
	format minvalue date9.;
RUN;
data &DSETNAME.;
	set final(rename=(aval=_aval));
	if PARAMCD = "BOD" THEN DO;
		if EVENTSEQ=1 and _aval=0 and cmiss(minvalue,randdt)=0 then aval= minvalue - randdt;
		else if EVENTSEQ=1 and _aval=1 and cmiss(adt,randdt)=0 then aval=adt-randdt;
		else if EVENTSEQ=1 and _aval=2 and cmiss(adt,randdt)=0 then aval=adt-randdt;
		else if EVENTSEQ=2 and _aval=2 and cmiss(adt,randdt)=0 then aval=(adt-randdt)+1*10**(-10);
		else if EVENTSEQ=1 and _aval=3 and cmiss(adt,randdt)=0 then aval=adt-randdt;
		else if EVENTSEQ=2 and _aval=3 and cmiss(adt,randdt)=0 then aval=(adt-randdt)+1*10**(-10);
		else if EVENTSEQ=3 and _aval=3 and cmiss(adt,randdt)=0 then aval=(adt-randdt)+2*10**(-10);
	end;
	if PARAMCD = "BOI" THEN DO;
		if EVENTSEQ=1 and _aval=0 and nmiss(minvalue,tr01sdt)=0 then aval= minvalue - tr01sdt;
		else if EVENTSEQ=1 and _aval=0.5 and cmiss(adt,tr01sdt)=0 then aval=adt-tr01sdt;
		else if EVENTSEQ=1 and _aval=1 and cmiss(adt,tr01sdt)=0 then aval=adt-tr01sdt;
		else if EVENTSEQ=2 and _aval=1 and cmiss(adt,tr01sdt)=0 then aval=(adt-tr01sdt)+1*10**(-10);
		else if EVENTSEQ=1 and _aval=2 and cmiss(adt,tr01sdt)=0 then aval=adt-tr01sdt;
		else if EVENTSEQ=2 and _aval=2 and cmiss(adt,tr01sdt)=0 then aval=(adt-tr01sdt)+1*10**(-10);
		else if EVENTSEQ=3 and _aval=2 and cmiss(adt,tr01sdt)=0 then aval=(adt-tr01sdt)+2*10**(-10);
		else if EVENTSEQ=4 and _aval=2 and cmiss(adt,tr01sdt)=0 then aval=(adt-tr01sdt)+3*10**(-10);
		else if EVENTSEQ=1 and _aval=3 and cmiss(adt,tr01sdt)=0 then aval=adt-tr01sdt;
		else if EVENTSEQ=2 and _aval=3 and cmiss(adt,tr01sdt)=0 then aval=(adt-tr01sdt)+1*10**(-10);
		else if EVENTSEQ=3 and _aval=3 and cmiss(adt,tr01sdt)=0 then aval=(adt-tr01sdt)+2*10**(-10);
		else if EVENTSEQ=4 and _aval=3 and cmiss(adt,tr01sdt)=0 then aval=(adt-tr01sdt)+3*10**(-10);
		else if EVENTSEQ=5 and _aval=3 and cmiss(adt,tr01sdt)=0 then aval=(adt-tr01sdt)+4*10**(-10);
		else if EVENTSEQ=6 and _aval=3 and cmiss(adt,tr01sdt)=0 then aval=(adt-tr01sdt)+5*10**(-10);
	end;
run;





%adam_dataset_update(
	ds=&DSETNAME,
	libin=work,
	libout=output,
	adsllib=adb,
	addcomvar=Y,
	addseq=,
	dropinfmt=Y,
	mapspecfile=&ADAM_SPEC,
	maploc=&ADAM_SPEC_LOC,
	debug=N
	);
	
	
**Generate Value Level Metadata values for the ad<xx> dataset**;
%* dod_vlm(        
	type=ADAM,               
	selmems=&DSETNAME,
	excmems=,
	specloc=&ADAM_SPEC_LOC,
	specname=&ADAM_SPEC,
	debug=N
	);

**Generate Enhanced Controlled Terminology for the ad<xx> dataset**;
%* dod_enhcd_ct(            
	type=ADAM,               
	selmems=&DSETNAME,
	excmems=,
	specloc=&ADAM_SPEC_LOC,
	specname=&ADAM_SPEC,
	map_ct_nm=,
	map_ct_loc=,
	debug=N
	);