*************************************************************************************************;
*           CLIENT: ModernaTX, Inc.
*         PROTOCOL: mRNA-1273-P301
*          PURPOSE: Create Inferential Statistical Analysis Macro for 95% CI results      
*      INPUT FILES: ADaM datasets
*     OUTPUT FILES: stat macro
*      USAGE NOTES: 
*************************************************************************************************;
*  Copyright 2020 Pharmaceutical Product Development, Inc.
*  All Rights Reserved.
*************************************************************************************************;

%macro clopper (libin=adb,datain=, vac=, sar=,sec=, dataout=, subset=, byvar=, );

%if (&datain.=ADAR or &datain.=ADARP7D) %then %do;
 %if &datain.=ADAR  %then %do;
  data &datain.;
  set &libin..&datain.;
  where &sar.='Y' and ATPTREF in &vac.;
  run;
  %end;

 %else %do;
  data &datain.;
  set &libin..&datain.;
  where &sar.='Y' and ATPTREF in &vac. and ANL06FL='Y';
  run;
 %end; 

  data temp;
  set &datain.;
  length trt $20;
  trt=trt01a;
  output;
  trt='Total';
  output;
  run;


  data temp2;
  set &libin..adar;
  where &sar.='Y' and ATPTREF in &vac.;
  run;

  data temp2;
  set temp2;
  length trt $20;
  trt=trt01a;
  output;
  trt='Total';
  output;
  run;

  %end;

  %else %do;

  data &datain.;
  set &datain.;
  where &sar.='Y' and ATPTREF in &vac. ;
  run;

  data temp2;
  set &datain.;
  length trt $20;
  trt=trt01a;
  output;
  trt='Total';
  output;
  run;


  data temp;
  set temp2;
  run;


  %end;


  %if &sec.='AR' %then %do;
    proc sort data=temp2 out=n1 nodupkey;
    by &subset. &byvar. subjid trt;
    where ATOXGRN^=.;
    run;

    proc sort data=temp out=any nodupkey;
    by &subset. &byvar. subjid trt;
    where ATOXGRN>0;
    run;
  %end;

 %if &sec.='LAR' %then %do;
    proc sort data=temp2 out=n1 nodupkey;
    by &subset. &byvar. subjid trt;
    where parcat1='LOCAL' and ATOXGRN^=.;
    run;

    proc sort data=temp out=any nodupkey;
    by &subset. &byvar. subjid trt;
    where parcat1='LOCAL' and ATOXGRN>0;
    run;
  %end;

  %if &sec.='SAR' %then %do;
    proc sort data=temp2 out=n1 nodupkey;
    by &subset. &byvar. subjid trt;
    where parcat1='SYSTEMIC' and ATOXGRN^=.;
    run;

    proc sort data=temp out=any nodupkey;
    by &subset. &byvar. subjid trt;
    where parcat1='SYSTEMIC' and ATOXGRN>0;
    run;
  %end;

 

  proc freq data=n1 noprint;
  table trt/norow nocol nopercent nocum out=denom;
  by &subset. &byvar.;
  run;


  proc freq data=any;
  table trt/norow nocol nopercent nocum out=num;
  by &subset. &byvar.;
  run;


  data ar;
  merge denom(rename=count=denom drop=percent) num(rename=count=n drop=percent);
  by &subset. &byvar. trt;
  run;

  data ar;
  set ar;
  if n=. then n=0;
  run;

  data clopper;
  set ar;
  n1=denom-n;
  rename n=Y n1=N;
  run;

  proc transpose data=clopper out=clopper_ar;
  by &subset. &byvar. trt ;
  var y n;
  run;

  proc freq data=clopper_ar;
  ods output binomialcls=ci;
  by &subset. &byvar. trt ;
  tables _name_/ nocum norow binomial (LEVEL="Y" ALL);
  weight col1 / zeros;
  run;


  data &dataout.;
  set ci;
  lowercl=lowercl*100;
  uppercl=uppercl*100;
  where type='Clopper-Pearson (Exact)';
  drop table proportion type;
  run;


%mend clopper;