Document text
file:///J/.../m5/datasets/c4591001/analysis/adam/programs-6mth/125742-45_S211_M5_c4591001-A_6mth-P-adae-s092-all-unb1-ped6-sas.txt[7/5/2023 10:22:58 AM]***********************************************************************************************;
** Program Name : adae-s092-all-unb1-ped6.sas **;** Date Created : 15Nov2021 **;
** Programmer Name :
**;
** Purpose : Create adae-s092-all-unb1-ped6 **;** Input data : adsl adae **;** Output data : adae-s092-all-unb1-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;%let codename=adae-s092-all-unb1-ped6;libname datvprot "&bprot.data_vai" access=readonly;%let outlog=&prot./analysis/eSUB/logs/&codename..log;%let outtable=&prot./analysis/eSUB/output/&codename..html;
proc printto log="&outlog." new;
run;
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;
where saffl="Y" and AGEGR4N=1 and HIVFL ne "Y" and (VAX101DT ne . and BDCSRDT
ne .);
run;
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;
analysis_subset='Y'; where AECAT='ADVERSE EVENT' and saffl="Y" and agegr4n=1 and vphasen>0
and .<VAX101DT<=ASTDT<=BDCSRDT and HIVFL ne "Y";
run;
(b) (4),
(b) (6)
FDA-CBER-2022-5812-0071596
file:///J/.../m5/datasets/c4591001/analysis/adam/programs-6mth/125742-45_S211_M5_c4591001-A_6mth-P-adae-s092-all-unb1-ped6-sas.txt[7/5/2023 10:22:58 AM]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;
if TRT01AN in (9) then
do; newtrtn=2; newtrt=coalescec("Placebo", TRT01A); output; end;run;
proc format;
value catlbl 1="Any event" 2="Any serious adverse event" 3="Severe" 4="Related(*ESC*){super f}" 5="Life-threatening" 6="Any nonserious adverse event" 7="Any adverse event leading to withdrawal" 8="Death"; value scatlbl 101, 102, 106, 107="Related(*ESC*){super f}" 201, 202, 206, 207="Severe" 301, 302, 306, 307="Life-threatening";run;
proc sort data=g_adsl_dsin out=_ds1;
by usubjid newtrtn;run;
proc sort data=g_a_dsin out=_ds2;
by usubjid newtrtn;run;
FDA-CBER-2022-5812-0071597
file:///J/.../m5/datasets/c4591001/analysis/adam/programs-6mth/125742-45_S211_M5_c4591001-A_6mth-P-adae-s092-all-unb1-ped6-sas.txt[7/5/2023 10:22:58 AM]data final;
merge _ds1(in=d1) _ds2(in=d2);
by usubjid newtrtn;
if d1;proc sort;
by newtrtn usubjid;run;
data final_;
set final; by newtrtn usubjid; _uniqid=_n_;run;
data _basetemplate(compress=no);
length _varname $8 _cvalue $35 _direct $20 _vrlabel $200 _rwlabel _colabel $800 _datatyp $5 _module $8 _pr_lbl $ 200; array _c _character_; delete;run;
data _data1;
set final_; where (NEWTRTN is not missing);
proc sort;
by NEWTRTN USUBJID;run;
data _data1;
retain _trt 0; length _str $200; _datasrt=1; set _data1 end=eof; 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;
FDA-CBER-2022-5812-0071598
file:///J/.../m5/datasets/c4591001/analysis/adam/programs-6mth/125742-45_S211_M5_c4591001-A_6mth-P-adae-s092-all-unb1-ped6-sas.txt[7/5/2023 10:22:58 AM]run;
proc sql;
create table trtbign as select distinct _trt, newtrt, compress(put(count(*), 5.) ) as bign, coalesce(sum(FUP1UNB)/(365.25*100), 0) as tenum from (select distinct USUBJID, _trt, newtrt, FUP1UNB from _data1 where NEWTRTN is not missing) group by _trt;quit;
proc sort data=_data1 out=_bydat1(keep=_datasrt _dummyby) nodupkey;
by _datasrt;run;
data _bydat1;
set _bydat1 end=eof; by _datasrt; retain _preby 0; drop _preby; _byvar1=0;
if eof then
do; call symput("_preby1", compress(put(_byvar1, 4.)));
if 0=0 then
output; end;run;
data _bydat1;
set _bydat1; by _datasrt; length _bycol _byindnt $50 _bylast $10; _bycol=" "; _byindnt=" "; _bylast=" ";
proc sort;
by _datasrt;run;
proc sort data=_data1;
by _trt usubjid aeterm descending ATOXGRN;run;
data tab1;
set _data1; where analysis_subset='Y' and aeterm ne ''; by _trt usubjid aeterm descending ATOXGRN;
if last.usubjid then
do; catvar=1;
output;
FDA-CBER-2022-5812-0071599
file:///J/.../m5/datasets/c4591001/analysis/adam/programs-6mth/125742-45_S211_M5_c4591001-A_6mth-P-adae-s092-all-unb1-ped6-sas.txt[7/5/2023 10:22:58 AM] end;
if last.ATOXGRN then
do; _catvar=1; output; end;run;
data rel_tab1;
set _data1; by _trt usubjid aeterm descending ATOXGRN; where analysis_subset='Y' and aeterm ne '' and upcase(AREL)='RELATED';
if last.usubjid then
do; catvar=1+100; output; end;
if last.ATOXGRN then
do; _catvar=1+100; output; end;run;
data sev_tab1;
set _data1; by _trt usubjid aeterm descending ATOXGRN; where analysis_subset='Y' and aeterm ne '' and ATOXGRN=3;
if last.usubjid then
do; catvar=1+200; output; end;
if last.ATOXGRN then
do; _catvar=1+200; output; end;run;
data lif_tab1;
set _data1; by _trt usubjid aeterm descending ATOXGRN; where analysis_subset='Y' and aeterm ne '' and (atoxgr="GRADE 4");
if last.usubjid then
do; catvar=1+300;
output;
FDA-CBER-2022-5812-0071600
file:///J/.../m5/datasets/c4591001/analysis/adam/programs-6mth/125742-45_S211_M5_c4591001-A_6mth-P-adae-s092-all-unb1-ped6-sas.txt[7/5/2023 10:22:58 AM] end;
if last.ATOXGRN then
do; _catvar=1+300; output; end;run;
data tab2;
set _data1; where analysis_subset='Y' and aeser='Y'; by _trt usubjid aeterm descending ATOXGRN;
if last.usubjid then
do; catvar=2; output; end;
if last.ATOXGRN then
do; _catvar=2; output; end;run;
data rel_tab2;
set _data1; by _trt usubjid aeterm descending ATOXGRN; where analysis_subset='Y' and aeser='Y' and upcase(AREL)='RELATED';
if last.usubjid then
do; catvar=2+100; output; end;
if last.ATOXGRN then
do; _catvar=2+100; output; end;run;
data sev_tab2;
set _data1; by _trt usubjid aeterm descending ATOXGRN; where analysis_subset='Y' and aeser='Y' and ATOXGRN=3;
if last.usubjid then
do; catvar=2+200;
output;
FDA-CBER-2022-5812-0071601
file:///J/.../m5/datasets/c4591001/analysis/adam/programs-6mth/125742-45_S211_M5_c4591001-A_6mth-P-adae-s092-all-unb1-ped6-sas.txt[7/5/2023 10:22:58 AM] end;
if last.ATOXGRN then
do; _catvar=2+200; output; end;run;
data lif_tab2;
set _data1; by _trt usubjid aeterm descending ATOXGRN; where analysis_subset='Y' and aeser='Y' and (atoxgr="GRADE 4");
if last.usubjid then
do; catvar=2+300; output; end;
if last.ATOXGRN then
do; _catvar=2+300; output; end;run;
data tab6;
set _data1; where analysis_subset='Y' and (aeser in (' ' 'N')); by _trt usubjid aeterm descending ATOXGRN;
if last.usubjid then
do; catvar=6; output; end;
if last.ATOXGRN then
do; _catvar=6; output; end;run;
data rel_tab6;
set _data1; by _trt usubjid aeterm descending ATOXGRN; where analysis_subset='Y' and (aeser in (' ' 'N')) and upcase(AREL)='RELATED';
if last.usubjid then
do; catvar=6+100;
output;
FDA-CBER-2022-5812-0071602
file:///J/.../m5/datasets/c4591001/analysis/adam/programs-6mth/125742-45_S211_M5_c4591001-A_6mth-P-adae-s092-all-unb1-ped6-sas.txt[7/5/2023 10:22:58 AM] end;
if last.ATOXGRN then
do; _catvar=6+100; output; end;run;
data sev_tab6;
set _data1; by _trt usubjid aeterm descending ATOXGRN; where analysis_subset='Y' and (aeser in (' ' 'N')) and ATOXGRN=3;
if last.usubjid then
do; catvar=6+200; output; end;
if last.ATOXGRN then
do; _catvar=6+200; output; end;run;
data lif_tab6;
set _data1; by _trt usubjid aeterm descending ATOXGRN; where analysis_subset='Y' and (aeser in (' ' 'N')) and (atoxgr="GRADE 4");
if last.usubjid then
do; catvar=6+300; output; end;
if last.ATOXGRN then
do; _catvar=6+300; output; end;run;
data tab7;
set _data1; where analysis_subset='Y' and (upcase(aeacn)='DRUG WITHDRAWN' or aesubjdc='Y'); by _trt usubjid aeterm descending ATOXGRN;
if last.usubjid then
do; catvar=7;
output;
FDA-CBER-2022-5812-0071603
file:///J/.../m5/datasets/c4591001/analysis/adam/programs-6mth/125742-45_S211_M5_c4591001-A_6mth-P-adae-s092-all-unb1-ped6-sas.txt[7/5/2023 10:22:58 AM] end;
if last.ATOXGRN then
do; _catvar=7; output; end;run;
data rel_tab7;
set _data1; by _trt usubjid aeterm descending ATOXGRN; where analysis_subset='Y' and (upcase(aeacn)='DRUG WITHDRAWN' or aesubjdc='Y') and upcase(AREL)='RELATED';
if last.usubjid then
do; catvar=7+100; output; end;
if last.ATOXGRN then
do; _catvar=7+100; output; end;run;
data sev_tab7;
set _data1; by _trt usubjid aeterm descending ATOXGRN; where analysis_subset='Y' and (upcase(aeacn)='DRUG WITHDRAWN' or aesubjdc='Y') and ATOXGRN=3;
if last.usubjid then
do; catvar=7+200; output; end;
if last.ATOXGRN then
do; _catvar=7+200; output; end;run;
data lif_tab7;
set _data1; by _trt usubjid aeterm descending ATOXGRN; where analysis_subset='Y' and (upcase(aeacn)='DRUG WITHDRAWN' or aesubjdc='Y') and (atoxgr="GRADE 4");
if last.usubjid then
FDA-CBER-2022-5812-0071604
file:///J/.../m5/datasets/c4591001/analysis/adam/programs-6mth/125742-45_S211_M5_c4591001-A_6mth-P-adae-s092-all-unb1-ped6-sas.txt[7/5/2023 10:22:58 AM] do;
catvar=7+300;
output; end;
if last.ATOXGRN then
do; _catvar=7+300; output; end;run;
data tab8;
set _data1; where analysis_subset='Y' and (upcase(AEOUT)="FATAL"); by _trt usubjid aeterm descending ATOXGRN;
if last.usubjid then
do; catvar=8; output; end;
if last.ATOXGRN then
do; _catvar=8; output; end;run;
data rel_tab8;
set _data1; by _trt usubjid aeterm descending ATOXGRN; where analysis_subset='Y' and (upcase(AEOUT)="FATAL") and upcase(AREL)='RELATED';
if last.usubjid then
do; catvar=8+100; output; end;
if last.ATOXGRN then
do; _catvar=8+100; output; end;run;
data sev_tab8;
set _data1; by _trt usubjid aeterm descending ATOXGRN; where analysis_subset='Y' and (upcase(AEOUT)="FATAL") and ATOXGRN=3;
FDA-CBER-2022-5812-0071605
file:///J/.../m5/datasets/c4591001/analysis/adam/programs-6mth/125742-45_S211_M5_c4591001-A_6mth-P-adae-s092-all-unb1-ped6-sas.txt[7/5/2023 10:22:58 AM] if last.usubjid then
do;
catvar=8+200; output; end;
if last.ATOXGRN then
do; _catvar=8+200; output; end;run;
data lif_tab8;
set _data1; by _trt usubjid aeterm descending ATOXGRN; where analysis_subset='Y' and (upcase(AEOUT)="FATAL") and (atoxgr="GRADE 4");
if last.usubjid then
do; catvar=8+300; output; end;
if last.ATOXGRN then
do; _catvar=8+300; output; end;run;
data _data1;
set _data1(in=a) tab1 sev_tab1 rel_tab1 lif_tab1 tab2 sev_tab2 rel_tab2 lif_tab2 tab6 sev_tab6 rel_tab6 lif_tab6 tab7 sev_tab7 rel_tab7 lif_tab7 tab8;
if a then
do; catvar=0; _catvar=0; end;
if _catvar ne . then
catvar=.;run;
proc format cntlout=tmpfmt;
select catlbl;run;
data _anal1;
length CATVAR 8; set _data1; where same and CATVAR is not missing;
_blcksrt=0;
FDA-CBER-2022-5812-0071606
file:///J/.../m5/datasets/c4591001/analysis/adam/programs-6mth/125742-45_S211_M5_c4591001-A_6mth-P-adae-s092-all-unb1-ped6-sas.txt[7/5/2023 10:22:58 AM] _cnt=1;
_cat=1;
if _trt <=0 then
delete; output;run;
proc sort data=_anal1;
by _datasrt _blcksrt CATVAR _trt _cat;run;
proc sort data=_anal1 out=_temp91 nodupkey;
by _datasrt _blcksrt _cat CATVAR _trt USUBJID;run;
proc freq data=_temp91;
format CATVAR; tables _datasrt*_blcksrt*_cat * CATVAR * _trt / sparse norow nocol nopercent out=_pct1(drop=percent);run;
Data temp;
catvar=1; output; catvar=101; output; catvar=201; output; catvar=301; output; catvar=2; output; catvar=102; output; catvar=202; output; catvar=302; output; catvar=6; output; catvar=106; output; catvar=206; output; catvar=306; output; catvar=7; output; catvar=107; output; catvar=207; output;
catvar=307;
FDA-CBER-2022-5812-0071607
file:///J/.../m5/datasets/c4591001/analysis/adam/programs-6mth/125742-45_S211_M5_c4591001-A_6mth-P-adae-s092-all-unb1-ped6-sas.txt[7/5/2023 10:22:58 AM] output;
catvar=8;
output;run;
proc sql;
create table temp2 as select distinct a._datasrt , a._blcksrt, a._cat, a._trt, b.* from _pct1 as a left join temp as b on 1;quit;
proc sql;
create table _pct2 as select a.*, coalesce(b.count, 0) as count from temp2 as a left join _pct1 as b on a._datasrt=b._datasrt and a._blcksrt=b._blcksrt and a._cat=b._cat and a._trt=b._trt and a.catvar=b.catvar;quit;
data rep1;
set _pct2; length _rwlabel $200. _cvalue $50.;
if catvar<100 then
do; _rwlabel=strip(put(CATVAR, catlbl.));
/* grp=1; */
end; else do;/* _rwlabel=repeat(byte(160), 2)|| strip(put(CATVAR, scatlbl.)); */ _rwlabel='~{nbspace 2}'|| strip(put(CATVAR, scatlbl.)); /* grp=2; */ end;
if catvar in (1, 101, 201, 301) then
_fixvar=1; else if catvar in (2, 102, 202, 302) then _fixvar=2; else if catvar in (6, 106, 206, 306) then _fixvar=3; else if catvar in (7, 107, 207, 307) then _fixvar=4; else if catvar in (8) then _fixvar=5; _cvalue=strip(put(count, best.));run;
proc sql;
create table rep2 as select a.*, b.bign, b.newtrt, b.tenum from rep1 as a left join trtbign as b on a._trt=b._trt;quit;
data rep2;
set rep2;
length _cpct _cvalue2 $40. CNP_CI $100.;
FDA-CBER-2022-5812-0071608
file:///J/.../m5/datasets/c4591001/analysis/adam/programs-6mth/125742-45_S211_M5_c4591001-A_6mth-P-adae-s092-all-unb1-ped6-sas.txt[7/5/2023 10:22:58 AM] newtrt=strip(newtrt)||"| (N(*ESC*){super a}="||strip(bign)||", TE(*ESC*){super b}="||strip(put(tenum,
8.1)) || ")";
percent=count / bign * 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; _cvalue2=strip(put((count/TENUM), 8.1));
if count ne 0 then
lcl=(cinv(0.05/2, 2*count))/(2*TENUM); else lcl=0; ucl=(cinv(1-0.05/2, 2*(count+1)))/(2*TENUM); CNP_CI=strip("(" || strip(put(lcl, 8.1)) || ",(*ESC*){nbspace 1}" || strip(put(ucl, 8.1)) || ")"); _dummy=1;
proc sort;
by _cat _fixvar catvar _rwlabel _trt newtrt _cvalue;run;
options topmargin=0.75in bottommargin=0.75in leftmargin=0.75in
rightmargin=0.75in;options orientation=LANDSCAPE papersize="LETTER";ods escapechar="~";option nobyline;title1 "Incidence Rates of at Least 1 Adverse Event From Dose 1 to Unblinding Date (*ESC*){unicode 2013} ";title2 "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 "a.~{nbspace 5}N = number of subjects in the specified group. This value is the denominator for the percentage calculations.";footnote2 "b.~{nbspace 5}TE = total exposure time in 100 person-years across all subjects in the specified group. Exposure time for a subject is the time from Dose 1 to the end of the blinded follow-up period. This value is the denominator for the incidence rate calculation.";footnote3 "%nrbquote(c.~{nbspace 5}n = Number of subjects reporting at least 1 occurrence of the specified event category. For "any event," n = number of subjects reporting at least 1 occurrence of any event.)";footnote4 "d.~{nbspace 5}Incidence rate (IR) is calculated as number of subjects reporting the event/total exposure time in 100 person-years (PY) across all subjects in the specified group.";footnote5 "e.~{nbspace 5}2-sided CI based on Poisson distribution.";footnote6 "f.~{nbspace 5}Assessed by the investigator as related to investigational product.";ods html file="&outtable.";
proc report data=rep2 nowd list missing contents="" split="|";
column _cat _fixvar catvar _rwlabel ("~S={just=center}Vaccine Group (as Administered)~{line}" newtrt,
(_cvalue _cvalue2 cnp_ci _dummy) );
FDA-CBER-2022-5812-0071609
file:///J/.../m5/datasets/c4591001/analysis/adam/programs-6mth/125742-45_S211_M5_c4591001-A_6mth-P-adae-s092-all-unb1-ped6-sas.txt[7/5/2023 10:22:58 AM] define _cat / group noprint;
define _fixvar / group order=internal noprint;
define catvar / group order=internal noprint; define _rwlabel / group "Adverse Event" order=data style(column)={just=left width=65mm} style(header)={just=left} left; define newtrt / across nozero "" style(column)={width=35mm leftmargin=12px} style(header)={just=center} center; define _cvalue / display nozero "n(*ESC*){super c} (%)" style(column)={leftmargin=12px} style(header)={just=center} center; define _cvalue2 / display nozero "IR(*ESC*){super d}" style(column)={leftmargin=12px} style(header)={just=center} center;
define cnp_ci / display nozero "(95% CI(*ESC*){super e})"
style(column)={leftmargin=12px} style(header)={just=center} center;
define _dummy / sum noprint;
compute before _cat;
line @1 " ~n";
endcomp;
compute after _cat;
line " ~n";
endcomp;
run;
ods html close;proc printto;
run;
FDA-CBER-2022-5812-0071610