Document text
file:///J/.../m5/datasets/c4591001/analysis/adam/programs-6mth/125742-45_S211_M5_c4591001-A_6mth-P-adae-s130-sae-unb2-ped6-sas.txt[7/5/2023 10:22:56 AM]***********************************************************************************************;
** Program Name : adae-s130-sae-unb2-ped6.sas **;** Date Created : 15Nov2021 **;** Programmer Name :
**;
** Purpose : Create adae-s130-sae-unb2-ped6 **;
** Input data : adae adsl **;** Output data : adae-s130-sae-unb2-ped6.html **;***********************************************************************************************;options mprint mlogic symbolgen mprint symbolgen mlogic nocenter missing=" ";**Setup the environment**;%let bprot=/Volumes/app/cdars/prod/sites/cdars4/
prjC459/nda2_unblinded_esub/sbla1215_esub_adam/saseng/cdisc3_0/;
%let prot=/Volumes/app/cdars/prod/sites/cdars4/prjC459/nda2_unblinded_esub/sbla1215_esub_adam/saseng/cdisc3_0;libname datvprot "&bprot.data_vai" access=readonly;%let codename=adae-s130-sae-unb2-ped6;
%let outlog=&prot./analysis/eSUB/logs/&codename..log;
%let outtable=&prot./analysis/eSUB/output/&codename..html;
proc printto log="&outlog." new;
run;********************************************************************************;*SPECIFICATION 1 -1) gen_cdisc_suminit *;* 2) null table when analysis dataset is empty *;* 3) Set Default value to ToT parameters *;********************************************************************************;
data g_adsl_dsin;
set datvprot.adsl;
if trt01an=8 and agegr4n=1 then
trtarn=1; else if trt01an=8 and agegr4n=2 then trtarn=2; else if trt01an=9 and agegr4n=1 then trtarn=3; else if trt01an=9 and agegr4n=2 then trtarn=4; trtar=trt01a;
if trt01an eq 7 and agegr1n eq 3 then
trtarn2=1; else if trt01an eq 9 and agegr1n eq 3 then trtarn2=2; else if trt01an eq 7 and agegr1n eq 4 then trtarn2=3; else if trt01an eq 9 and agegr1n eq 4 then trtarn2=4; where saffl="Y" and agegr4n eq 1 and phasen in (2, 3, 4) and HIVFL ne "Y" and (VAX101DT ne . and BDCSRDT ne .) and (EOSDCDT gt input("13MAR2021", date9.) or EOSDCDT eq .);run;
(b) (4), (b)
(6)
FDA-CBER-2022-5812-0071626
file:///J/.../m5/datasets/c4591001/analysis/adam/programs-6mth/125742-45_S211_M5_c4591001-A_6mth-P-adae-s130-sae-unb2-ped6-sas.txt[7/5/2023 10:22:56 AM]data g_a_dsin;
set datvprot.adae;
if trt01an=8 and agegr4n=1 then
trtarn=1; else if trt01an=8 and agegr4n=2 then trtarn=2; else if trt01an=9 and agegr4n=1 then trtarn=3; else if trt01an=9 and agegr4n=2 then trtarn=4; trtar=trt01a;
if trt01an eq 7 and agegr1n eq 3 then
trtarn2=1; else if trt01an eq 9 and agegr1n eq 3 then trtarn2=2; else if trt01an eq 7 and agegr1n eq 4 then trtarn2=3; else if trt01an eq 9 and agegr1n eq 4 then trtarn2=4; analysis_subset='Y'; where DATCHGFL="Y" and AECAT='ADVERSE EVENT' and saffl="Y" and AESER='Y' and agegr4n eq 1 and PHASEN in (2, 3, 4) and vphasen>0 and .<VAX101DT<=ASTDT<=BDCSRDT and HIVFL ne "Y";run;
data g_adsl_dsin;
set g_adsl_dsin;
if TRT01AN in (8) then
do; newtrtn=1; newtrt=coalescec("BNT162b2 (30 (*ESC*){unicode 03BC}g)", TRT01A); output; end;
if TRT01AN in (9) then
do; newtrtn=2; newtrt=coalescec("Placebo", TRT01A); output; end;run;
data g_a_dsin;
set g_a_dsin;
if TRT01AN in (8) then
do; newtrtn=1; newtrt=coalescec("BNT162b2 (30 (*ESC*){unicode 03BC}g)", TRT01A); output;
end;
FDA-CBER-2022-5812-0071627
file:///J/.../m5/datasets/c4591001/analysis/adam/programs-6mth/125742-45_S211_M5_c4591001-A_6mth-P-adae-s130-sae-unb2-ped6-sas.txt[7/5/2023 10:22:56 AM] if TRT01AN in (9) then
do; newtrtn=2; newtrt=coalescec("Placebo", TRT01A); output; end;run;
********************************************************************************;
*SPECIFICATION 2 -1) determine the no of tiers from g_a_tiervar *;* 2) any uncoded terms set to uncoded||term label *;********************************************************************************;;
data g_a_dsin1;
set g_a_dsin; where ^missing(aeterm);
if missing(aedecod) then
aedecod=aeterm;
if missing(AEBODSYS) then
AEBODSYS='**Uncoded Terms Being Queried';
if missing(AEDECOD) then
AEDECOD='**Uncoded Terms Being Queried'; aebodsys=upcase(substr(aebodsys, 1, 1))||strip(upcase(substr(aebodsys, 2, (length(aebodsys)-1))));run;
********************************************************************************;
*SPECIFICATION 3 -1) Remove Duplicate observations from AE data. *;* 2) create flags _anyae _event to identify summary counts *;* for summary rows *;* 3) merge adsl and analysis dataset *;********************************************************************************;
proc sort data=g_a_dsin1 out=_a_dsin nodupkey;
by newtrtn usubjid aedecod astdt ATOXGR;run;
proc sort data=_a_dsin;
by newtrtn usubjid AEBODSYS AEDECOD;run;
data _a_dsin;
set _a_dsin; by newtrtn usubjid AEBODSYS AEDECOD;
if first.usubjid then
_anyae=1;
if aeterm ne '' then
FDA-CBER-2022-5812-0071628
file:///J/.../m5/datasets/c4591001/analysis/adam/programs-6mth/125742-45_S211_M5_c4591001-A_6mth-P-adae-s130-sae-unb2-ped6-sas.txt[7/5/2023 10:22:56 AM] _event=1;
_uniqid=_n_;
run;
proc sort data=g_adsl_dsin out=_ds1;
by usubjid newtrtn;run;
proc sort data=_a_dsin out=_ds2;
by usubjid newtrtn;run;
data final;
merge _ds1(in=d1) _ds2(in=d2); by usubjid newtrtn;
if d1;
run;
data final;
set final;
if nmiss(_anyae) then
_anyae=0;
if nmiss(_event) then
_event=0;run;
********************************************************************************;
*SPECIFICATION 4 -1) minitial - initialize isam *;* 2) mentry - setup bigN, treatment, by variables & subgroups *;* 3) apply PCTCUTOFF when G_A_PCTOFF not null *;********************************************************************************;
data _data1;
set final; where (NEWTRTN is not missing);run;
proc sql noprint;
select count(unique NEWTRTN) into :_trtn from _data1 where NEWTRTN is not missing;quit;
proc sort data=_data1;
by NEWTRTN USUBJID;run;
data _data1;
retain _trt 0; length _str $200; _datasrt=1;
set _data1 end=eof;
FDA-CBER-2022-5812-0071629
file:///J/.../m5/datasets/c4591001/analysis/adam/programs-6mth/125742-45_S211_M5_c4591001-A_6mth-P-adae-s130-sae-unb2-ped6-sas.txt[7/5/2023 10:22:56 AM] by NEWTRTN USUBJID;
drop _str;
_str=' '; _lastby=1; _dummyby=0;
if first.NEWTRTN then
do;
if not missing(NEWTRTN) then
do; _trt=_trt + 1; end; _str=NEWTRT;
if _trt > 0 then
call symput('_trtlb'||compress(put(_trt, 4.)), trim(left(_str))); end;run;
*----------------------------------------------------------------------;
* Count number of patients in each treatment. ;*----------------------------------------------------------------------;
proc sql noprint;
select compress(put(count(*), 5.) ) into :_trt1 - :_trt2 from (select distinct USUBJID, _trt from _data1 where NEWTRTN is not missing) group by _trt; select compress(put(count(*), 5.) ) into :_trt3 from (select distinct USUBJID from _data1 where NEWTRTN is not missing);quit;
*----------------------------------------------------------------------;
* Generate a dataset containing all by-variables ;*----------------------------------------------------------------------;
proc sort data=_data1 out=_bydat1(keep=_datasrt _dummyby) nodupkey;
by _datasrt;run;
proc sort data=_data1 out=_data1;
by _datasrt;run;
********************************************************************************;
*SPECIFICATION 5 -1) Any AE counts and percent *;********************************************************************************;
data _null_;
set _data1 end=eof;
if eof then
call symput('dptlab', vlabel(_ANYAE));run;
FDA-CBER-2022-5812-0071630
file:///J/.../m5/datasets/c4591001/analysis/adam/programs-6mth/125742-45_S211_M5_c4591001-A_6mth-P-adae-s130-sae-unb2-ped6-sas.txt[7/5/2023 10:22:56 AM]data _anal1;
length _ANYAE 8;
set _data1; where same and _ANYAE is not missing; _blcksrt=1; _cnt=1; _cat=1;
if _trt <=0 then
delete; output;run;
proc sort data=_anal1;
by _datasrt _blcksrt _ANYAE _trt _cat;run;
*--- Counts for each by-sequence, dependant var, and treatment combination ---*;data _temp1;
set _anal1; output;run;
proc sort data=_temp1 out=_temp91 nodupkey;
by _datasrt _blcksrt _cat _ANYAE _trt USUBJID; ;run;
proc freq data=_temp91;
format _ANYAE; tables _datasrt*_blcksrt*_cat * _ANYAE * _trt / sparse norow nocol nopercent out=_pct1(drop=percent);run;
proc sort data=_anal1 out=_denom1(keep=_datasrt _cat) nodupkey;
; by _datasrt _cat;run;
data _denom1;
set _denom1; by _datasrt _cat; label count='count'; _trt=1; count=&_TRT1.; output; _trt=2; count=&_TRT2.; output;run;
*----------------------------------------------------------------------;
* Create _DENOMF a frame dataset for the denominators ;
FDA-CBER-2022-5812-0071631
file:///J/.../m5/datasets/c4591001/analysis/adam/programs-6mth/125742-45_S211_M5_c4591001-A_6mth-P-adae-s130-sae-unb2-ped6-sas.txt[7/5/2023 10:22:56 AM]*----------------------------------------------------------------------;
data _denomf1;
_datasrt=1; set _bydat1(keep=); * All treatment groups ; _trt1=0; _trt2=0; * _CAT is the subgroup variable ; _cat=1; output;run;
*----------------------------------------------------------------------;
* Transpose _DENOM into _DENOMIN to get COUNT as _TRTn columns ;*----------------------------------------------------------------------;
proc transpose data=_denom1 out=_denomin1(drop=_name_ _label_) prefix=_trt;
by _datasrt _cat; var count; id _trt;run;
*----------------------------------------------------------------------;
* Create _FRAME dataset using all combinations of category variable ;*----------------------------------------------------------------------;
data _frame1;
_datasrt=1; set _bydat1(keep=); _blcksrt=1; length _ANYAE 8; _catLabl=" "; _trt=1; _ANYAE=1; _catord=1; _cat=1; output; _trt=2; _ANYAE=1; _catord=1; _cat=1; output;run;
*----------------------------------------------------------------------;
* Merge the _PCT dataset with its frameup dataset(_FRAME) ;*----------------------------------------------------------------------;
proc sort data=_frame1;
by _datasrt _blcksrt _cat _ANYAE _trt;run;
proc sort data=_pct1;
FDA-CBER-2022-5812-0071632
file:///J/.../m5/datasets/c4591001/analysis/adam/programs-6mth/125742-45_S211_M5_c4591001-A_6mth-P-adae-s130-sae-unb2-ped6-sas.txt[7/5/2023 10:22:56 AM] by _datasrt _blcksrt _cat _ANYAE _trt;
run;
data _pct1;
merge _frame1(in=_inframe) _pct1; by _datasrt _blcksrt _cat _ANYAE _trt;
if _inframe; if count=. then
count=0;run;
*----------------------------------------------------------------------;
* Delete Zero filled MISSING category rows for each combination of;* _datasrt &_byvar _blcksrt;*----------------------------------------------------------------------;
proc sort data=_pct1;
by _datasrt _blcksrt _ANYAE;run;
data _miss1(keep=_datasrt _blcksrt _ANYAE totcount);
set _pct1; where _ANYAE=9998; retain totcount; by _datasrt _blcksrt _ANYAE;
if first._ANYAE then
totcount=0; totcount=totcount+count;
if last._ANYAE;
run;
data _pct1(drop=totcount);
merge _pct1 _miss1; by _datasrt _blcksrt _ANYAE;
if totcount=0 then
delete;run;
*******************************************************************;
*IF PCTDISP=CAT/DPTVAR then add dptvar into denomitor frame dataset;*******************************************************************;*----------------------------------------------------------------------;* Merge the _DENOMIN with its frame up dataset (_denomf) ;*----------------------------------------------------------------------;
proc sort data=_denomf1;
by _datasrt _cat;run;
FDA-CBER-2022-5812-0071633
file:///J/.../m5/datasets/c4591001/analysis/adam/programs-6mth/125742-45_S211_M5_c4591001-A_6mth-P-adae-s130-sae-unb2-ped6-sas.txt[7/5/2023 10:22:56 AM]proc sort data=_denomin1;
by _datasrt _cat;
run;
data _denomin1;
merge _denomf1(in=_inframe) _denomin1; by _datasrt _cat;
if _inframe;
_blcksrt=1;run;
*----------------------------------------------------------------------;
* Merge in _PCT(counts) with the _DENOMIN(denominator for percents) ;*----------------------------------------------------------------------;
proc sort data=_pct1;
by _datasrt _cat;run;
*----------------------------------------------------------------------;
* Create _VARNAME variable to hold depend variable name. ;* Create _VRLABEL variable to display Group label. ;* Create _RWLABEL variable to display &dptvar categories. ;*----------------------------------------------------------------------;
data _pct1;
merge _denomin1(in=_a) _pct1; by _datasrt _cat;
if _a;
_varname="_ANYAE "; _vrlabel=" "; _rwlabel="Any event ";
if _ANYAE=9998 then
do; _rwlabel="Missing "; _catord=9998; end; else if _ANYAE=9999 then do; _rwlabel="Total "; _catord=9999; end;
if _catord=. then
_catord=9997;run;
proc sort data=_pct1;
by _datasrt _blcksrt _catord _ANYAE _trt _cat;run;
FDA-CBER-2022-5812-0071634
file:///J/.../m5/datasets/c4591001/analysis/adam/programs-6mth/125742-45_S211_M5_c4591001-A_6mth-P-adae-s130-sae-unb2-ped6-sas.txt[7/5/2023 10:22:56 AM]*----------------------------------------------------------------------;
* Create _CVALUE variable to display results. ;
* Create _ROWSRT variable to order results. ;*----------------------------------------------------------------------;
data _base1;
length _catlabl $200 _cvalue $30.; set _pct1 end=eof; by _datasrt _blcksrt _catord _ANYAE _trt _cat; retain _rowsrt 0 _rowmax 0; array _trtcnt(*) _trt1-_trt3; drop _rowmax _cpct; length _cpct $100; _cpct=' '; _module='mcatstat';
if count > . then
_cvalue=put(count, 5.); else _cvalue=put(0, 5.); *----------------------------------------------------------------------; * Format percent to append to display value in _CVALUE ; *----------------------------------------------------------------------;
if _trt ne . then
do;
if _trtcnt(_trt) > 0 then
do; percent=count / _trtcnt(_trt) * 100;
if percent > 0 then
do;
if round(percent, 0.1) GE 0.1 then
_cpct="(*ESC*){nbspace 1}("||strip(put(percent, 5.1))||")"; else _cpct="(*ESC*){nbspace 1}(0.0)"; _cvalue=trim(_cvalue)||_cpct; end; end; end;
/* if length(_cvalue) < 13 then */
/* do; */ *----------------------------------------------------------------------; * Put character A0x at right most character to pad text; *----------------------------------------------------------------------;/* substr(_cvalue, 13, 1)='A0'x; *//* end; */
if first._ANYAE then
do;
_rowsrt=_rowsrt + 1;
FDA-CBER-2022-5812-0071635
file:///J/.../m5/datasets/c4591001/analysis/adam/programs-6mth/125742-45_S211_M5_c4591001-A_6mth-P-adae-s130-sae-unb2-ped6-sas.txt[7/5/2023 10:22:56 AM] _rowmax=max(_rowsrt, _rowmax);
end;
_datatyp='data'; _indent=0; _dptindt=0; _vorder=1; _rowjump=1;
if upcase(_rwlabel)='_NONE_' then
_rwlabel=' '; _indent=0; _dptindt=0;
if _trt=2 +1 then
_trt=9999;
if eof then
call symput('_rowsrt', compress(put(_rowmax, 4.))); _direct="TOP "; _p=2;run;
********************************************************************************;
*SPECIFICATION 5.1 - *;* 1) if user requested to calculate Observed proportion using Clopper & *;* Pearson method then call macro cnp_obsprop. *;********************************************************************************;***hup02 modified to correct CI;
data _cnp _tmp_cnp;
set _base1;
if count=. then
count=0; indc=1; output _cnp; indc=2; count=input(compress(symget('_trt'||compress(put(_trt, 8.)))), 8.) - count; output _cnp;
if indc=2 and count=0 then
output _tmp_cnp;run;
proc sort data=_cnp;
by _cat _rowsrt _rwlabel _trt;run;
proc sort nodupkey data=_tmp_cnp(keep=_cat _rowsrt _rwlabel _trt);
by _cat _rowsrt _rwlabel _trt;run;
proc freq data=_cnp noprint;
by _cat _rowsrt _rwlabel _trt;
FDA-CBER-2022-5812-0071636
file:///J/.../m5/datasets/c4591001/analysis/adam/programs-6mth/125742-45_S211_M5_c4591001-A_6mth-P-adae-s130-sae-unb2-ped6-sas.txt[7/5/2023 10:22:56 AM] table indc/binomial alpha=0.05;
output out=obsprop binomial;
weight count;run;
data obsprop;
merge obsprop _tmp_cnp(in=a); by _cat _rowsrt _rwlabel _trt;
if _bin_=1 and not a then
do; xl_bin_=1 - xu_bin; xu_bin_=1 - xl_bin; end; else do; xl_bin_=xl_bin; xu_bin_=xu_bin; end;run;
data cnpobsprop1(keep=_cat _rowsrt _rwlabel _trt cnp_ci);
set obsprop; by _cat _rowsrt _rwlabel _trt; cnp_ci='(' || compress(put(xl_bin_ * 100, 5.1)) || ',(*ESC*){nbspace 1}' || compress(put(xu_bin_ * 100, 5.1)) || ')'; label cnp_ci='95% CI';run;
proc datasets lib=work nolist gennum=all;
delete _cnp obsprop; run; ;
proc sort data=_base1;
by _cat _rowsrt _rwlabel _trt;run;
proc sort data=cnpobsprop1;
by _cat _rowsrt _rwlabel _trt;run;
data _base1;
length _varname $8 _vrlabel $200 _direct $20 _module $8 _rwlabel $800; ; merge _base1(in=a) cnpobsprop1; by _cat _rowsrt _rwlabel _trt;
if a;
run;
********************************************************************************;
*SPECIFICATION 6 -1) G_A_TIERVAR - counts and percent *;
********************************************************************************;
FDA-CBER-2022-5812-0071637
file:///J/.../m5/datasets/c4591001/analysis/adam/programs-6mth/125742-45_S211_M5_c4591001-A_6mth-P-adae-s130-sae-unb2-ped6-sas.txt[7/5/2023 10:22:56 AM]proc transpose data=_data1 name=name out=lvlvars;
var AEBODSYS AEDECOD;run;
data _dsin;
set _data1; output;run;
data dsin;
set _dsin; _cat=1; output;run;
data frame;
set _bydat1(keep=); _cat=1; _trt=1; output; _cat=1; _trt=2; output;run;
proc sort data=frame;
by _cat _trt;run;
*******************************************************************************;
* SPECIFICATION 4 -1) denominator dataset and denominator variables *;* 2) TRTN is N by treatment *;* 3) SUBGRPN is N by treatment, by variables & subgroup or *;* N by treatment and subgroup when PCTDISP=SGRPN *;*******************************************************************************;
data denom(drop=_col) temp;
_trt=1; trtn=input(symget(cats('_trt', _trt)), best.); _cat=1; subgrpn=trtn; output denom; _col=_trt; output temp; _trt=2; trtn=input(symget(cats('_trt', _trt)), best.); _cat=1; subgrpn=trtn; output denom; _col=_trt; output temp;run;
FDA-CBER-2022-5812-0071638
file:///J/.../m5/datasets/c4591001/analysis/adam/programs-6mth/125742-45_S211_M5_c4591001-A_6mth-P-adae-s130-sae-unb2-ped6-sas.txt[7/5/2023 10:22:56 AM]*******************************************************************************;
* SPECIFICATION 5 -1) create _COL that reflect report column number *;
* 2) Call %util_num_obs and if no. of obs <=0 then exit *;* out of macro. *;* 3) reinitialize _rowsrt and _blcksrt based on joinyn *;*******************************************************************************;
proc sql noprint;
create table numin as select a.*, b._col from dsin as a left join temp as b on a._trt=b._trt;quit;
data numin;
set numin; where aeterm is not missing;run;
*******************************************************************************;
* SPECIFICATION 6 -1) compute n by tier variables *;* 2) setup sorting either by ALPHA/FREQ based on dptsort *;*******************************************************************************;
data _null_;
set lvlvars end=eof; length cclass cclasst $200; retain cclass cclasst; cclass=catx(' ', cclass, name); cclasst=catx(' ', cclasst, cats(name, '_n')); call symputx(cats('_cclass', _n_), cclass);
if eof then
do; call symputx('_cclasst', cclasst); end;run;
proc sort data=numin out=class1(keep=AEBODSYS) nodupkey;
by AEBODSYS;run;
data classo1;
set frame;
do i=1 to cobs;
set class1 nobs=cobs point=i; output; end;run;
proc sort data=numin out=level1 NODUPKEY;
by _cat _trt AEBODSYS usubjid;run;
proc summary data=level1 nway classdata=classo1 missing;
FDA-CBER-2022-5812-0071639
file:///J/.../m5/datasets/c4591001/analysis/adam/programs-6mth/125742-45_S211_M5_c4591001-A_6mth-P-adae-s130-sae-unb2-ped6-sas.txt[7/5/2023 10:22:56 AM] class _cat _trt AEBODSYS;
output out=count1(drop=_type_ rename=(_freq_=count));
run;
data sort1;
set class1; AEBODSYS_n=_n_;run;
proc sort data=count1;
by AEBODSYS;run;
proc sort data=sort1 out=sorto1(keep=AEBODSYS AEBODSYS_n);
by AEBODSYS;run;
data countf1;
length _rwlabel $800; merge count1 sorto1; by AEBODSYS; _level=1;/* _rwlabel=ifc(1>1, repeat(byte(160), 0)||AEBODSYS, AEBODSYS); */ _rwlabel=ifc(1>1, repeat('~{nbspace 1}', 0)||AEBODSYS, AEBODSYS);run;
proc sort data=numin out=class2(keep=AEBODSYS AEDECOD) nodupkey;
by AEBODSYS AEDECOD;run;
data classo2;
set frame;
do i=1 to cobs;
set class2 nobs=cobs point=i; output; end;run;
proc sort data=numin out=level2 NODUPKEY;
by _cat _trt AEBODSYS AEDECOD usubjid;run;
proc summary data=level2 nway classdata=classo2 missing;
class _cat _trt AEBODSYS AEDECOD; output out=count2(drop=_type_ rename=(_freq_=count));run;
proc sort data=level2 out=flevel2 nodupkey;
by AEBODSYS AEDECOD usubjid; ;run;
proc summary data=flevel2 nway classdata=class2 missing;
FDA-CBER-2022-5812-0071640
file:///J/.../m5/datasets/c4591001/analysis/adam/programs-6mth/125742-45_S211_M5_c4591001-A_6mth-P-adae-s130-sae-unb2-ped6-sas.txt[7/5/2023 10:22:56 AM] class AEBODSYS AEDECOD;
output out=fcount2(drop=_type_ rename=(_freq_=count));
run;
proc sort data=fcount2 out=freq2(keep=AEBODSYS AEDECOD count);
by descending count AEBODSYS AEDECOD;run;
data sort2;
set freq2; AEDECOD_n=_n_;run;
proc sort data=count2;
by AEBODSYS AEDECOD;run;
proc sort data=sort2 out=sorto2(keep=AEBODSYS AEDECOD AEDECOD_n);
by AEBODSYS AEDECOD;run;
data countf2;
length _rwlabel $800; merge count2 sorto2; by AEBODSYS AEDECOD; _level=2;/* _rwlabel=ifc(2>1, repeat(byte(160), 5)||AEDECOD, AEDECOD); */ _rwlabel=ifc(2>1, repeat('~{nbspace 1}', 5)||AEDECOD, AEDECOD);run;
proc sort data=countf2;
by AEBODSYS;run;
data countf2;
merge countf2 sorto1; by AEBODSYS;run;
data alln;
set countf1 countf2;run;
*******************************************************************************;
* 1) gender specific denominator *;* 2) compute percents *;*******************************************************************************;
proc sort data=denom out=denomf(keep=_trt trtn) nodupkey;
by _trt;run;
proc sort data=alln out=alln;
by _trt;
FDA-CBER-2022-5812-0071641
file:///J/.../m5/datasets/c4591001/analysis/adam/programs-6mth/125742-45_S211_M5_c4591001-A_6mth-P-adae-s130-sae-unb2-ped6-sas.txt[7/5/2023 10:22:56 AM]run;
data final;
merge alln(in=a) denomf; by _trt;
if a;
length _cvalue $30;
if count > . then
_cvalue=put(count, 5.); else _cvalue=put(0, 5.);
if count > 0 and trtn > 0 then
do; pct=(count/trtn)*100; _cvalue=trim(_cvalue)||" ("||strip(put(pct, 5.1))||")"; end;
/* if length(_cvalue) < 13 then */
/* do; */ *-------------------------------------------------------------; * Put character A0x at right most character to pad text; *-------------------------------------------------------------;/* substr(_cvalue, 13, 1)='A0'x; *//* end; */
if _trt=3 then
_trt=9999; _p=2;run;
proc sort data=final;
by _cat _trt AEBODSYS_n AEDECOD_n;run;
data _base2;
set final; by _cat _trt AEBODSYS_n AEDECOD_n; length _varname $8 _vrlabel $200 _direct $20 _module $8;
if first._trt then
_rowsrt=0; _rowsrt++1; _varname=" "; _vrlabel=""; _vorder=1; _indent=coalesce(0, 0); _dptindt=coalesce(0, 0); _direct="TOP"; _rowjump=1; _datatyp='data';
_module="MCATSTAT";
FDA-CBER-2022-5812-0071642
file:///J/.../m5/datasets/c4591001/analysis/adam/programs-6mth/125742-45_S211_M5_c4591001-A_6mth-P-adae-s130-sae-unb2-ped6-sas.txt[7/5/2023 10:22:56 AM] _datasrt=1;
_blcksrt=1+ AEBODSYS_n;
if _indent+_dptindt > 0 then
/* _rwlabel=cats(repeat(byte(160), sum(_indent, _dptindt, 1)), _rwlabel); */ _rwlabel=cats(repeat('~{nbspace 1}', sum(_indent, _dptindt, 1)), _rwlabel);run;
proc sort data=_base2;
by _datasrt _blcksrt _rowsrt;run;
proc sort data=_base2 out=_dsnin1;
by _rowsrt _rwlabel; where ^missing(_rwlabel);run;
data _dsnin1 (keep=_rowsrt _rwlabel);
set _dsnin1; by _rowsrt _rwlabel;
if last._rwlabel;
run;
proc sort data=_dsnin1 out=_dsninx nodupkey dupout=_dupevent;
by _rwlabel;run;
proc datasets library=work;
delete _dupevent _dsninx _dsnin1;quit;
********************************************************************************;
*SPECIFICATION 6.1 - *;* 1) if user requested to calculate Observed proportion using Clopper & *;* Pearson method then call macro cnp_obsprop. *;********************************************************************************;***hup02 modified to correct CI;
data _cnp _tmp_cnp;
set _base2;
if count=. then
count=0; indc=1; output _cnp; indc=2; count=input(compress(symget('_trt'||compress(put(_trt, 8.)))), 8.) - count; output _cnp;
if indc=2 and count=0 then
output _tmp_cnp;run;
FDA-CBER-2022-5812-0071643
file:///J/.../m5/datasets/c4591001/analysis/adam/programs-6mth/125742-45_S211_M5_c4591001-A_6mth-P-adae-s130-sae-unb2-ped6-sas.txt[7/5/2023 10:22:56 AM]proc sort data=_cnp;
by _cat AEBODSYS AEDECOD _rowsrt _rwlabel _trt;
run;
proc sort nodupkey data=_tmp_cnp(keep=_cat AEBODSYS AEDECOD _rowsrt _rwlabel
_trt); by _cat AEBODSYS AEDECOD _rowsrt _rwlabel _trt;run;
proc freq data=_cnp noprint;
by _cat AEBODSYS AEDECOD _rowsrt _rwlabel _trt; table indc/binomial alpha=0.05; output out=obsprop binomial; weight count;run;
data obsprop;
merge obsprop _tmp_cnp(in=a); by _cat AEBODSYS AEDECOD _rowsrt _rwlabel _trt;
if _bin_=1 and not a then
do; xl_bin_=1 - xu_bin; xu_bin_=1 - xl_bin; end; else do; xl_bin_=xl_bin; xu_bin_=xu_bin; end;run;
data cnpobsprop2(keep=_cat AEBODSYS AEDECOD _rowsrt _rwlabel _trt cnp_ci);
set obsprop; by _cat AEBODSYS AEDECOD _rowsrt _rwlabel _trt; cnp_ci='(' || compress(put(xl_bin_ * 100, 5.1)) || ',(*ESC*){nbspace 1}' || compress(put(xu_bin_ * 100, 5.1)) || ')'; label cnp_ci='95% CI';run;
proc datasets lib=work nolist gennum=all;
delete _cnp obsprop; run; ;
proc sort data=_base2;
by _cat AEBODSYS AEDECOD _rowsrt _rwlabel _trt;run;
proc sort data=cnpobsprop2;
by _cat AEBODSYS AEDECOD _rowsrt _rwlabel _trt;run;
data _base2;
FDA-CBER-2022-5812-0071644
file:///J/.../m5/datasets/c4591001/analysis/adam/programs-6mth/125742-45_S211_M5_c4591001-A_6mth-P-adae-s130-sae-unb2-ped6-sas.txt[7/5/2023 10:22:56 AM] merge _base2(in=a) cnpobsprop2;
by _cat AEBODSYS AEDECOD _rowsrt _rwlabel _trt;
if a;
run;
********************************************************************************;
*SPECIFICATION 12 -1) titles and footnotes *;* 2) display *;********************************************************************************;
data _final;
set _base1 _base2;run;
proc sort data=_final;
by _datasrt _blcksrt _rowsrt;run;
data ADAE_S130_SAE_UNB2_PED6;
length _rvalue $200; set _final end=eof; _rwindt=sum(_indent, _dptindt);
if _rwindt <=0 then
_rvalue=_rwlabel; else/* _rvalue=repeat(byte(160), _rwindt-1)||_rwlabel; */ _rvalue=repeat('~{nbspace 1}', _rwindt-1)||_rwlabel; _dummy=1;
if _trt=. then
_trt=1;run;
proc sort data=ADAE_S130_SAE_UNB2_PED6;
by _datasrt _trt _blcksrt _rowsrt;run;
data treat;
length FMTNAME $8 start 8 label $200; fmtname='TREAT';
do start=1 to 2 + ("N"="Y");
label=symget('_TRTLB'|| compress(put(start, 4.))); label=trim(label) || "| (N(*ESC*){super a}=" || compress(symget("_TRT" || compress(put(start, 4.)))) || ")"; output; end;run;
proc format cntlin=treat;
run;
FDA-CBER-2022-5812-0071645
file:///J/.../m5/datasets/c4591001/analysis/adam/programs-6mth/125742-45_S211_M5_c4591001-A_6mth-P-adae-s130-sae-unb2-ped6-sas.txt[7/5/2023 10:22:56 AM]data report;
set ADAE_S130_SAE_UNB2_PED6;
if _trt=9999 then
_trt=2 +1; _rvalue=tranwrd(_rvalue, "|", '036e'x);run;
proc sort data=report;
by _datasrt _blcksrt _rowsrt _rvalue _trt;run;
data data_1 (keep=_datasrt _blcksrt _rowsrt _rvalue COL:);
set report; where _trt=1; rename _cvalue=COL11 cnp_ci=COL12;run;
data data_2 (keep=_datasrt _blcksrt _rowsrt _rvalue COL:);
set report; where _trt=2; rename _cvalue=COL21 cnp_ci=COL22;run;
proc sort data=report out=extradata (keep=_datasrt _blcksrt _rowsrt _rvalue)
nodupkey; by _datasrt _blcksrt _rowsrt _rvalue;run;
data report;
merge data_1 data_2 extradata; by _datasrt _blcksrt _rowsrt _rvalue;run;
data report;
set report; _fixvar=1; _fix2var=1; _dummy=1;run;
proc sort data=report out=outdata1;
by _datasrt _blcksrt _rowsrt _rvalue;run;
ods escapechar="~";
title1 "Number (%) of Subjects Reporting at Least 1 New Serious Adverse Event After the EUA Snapshot, From Dose 1 to ";title2 "Unblinding Date, by System Organ Class and Preferred Term (*ESC*){unicode 2013} Blinded Placebo-Controlled Follow-up Period (*ESC*){unicode 2013}";title3 "Phase 2/3 Subjects 12 Through 15 Years of Age (*ESC*){unicode 2013} Safety Population";footnote1 "Abbreviation: EUA = emergency use authorization.";
footnote2 "Note: MedDRA (v24.0) coding dictionary applied.";
FDA-CBER-2022-5812-0071646
file:///J/.../m5/datasets/c4591001/analysis/adam/programs-6mth/125742-45_S211_M5_c4591001-A_6mth-P-adae-s130-sae-unb2-ped6-sas.txt[7/5/2023 10:22:56 AM]footnote3 "Note: Adverse events that occurred on the day of or after subjects were unblinded are excluded from this
summary.";
footnote4 "a.~{nbspace 5}N = number of subjects in the specified group, subjects who withdrew from the study before EUA snapshot 25Mar2021 with the cutoff date 13Mar2021 are not included. This value is the denominator for the percentage calculations.";footnote5 "b.~{nbspace 5}n = Number of subjects reporting at least 1 occurrence of the specified event. For (*ESC*){unicode 0022}any event,(*ESC*){unicode 0022} n = number of subjects reporting at least 1 occurrence of any event.";footnote6 "c.~{nbspace 5}Exact 2-sided CI based on the Clopper and Pearson method.";ods html file="&outtable.";
proc report data=outdata1 nowd list missing contents="" split="|"
style(report)={} style(header)={} style(column)={}; column _fixvar _fix2var _datasrt _blcksrt _rowsrt ("" _rvalue) (" " (" " ("Vaccine Group (as Administered)~{line}" ("BNT162b2 (30 (*ESC*){unicode 03BC}g)| (N(*ESC*){super a}=&_TRT1.)" (COL11 COL12)) ("Placebo| (N(*ESC*){super a}=&_TRT2.)" (COL21 COL22))) ) ) _dummy; define _fixvar / group noprint; define _fix2var / group noprint; define _datasrt / group order=internal noprint; define _blcksrt / group order=internal noprint; define _rowsrt / group order=internal noprint; define _rvalue / group "System Organ Class|~{nbspace 5}Preferred Term" order=data style(column)={just=left width=60mm} style(header)={just=left} left; ; define COL11 / group nozero " n(*ESC*){super b} (%)" style(column)={leftmargin=12px} style(header)={just=center} center; define COL12 / group nozero " (95%~{nbspace 1}CI(*ESC*){super c})" style(column)={leftmargin=12px} style(header)={just=center} center; define COL21 / group nozero " n(*ESC*){super b} (%)" style(column)={leftmargin=12px} style(header)={just=center} center; define COL22 / group nozero " (95%~{nbspace 1}CI(*ESC*){super c})" style(column)={leftmargin=12px} style(header)={just=center} center; define _dummy / sum noprint; break before _fixvar / contents="" page; compute before _fix2var; line @1 " ~n "; endcomp; compute after _blcksrt; line " ~n "; endcomp;run;
FDA-CBER-2022-5812-0071647