*************************************************************************
*        CLIENT: MODMRNA  
*      PROTOCOL:  mRNA-1273-P201 
*       PURPOSE:  
*   INPUT FILES:  _adsl_vars_.sas/_adis_vars_.sas, sdtm
*  OUTPUT FILES: PP_Listing.dat/xls format 
*   USAGE NOTES:  
************************************************************************* 
*  Copyright 2020 PPD
*  All Rights Reserved. 
*************************************************************************;

/* DELETE this comment block before writing code.
   Reference: http://wiki.ppdi.com/BioWiki/index.php/SAS_Program_Headers
*/
*options mprint;

%include ".\_adsl_vars_.sas";
%let adslvar=tr01sdt dose2dt tr01sdtm tr01edtm dose1fl dose2fl eosdt dthdt randfl sex;

data adsl;
  set final;
run;

/*
data z;
  set adsl;
   by usubjid;
    if first.usubjid then s=-1;
  else s=0;
  keep usubjid subjid s;
  run;*/
%include ".\_adis_vars_.sas";

/*
data z;
  set final;
  run;

  proc sql;
   create table z as
      select distinct dtype,iscat,istestcd,avisit,ady,isstresc
	      from final;
		  quit;*/

data adis;
  set final;

  ***    if missing(avisit) then avisit="Baseline";
if ^missing(avisit) and ^missing(usubjid);
if (index(upcase(iscat),'NEUTRALIZING') and istestcd='MNET' and lloq=160) or (index(upcase(iscat),'NEUTRALIZING') and istestcd='MN50' and lloq=318.46) then delete;

keep ISC: usubjid ady avisit vis: paramcd ISSTRESC dtype adt aval paramtyp;
run;



 data adis;
    set adis;
 
	if iscat="Serum SARS-CoV-2 Binding Antibodies" then do; iscat1="BIND";   iscat2="BIND_DY"; iscat3="BIND_DT"; end;
	else if iscat="Serum SARS-CoV-2 Neutralizing Antibodies" then do;  iscat1="NEUT";   iscat2="NEUT_DY"; iscat3="NEUT_DT"; end;
   /*istresc=isorres;*/
	if missing(paramtyp) /*and indexc(ISsTRESC ,"0123456789") gt 0  aval>. */;
	output;
   /*  iscat="Serum SARS-CoV-2 Binding Antibodies";iscat1="BIND";   usubjid="";  iscat2="BIND_DY";  output;*/   /*!!!!!!!!!!!  remove later*/
 run;



 proc sort data=adis;
    by usubjid  iscat adt  avisit;
run;

data adis;
   set adis;
   by usubjid  iscat avisit notsorted;
    if first.avisit;
 run;


 proc sort data=adis;
      by usubjid /*paramcd*/  avisit adt/* ady*/  /*VISITTPT:*/ ;

 run;
/**/
/* data chk;*/
/* set adis;*/
/*      by usubjid  adt avisit ;*/
/*if avisit ne '' then avisit_s=lag(avisit);*/
/*run;*/

/*data issue adt for Day 43 after Day 57 usubjid='mRNA-1273-P201-US203-1093'*/

 proc transpose data=adis   out=adis_tr(drop=_name_);
     by usubjid  avisit  /* ady  VISITTPT: */;
   id iscat1;
   var ISSTRESC;
   where aval>.;
	 run;
 

	 
 proc transpose data=adis   out=adis_tr2(drop=_name_);
     by usubjid  avisit  /* ady  VISITTPT: */;
   id iscat2;
   var ady;
	 run;
 

 proc transpose data=adis   out=adis_tr3(drop=_name_);
     by usubjid  avisit  /* ady  VISITTPT: */;
   id iscat3;
   var adt;
	 run; 

%revsupp(libin=TRANS
       , libout=work
       , ds=ds
       , supp=suppds
       , maploc=&G_PROJECTPATH.&G_TOPLEVEL.\Databases\Transformed 
       , mapspec=&g_nickname._mapping_spec.xlsx
       );

	    	   %revsupp(libin=TRANS
       , libout=work
       , ds=dv
       , supp=suppdv
       , maploc=&G_PROJECTPATH.&G_TOPLEVEL.\Databases\Transformed 
       , mapspec=&g_nickname._mapping_spec.xlsx
       );

	  /* %revsupp(libin=TRANS
       , libout=work
       , ds=dm
       , supp=suppdm
       , maploc=&G_PROJECTPATH.&G_TOPLEVEL.\Databases\Transformed 
       , mapspec=&g_nickname._mapping_spec.xlsx
       );



	  */


	  /* %revsupp(libin=TRANS
       , libout=work
       , ds=ie
       , supp=suppie
       , maploc=&G_PROJECTPATH.&G_TOPLEVEL.\Databases\Transformed 
       , mapspec=&g_nickname._mapping_spec.xlsx
       );
	   quit;*/

data ie;
 set trans.ie;
     keep usubjid subjid;

run;


proc sort data=ie nodupkey;
   by usubjid;
run;


data pp_listing_dm;
    set trans.dm;
    keep usubjid subjid ;
run;


data pp_listing_ds;
    set ds;
	if ENROLLYN="N" or DSSCAT='SCREEN FAILURE' then delete;
  ***  keep usubjid subjid cohort;
run;


proc sort data=pp_listing_ds nodupkey;
   by usubjid;
run;

data pp_listing;
   merge pp_listing_ds(in=a drop=subjid) pp_listing_dm ;
     by usubjid ;
	 if a;
run;
 
data pp_listing;
   merge pp_listing(in=ina) ie(in=inb);
   by usubjid subjid;
   if inb then iefl="N";
   else iefl="Y";
   if ina;
run;


/*Positive PCR*/

data mbpos;
	set trans.mb;
	if mborres in ('DETECTED', 'POSITIVE') and mbtestcd='SARSCOV2';
	mbdt=input(substr(mbdtc,1,10), yymmdd10.);
	format mbdt date9.;
run;

data aepos;
	set trans.ae;
	if AEDECOD in ('COVID-19', 'Asymptomatic COVID-19', 'SARS-CoV-2 test positive');
	mbdt=input(substr(aestdtc,1,10), yymmdd10.);
	format mbdt date9.;
run;


data pos;
	set mbpos aepos (in=a);
	if a then mborres=aedecod;
run;

proc sort data=pos nodupkey;
	by usubjid;
run;
 
proc format;
   value $vis
      "1"="Baseline"
      "4"="Day 15"
      "5"="Day 29"
      "7"="Day 43"
	  "8"="Day 57"
	  "9"= "Day 209"
	  "10"="Day 394"
         ;
   run;


data vist_templ(drop=VISITTPTN_  );
   set adsl(keep=usubjid);
   length avisit $50;
            do VISITTPTN_  ="1 ","4","5","7","8","9","10";
                      _VISITTPT=put(VISITTPTN_,$vis.);
                      _VISITTPTN=input(VISITTPTN_,best.);
					  avisit=_VISITTPT;
					   VISITTPT =_VISITTPT;
 VISITTPTN =_VISITTPTN;
				output;
            end;
        			
run;

proc sort data=adsl;
     by usubjid ;
run;
 
proc sort data=vist_templ;
     by usubjid avisit;
run;
 

data adsl_vis;
   merge adsl (drop=_: STUDYID DOMAIN  /*TR01SDTM*/ in=adsl) vist_templ ;
     by usubjid;
	 if adsl;
run;

 

data adis_tr_sum;
  merge adis_tr adis_tr2 adis_tr3;
    by usubjid  avisit;
	run;


 

data adsl_adis;
   merge adsl_vis ( in=adsl)   adis_tr_sum ;
     by usubjid avisit;
	 if adsl;
run;


data pp_listing;
  set pp_listing;
drop      DSREFID  DSDECOD  ENROLLYN  DSSCAT  /*avisit  _VISITTPT
 _VISITTPTN  VISITTPT VISITTPTN */;
  run;




data adsl_adis_vis;
    merge adsl_adis (in=inadsl) /*vist_templ*/ pp_listing (in=inpp);

   by usubjid subjid ;
   if inadsl;
run;

data adsl_adis_vis;
    merge adsl_adis_vis (in=inadsl) pos (keep=usubjid  mbdt mborres);

   by usubjid  ;
   if inadsl;
run;


data ve;
 set trans.ve;
 d29="Y";
 if find(upcase(visit),"DAY 29");
 keep usubjid visit vestdtc d29;
 run;

 data adsl_adis_vis;
    merge adsl_adis_vis ve;
	by usubjid;
	run;

data adsl_adis_vis;
length DOSE2FL $1;
   set adsl_adis_vis;
        VISITTPT =_VISITTPT;
  VISITTPTN =_VISITTPTN;

  if ^missing(bind) or ^missing(neut) then DVISFL="N";
  else DVISFL="Y";
/*if VISITTPTN <=5 then DOSE2FL="NA";*/
 

/*
Refer to ADSL for DOSE2DT and TR01SDT for derivation:  
 
for subjects who don't have record in VE where VE.VISIT contains 'Day 29', use the following window for Day 29: 
"Y" if ADSL.DOSE2DT is >=ADSL.TR01SDT+25 and <=ADSL.TR01SDT+35; 
for subjects who have record in VE where VE.VISIT contains 'Day 29', use the following window for Day 29: 
"Y" if ADSL.DOSE2DT is >=ADSL.TR01SDT+25 and <=ADSL.TR01SDT+49 (-3/+21);
"N" otherwise
(2nd vaccination should be 29 + 7/- 3 days after the first vaccination);
*/
 
if missing(d29) and DOSE2DT ge TR01SDT+25 and DOSE2DT le TR01SDT+35 then PDOS2WFL="Y";
else if ^missing(d29) and DOSE2DT ge TR01SDT+25 and DOSE2DT le TR01SDT+49 then PDOS2WFL="Y";
else PDOS2WFL="N";

 /*
 if VISITTPTN <=5 then PDOS2WFL="NA";
 else if DOSE2DT >=TR01SDT+25 and DOSE2DT<=TR01SDT+35 then PDOS2WFL="Y";
 else PDOS2WFL="N";
 */
 if /*indexc(ISSTRESC ,"0123456789") gt 0  and  ISCAT='Serum SARS-CoV-2 Binding Antibodies'*/ ^missing(bind) then PBABISFL="Y";
 else  PBABISFL="N";


  if /*indexc(ISSTRESC ,"0123456789") gt 0 and  ISCAT='Serum SARS-CoV-2 Neutralizing Antibodies'*/ ^missing(neut)  then PNABISFL="Y";
 else  PNABISFL="N";

/*if visitdy=1*/
/*ady=visitdy;*/ /*remove later*/

 /*if ^missing(bind) and AVISIT="Baseline" then bind_dy=1;  
 if ^missing(neut) and AVISIT="Baseline" then neut_dy=1;*/ 


 
if nmiss(bind_dt,DOSE2DT)=0 then spadt_b=bind_dt-DOSE2DT+1;
if nmiss(neut_dt,DOSE2DT)=0 then spadt_n=neut_dt-DOSE2DT+1;

if /*ISCAT='Serum SARS-CoV-2 Binding Antibodies'*/ ^missing(bind_dy) and ^missing(avisit) then do;
	if AVISIT="Baseline" and bind_dy=1 then PBABISW="Y";
	else if  AVISIT="Day 15" and 12 <= bind_dy<= 18 then PBABISW="Y" ; 
	else if AVISIT="Day 29" and missing(d29) and 26 <= bind_dy <= 36  then PBABISW="Y";
	else if AVISIT="Day 29" and ^missing(d29) and 26 <= bind_dy <= 50  then PBABISW="Y";


	else if  AVISIT="Day 43"  and ^missing(spadt_b) and   12 <= spadt_b<= 18  then PBABISW="Y";
	else if   AVISIT="Day 57" and ^missing(spadt_b) and   26 <=spadt_b <= 36 then PBABISW="Y";
	else if   AVISIT="Day 209"  and ^missing(spadt_b)  and   167 <=spadt_b <= 195 then PBABISW="Y";
	else if AVISIT="Day 394"  and ^missing(spadt_b)  and 352 <=spadt_b <= 380 then PBABISW="Y";
	else PBABISW="N";

	if cov19bl ne 'Detected' and bind_dt>=mbdt>.  then POSCOVFL='Y';
end;
 

if /*ISCAT='Serum SARS-CoV-2 Binding Antibodies'*/ ^missing(neut_dy) then do;
		if AVISIT="Baseline" and neut_dy=1 then PNABISW="Y";
		else if  AVISIT="Day 15" and 12 <= neut_dy<= 18 then PNABISW="Y" ;
		else if AVISIT="Day 29" and missing(d29) and 26 <= neut_dy <= 36  then PNABISW="Y";
		else if AVISIT="Day 29" and ^missing(d29) and 26 <= neut_dy <= 50  then PNABISW="Y";
		else if  AVISIT="Day 43"  and ^missing(spadt_n)  and /*40 <= bind_dy <= 46*/ 12 <= spadt_n <= 18  then PNABISW="Y";
		else if   AVISIT="Day 57"  and ^missing(spadt_n)  and /*54 <= bind_dy <= 64*/ 26 <=spadt_n<= 36 then PNABISW="Y";
		else if   AVISIT="Day 209"  and ^missing(spadt_n)  and /*195 <= bind_dy <= 223*/ 167 <= spadt_n<= 195 then PNABISW="Y";
		else if AVISIT="Day 394"  and ^missing(spadt_n)  and /*380 <= bind_dy <= 408*/ 352 <= spadt_n<= 380 then PNABISW="Y";
		else PNABISW="N";

		if cov19bl ne 'Detected' and neut_dt>=mbdt>.  then POSCOVFL='Y';
end;



if missing(PNABISW) then PNABISW="N";
if missing(PBABISW)  then PBABISW="N";
if missing(POSCOVFL) and (neut_dt>. OR bind_dt>.) then POSCOVFL="N";

 keep   /*NABISW PBABISW  DOSE2DT bind_dy neut_dy avisit spadt_n spadt_b mbdt bind_dt neut_dt*/
 PNABISW
 PBABISW
FASBABFL
FASNABFL


PNABISFL
 PBABISFL
  


PDOS2WFL
DOSE2FL PDOS2WFL
USUBJID
SUBJID
COHORT
 VISITTPT 
 VISITTPTN 
DVISFL
IEFL
COV19BL
DOSE1FL
avisit bind_dy neut_dy
POSCOVFL
sentlfl

;


run;


proc sort data= adsl_adis_vis (rename=(poscovfl=poscovfl_));
by usubjid visittptn;
run;

data adsl_adis_vis;
set adsl_adis_vis;
retain poscovfl;
if poscovfl_ ne '' then poscovfl=poscovfl_;
run;



proc sort data=dv out=dv1(keep=usubjid sevdes spectpt);
	by usubjid sevdes spectpt; 
	where sevdes in ('3 - Exclude from per-protocol analysis set only'
					 '4 - Exclude from bAb per-protocol analysis set only' 
					 '5 - Exclude from nAb per-protocol analysis set only');
run;

data dv2; 
	set dv1; 
	if index(spectpt,'Baseline')>0 then tptn = 1; 
	if index(spectpt,'Day 15')>0 then tptn = 4;
	if index(spectpt,'Day 29')>0 then tptn = 5; 
	if index(spectpt,'Day 43')>0 then tptn = 7; 
	if index(spectpt,'Day 57')>0 then tptn = 8; 
	if index(spectpt,'Day 209')>0 then tptn = 9; 
	if index(spectpt,'Day 394')>0 then tptn = 10; 
	if index(spectpt, 'Exclude from all visits') then tptn = 99;

	if index(upcase(spectpt),'AFTER VISIT DAY 15')>0 then tptn = 4.01;
	if index(upcase(spectpt),'AFTER VISIT DAY 29')>0 then tptn = 5.01; 
	if index(upcase(spectpt),'AFTER VISIT DAY 43')>0 then tptn = 7.01; 
	if index(upcase(spectpt),'AFTER VISIT DAY 57')>0 then tptn = 8.01; 
	if index(upcase(spectpt),'AFTER VISIT DAY 209')>0 then tptn = 9.01; 
	if index(upcase(spectpt),'AFTER VISIT DAY 394')>0 then tptn = 10.01;
run;

**EXCLUSION FROM bAb DUE TO STUDY DEVIATIONS;

proc transpose data=dv2 out=babdv(drop=_name_) prefix=babtpt;
	where sevdes in ('3 - Exclude from per-protocol analysis set only'
					 '4 - Exclude from bAb per-protocol analysis set only');
	by usubjid;
	var tptn;
run;


data adsl_adis_vis;
     merge  adsl_adis_vis(in=inm)  babdv;
	 by usubjid;
	 array babdv babtpt:;
	  do i = 1 to dim(babdv);
	    if babdv(i) ne . and index(put(babdv(i), best.),'.')>0 then do; 
		  if VISITTPTN > input(scan(put(babdv(i), best.),2,'.'), best.) then PBABPDFL = "Y";
		end;
	    else if babdv(i)=99 then PBABPDFL = 'Y'; 
		else if babdv(i)=VISITTPTN then PBABPDFL = 'Y';

		if PBABPDFL = "" then PBABPDFL = "N";
		*else PBABPDFL = 'N';
	  end;
run;

**EXCLUSION FROM nAb DUE TO STUDY DEVIATIONS;

proc transpose data=dv2 out=nabdv(drop=_name_) prefix=nabtpt;
	where sevdes in ('3 - Exclude from per-protocol analysis set only'
					 '5 - Exclude from nAb per-protocol analysis set only');
	by usubjid;
	var tptn;
run;

data adsl_adis_vis;
     merge  adsl_adis_vis(in=inm)  nabdv;
	 by usubjid;
	 array nabdv nabtpt:;
	  do j = 1 to dim(nabdv);
	    if nabdv(j) ne . and index(put(nabdv(j), best.),'.')>0 then do; 
		  if VISITTPTN > input(scan(put(nabdv(j), best.),2,'.'), best.) then PNABPDFL = "Y";
		end;
	    else if nabdv(j)=99 then PNABPDFL = 'Y'; 
		else if nabdv(j)=VISITTPTN then PNABPDFL = 'Y';

		if PNABPDFL = "" then PNABPDFL = "N";
		*else PNABPDFL = 'N';
	  end;
run;



proc sort data=adsl_adis_vis;
    by usubjid avisit;
run;
/**/
/*data adsl_adis_vis;*/
/*     merge  adsl_adis_vis(in=inm) PBABPDFL PNABPDFL;*/
/*	 by usubjid avisit;*/
/*	  if inm;*/
/*run;*/
/**/
data adsl_adis_vis;
 set adsl_adis_vis;
 if missing(PBABPDFL) then PBABPDFL="N";
 if missing(PNABPDFL) then PNABPDFL="N";
run;



data _PBABISFL_;
  set adsl_adis_vis;
    if  PBABISFL="Y" then _PBABISFL_="Y";
    else _PBABISFL_="N";

       keep usubjid _PBABISFL_ avisit /*iefl PBABPDFL*/;
  run;

  proc sort data= _PBABISFL_;
     by usubjid avisit _PBABISFL_;
	 run;

	 data _PBABISFL_;
	    set _PBABISFL_;
	     by usubjid avisit _PBABISFL_;
          if last._PBABISFL_;
	 run;


	 proc sort data=adsl_adis_vis;
            by usubjid  avisit;
	 run;

data adsl_adis_vis;
   merge  adsl_adis_vis _PBABISFL_;
    by usubjid  avisit;
run;

data adsl_adis_vis;
  set adsl_adis_vis;
    if /*IEFL="Y" and*/ DOSE1FL="Y" and DOSE2FL="Y" and PDOS2WFL="Y" and PBABISW="Y" and FASBABFL="Y" and PBABPDFL="N" and COV19BL ne "Detected" and POSCOVFL ne 'Y' then PVSBABFL="Y";
	else  PVSBABFL="N";
run;
 


data _PNABISFL_;
  set adsl_adis_vis;
    if  PNABISFL="Y" then _PNABISFL_="Y";
    else _PNABISFL_="N";

       keep usubjid _PNABISFL_ avisit /*iefl PNABPDFL*/;
  run;

  proc sort data= _PNABISFL_;
     by usubjid avisit _PNABISFL_;
	 run;


	 data _PNABISFL_;
	    set _PNABISFL_;
	     by usubjid avisit _PNABISFL_;
          if last._PNABISFL_;
	 run;

 proc sort data=adsl_adis_vis;
            by usubjid  avisit;
	 run;
	 proc sort data=_PNABISFL_;
               by usubjid avisit;
	 run;

data adsl_adis_vis;
   merge  adsl_adis_vis _PNABISFL_;
    by usubjid avisit;
run;

data adsl_adis_vis;;
  set adsl_adis_vis;;
  if /*IEFL="Y" and*/ DOSE1FL="Y" and DOSE2FL="Y" and PDOS2WFL="Y" and _PNABISFL_="Y" and PNABISW="Y" and FASNABFL="Y" and PNABPDFL="N" and COV19BL ne "Detected" and POSCOVFL ne 'Y' then PVSNABFL="Y";
  else PVSNABFL="N";

  run;

 

	proc sql;
        create table PB_flag as 
		    select distinct usubjid, count(distinct PVSBABFL) as cnt_PVSBABFL,PVSBABFL as PVSBABFL_u,avisit
			   from adsl_adis_vis
			     group by usubjid,avisit;
				 quit;


data PB_flag;
   set PB_flag;
    if  cnt_PVSBABFL=1 and PVSBABFL_u="N";
	keep usubjid avisit PVSBABFL_u;
run;
				 	proc sql;
        create table PN_flag as 
		    select distinct usubjid, count(distinct PVSNABFL) as cnt_PVSNABFL, PVSNABFL as PVSNABFL_u,avisit
			   from adsl_adis_vis
			     group by usubjid,avisit;
				 quit;

				 data PN_flag;
                   set PN_flag;
				     if cnt_PVSNABFL=1 and  PVSNABFL_u="N";
					 keep usubjid PVSNABFL_u avisit;
				 run;


data adsl_adis_vis;
  merge adsl_adis_vis PB_flag PN_flag;
  by usubjid avisit;
  run;



  data adsl_adis_vis;
     set adsl_adis_vis;
	 length r34 r56 PBABREAS PNABREAS  $200;
    if PVSBABFL_u="N" then do;
        *if IEFL="N" then reason1="Did not meet all eligibility criteria";
		if DOSE1FL="N" then  reason2="Did not receive Vaccination #1";
			if DOSE2FL="N" then  reason3="Did not receive Vaccination #2";
            if PDOS2WFL="N" then reason4="Vaccination #2 out of window"; 
			if _PBABISFL_="N"  then reason5="There was no immunogenicity result at corresponding visit";
			if PBABISW="N"  then reason6="Serum collection out of window";
			if FASBABFL="N" then reason7="Not in Full Analysis Set";
			if PBABPDFL="Y"  then  reason8="Other study deviation"; 
			if COV19BL ="Detected" then reason9="COVID-19 infection at baseline";
			if POSCOVFL='Y' then reason10="Post-baseline COVID-19 infection prior to the visit";
		
			r34=coalescec(reason3,reason4);
            r56=coalescec(reason5,reason6);   
/*               PBABREAS=catx("; ",reason1,reason2,r34,r56,reason7,reason8,reason9, reason10);*/
			PBABREAS=catx("; ",reason2,r34,r56,reason7,reason8,reason9, reason10);

	end;

    


    if PVSNABFL_u="N" then do;
            *if IEFL="N" then reason1_="Did not meet all eligibility criteria";
		    if DOSE1FL="N" then  reason2_="Did not receive Vaccination #1";
			if DOSE2FL="N" then  reason3_="Did not receive Vaccination #2";
            if PDOS2WFL="N" then reason4_="Vaccination #2 out of window"; 
			if _PNABISFL_="N"  then reason5_="There was no immunogenicity result at corresponding visit";
			if PNABISW="N"  then reason6_="Serum collection out of window";
			if FASNABFL="N" then reason7_="Not in Full Analysis Set";
			if PNABPDFL="Y"  then  reason8_="Other study deviation"; 
			if  COV19BL ="Detected" then reason9_="COVID-19 infection at baseline";
			if POSCOVFL='Y' then reason10_="Post-baseline COVID-19 infection prior to the visit";

			r34_=coalescec(reason3_,reason4_);
            r56_=coalescec(reason5_,reason6_);   
/*            PNABREAS=catx("; ",reason1_,reason2_,r34_,r56_,reason7_,reason8_,reason9_, reason10_);*/
            PNABREAS=catx("; ",reason2_,r34_,r56_,reason7_,reason8_,reason9_, reason10_);

	end;

   run;
 
 

  /* data z;
    set adsl_adis_vis; 
	if usubjid in ("mRNA-1273-P201-US201-1007");

keep  r: PVSNABFL_u PVSBABFL_u IEFL DOSE1FL DOSE2FL PDOS2WFL _PNABISFL_ PNABISW FASNABFL PNABPDFL COV19BL PNABREAS;
   run;*/

 data adsl_adis_vis;
    set adsl_adis_vis (rename=(sentlfl=sentl));
	length sentlfl $1;
  	sentlfl=sentl;
	drop sentl;
run;

proc sort data=adsl_adis_vis;
   by usubjid VISITTPTN;
run;

data templt;
  	attrib
USUBJID  label="Usubjid" length=$25
SUBJID  label="Subjid"  length=$9
 	
COHORT	label ="Cohort" length =$48
SENTLFL label="Sentinel Participant Flag" length=$1
VISITTPT label="Visit Timepoint"	length =$50
VISITTPTN  label="Visit Timepoint (N)"
DVISFL	label="Dummy Visit Flag"	length =$1
IEFL label="Meet all eligibility criteria"	length= $1
COV19BL	label="Baseline COVID Infection"	length= $20
DOSE1FL	label="Received Vaccination #1"	length= $1
DOSE2FL	label="Received Vaccination #2" length=	$1
PDOS2WFL label="Vaccination #2 within window"	length= $1
POSCOVFL label="Post-baseline COVID Infection" length= $1
PBABISFL label="bAb result (for at least 1 assay)" length=	$1
PNABISFL label="nAb result (for at least 1 assay)"	length= $1
PBABISW	label="Serum bAb collection within window"	length= $1
PNABISW	label ="Serum nAb collection within window" length=	$1
FASBABFL label="In bAb FAS" length=	$1
FASNABFL label="In nAb FAS"	length= $1
PBABPDFL label="Exclusion from bAb due to major PD" length=	$1
PNABPDFL label="Exclusion from nAb due to major PD"	length= $1
PVSBABFL label="bAb PP flag at each visit" length=	$1
PVSNABFL label="nAb PP flag at each visit" length=	$1
PBABREAS label="Reason exclusion from bAb PP"	length= $200
PNABREAS  label="Reason exclusion from nAb PP"	length =$200;

usubjid="";SUBJID="";COHORT="";SENTLFL="";VISITTPT="";VISITTPT="";VISITTPTN=.;DVISFL="";IEFL="";COV19BL="";DOSE1FL="";DOSE2FL="";
PDOS2WFL=""; POSCOVFL=""; PBABISFL="";PNABISFL="";PBABISW="";PNABISW="";FASBABFL="";FASNABFL="";PBABPDFL="";PVSBABFL="";PVSNABFL="";PBABREAS="";PNABREAS="";
PNABPDFL="";
run;


data final;
    set templt adsl_adis_vis;
	attrib
USUBJID  label="Unique Subject Identifier" length=$25
SUBJID  label="Subject Identifier for the Study"  length=$9
COHORT	label ="Cohort" length =$48
SENTLFL label="Sentinel Participant Flag" length=$1
VISITTPT label="Visit Timepoint"	length =$50
VISITTPTN  label="Visit Timepoint (N)"
DVISFL	label="Dummy Visit Flag"	length =$1
IEFL label="Meet all eligibility criteria"	length= $1
COV19BL	label="Baseline COVID Infection"	length= $20
DOSE1FL	label="Received Vaccination #1"	length= $1
DOSE2FL	label="Received Vaccination #2" length=	$1
PDOS2WFL label="Vaccination #2 within window"	length= $1
POSCOVFL label="Post-baseline COVID Infection" length= $1
PBABISFL label="bAb result (for at least 1 assay)" length=	$1
PNABISFL label="nAb result (for at least 1 assay)"	length= $1
PBABISW	label="Serum bAb collection within window"	length= $1
PNABISW	label ="Serum nAb collection within window" length=	$1
FASBABFL label="In bAb FAS" length=	$1
FASNABFL label="In nAb FAS"	length= $1
PBABPDFL label="Exclusion from bAb due to major PD" length=	$1
PNABPDFL label="Exclusion from nAb due to major PD"	length= $1
PVSBABFL label="bAb PP flag at each visit" length=	$1
PVSNABFL label="nAb PP flag at each visit" length=	$1
PBABREAS label="Reason exclusion from bAb PP"	length= $200
PNABREAS  label="Reason exclusion from nAb PP"	length =$200;
/*
col1  label="Usubjid" length=$200
col2  label="Subjid"  length=$200
col3	label ="Cohort" length =$200
col4 label="Visit Timepoint"	length =$50
col5  label="Visit Timepoint (N)"
col6	label="Dummy Visit Flag"	length =$1
col7 label="Meet all eligibility criteria"	length= $1
col8	label="Baseline COVID Infection"	length= $20
col9	label="Received Vaccination #1"	length= $1
col10	label="Received Vaccination #2" length=	$2
col11 label="Vaccination #2 within window"	length= $2
col12 label="bAb result (for at least 1 assay)" length=	$1
col13 label="nAb result (for at least 1 assay)"	length= $1
col14	label="Serum bAb collection within window"	length= $1
col15	label ="Serum nAb collection within window" length=	$1
col16 label="In bAb FAS" length=	$1
col17 label="In nAb FAS"	length= $1
col18 label="Exclusion from bAb due to major deviations" length=	$1
col19 label="Exclusion from nAb due to major deviations"	length= $1
col20 label="bAb PP flag at each visit" length=	$1
col21 label="nAb PP flag at each visit" length=	$1
col22 label="Reason exclusion from bAb PP"	length= $200
col23  label="Reason exclusion from nAb PP"	length =$200;



col1=USUBJID; 
col2=SUBJID;
col3=COHORT;
col4=VISITTPT;
col5=VISITTPTN;
col6=DVISFL;
col7=IEFL;
col8=COV19BL;
col9=DOSE1FL;
col10=DOSE2FL;
col11=PDOS2WFL;
col12=PBABISFL;
col13=PNABISFL;
col14=PBABISW;
col15=PNABISW;
col16=FASBABFL;
col17=FASNABFL;
col18=PBABPDFL;
col19=PNABPDFL;
col20=PVSBABFL;
col21=PVSNABFL;
col22=PBABREAS;
col23=PNABREAS;
*/

keep /* col1--col23*/
USUBJID
SUBJID
COHORT
SENTLFL
VISITTPT
VISITTPTN
DVISFL
/*IEFL*/
COV19BL
DOSE1FL
DOSE2FL
PDOS2WFL
POSCOVFL
PBABISFL
PNABISFL
PBABISW
PNABISW
FASBABFL
FASNABFL
PBABPDFL
PNABPDFL
PVSBABFL
PVSNABFL
PBABREAS
PNABREAS
;
if missing(PBABPDFL) then PBABPDFL="N";
if missing(PNABPDFL)  then PNABPDFL="N";
if ^missing(usubjid);
run;

/*remove Day 15 for Day 57 IA*/
data final;
	set final;
	if visittpt ne 'Day 15';
run;
 
proc sort data=final out=Per_Protocol_Analysis/*(keep=COL1-COL23)*/ ;
	by USUBJID  VISITTPTN;
run;
data PP_Listing (label='Per Protocol Evaluation Listing');;
   set Per_Protocol_Analysis;
   run;

data output.PP_List(label='Per Protocol Evaluation Listing');
	set Per_Protocol_Analysis; 
	rename VISITTPTN=VISITPTN;
run;


data foot;
length usubjid $200;
usubjid='';
output;
usubjid='Note: Subjects who have dosing error will be additionally excluded at ADaM level';
output;
run;

data Per_Protocol_Analysis;
	length usubjid $200;
	set Per_Protocol_Analysis foot; 
run;

data _null_;
call symput('tdate', compress(put(today(), date9.)));
run;

%put tdate = &tdate;

** Output to EXCEL file ;
libname dmrpt "&g_fullpath";

%let footnote1 = Note: Subjects who have dosing error will be additionally excluded at ADaM level;

*****************************************************************************
*STEP 11: CALL THE PATIENTVIEW_TYPE_OUTPUT macro for outputting the report
*****************************************************************************;

%PatientView_Type_Output ( In_Data = output.pp_list, 
			   Out_File =Moderna mRNA1273P201 per-protocol analysis from the First Lot &tdate,  			    			  
                           Deliv_Type = E);