****************************************************************************************************
* PROGRAM OVERVIEW
****************************************************************************************************
*
* PROGRAM: create_tableofcontents.sas
* Created (mm/dd/yyyy): 02/09/2021
*
*--------------------------------------------------------------------------------------------------
* PURPOSE: This macro createas a dataset with 1 row per table and figure that is used as the
* report table of contents
*
* Program inputs:
*
* Program outputs:
* -tableofcontents: dataset containing table of contents
*
* PARAMETERS:
*
* Programming Notes:
*
*
*--------------------------------------------------------------------------------------------------
* CONTACT INFO:
* Sentinel Coordinating Center
* info@sentinelsystem.org
*
***************************************************************************************************;
%macro create_tableofcontents();
%put =====> MACRO CALLED: create_tableofcontents;
/*********************************************************************************************/
/* Utility macro to add row to tableofcontents file */
/*********************************************************************************************/
%macro addtotoc(tabnum=, caption=, appendixtype=);
data tableofcontents;
set tableofcontents end=eof;
output;
if eof then do;
tabnum = "&tabnum.";
caption = "&caption.";
appendixtype = "&appendixtype.";
output;
end;
run;
%mend;
/*********************************************************************************************/
/* Initialize empty table and table number */
/*********************************************************************************************/
data tableofcontents;
length tabnum $25 caption $500 appendixtype $30;
call missing(tabnum, caption, appendixtype);
run;
%let number = 1;
%let tablenum = 1;
/*********************************************************************************************/
/* Build table of contents */
/*********************************************************************************************/
/*********************************************************************************************/
/* Glossary rows */
/*********************************************************************************************/
%addtotoc(tabnum=Glossary (CIDA), caption=List of Terms to Define the Cohort Identification and Descriptive Analysis (CIDA) Found in this Report);
%if %str("&reporttype") = %str("T2L2") | %str("&reporttype") = %str("T4L2") %then %do;
%addtotoc(tabnum=Glossary (PSA), caption=List of Terms to Define the Propensity Score Analysis (PSA) Found in this Report);
%end;
/*temporary - L2 reporting code out of date*/
%if %str("&reporttype") ne %str("T2L2") & %str("&reporttype") ne %str("T4L2") %then %do;
/*********************************************************************************************/
/* Baseline Table */
/*********************************************************************************************/
%if %eval(&numbaselinetablegrp.>0) %then %do;
/*counter for determining table letter*/
%let tablecount = 1;
/* counter for determining table number */
%let tablenum = 2;
/*loop through each baseline table*/
%do b = 1 %to &numbaselinetablegrp.;
%let analysisgrp = ;
%let analysisgrp2 = ;
%let baselinegroupnum = ;
%let pregnancylabel = ;
%let includenonpregnant = N;
/*for L2 tables - need to reference PS/CS specific files to pull additional parameters*/
%let ratio = F;
%let psfile = ;
%let weightlabel = ;
%let weightscheme = ;
%let pstrim = ;
%let percentiles=;
%let ratiolabel = ;
%let caliperlabel = ;
%let truncationlabel = ;
%let psestimategrp = ;
%let unadjusted = ;
data _null_;
set baselinefile(where=(order=&b.));
if _n_ = 1 then do;
call symputx('analysisgrp', analysisgrp);
call symputx('runid', runid);
call symputx('cohort', cohort);
call symputx('unique_psestimate',unique_psestimate);
%if %sysfunc(prxmatch(m/T4L1/i,&reporttype.)) > 0 %then %do;
if cohort in ('preg', 'nopreg') then do;
if upcase(includenonpregnant) = 'Y' then call symput('pregnancylabel', ' Pregnancy Cohort and Non-Pregnancy Cohort');
else call symput('pregnancylabel', ' Pregnancy Cohort');
end;
call symputx('includenonpregnant', upcase(includenonpregnant));
%end;
if missing(baselinegroupnum)=0 then call symputx('baselinegroupnum', baselinegroupnum);
end;
/*if baselinegroupnum is specified, a 2nd row will exist in the file*/
if _n_ = 2 then do;
if missing(baselinegroupnum)=0 then do;
call symputx('analysisgrp2',analysisgrp);
end;
end;
run;
%if %sysfunc(prxmatch(m/T2L2|T4L2/i,&reporttype.)) > 0 %then %do;
data _null_;
set pscs_masterinputs(where=(analysisgrp = "&analysisgrp." and missing(subgroup)));
call symputx('psfile', strip(file));
call symputx('psestimategrp', psestimategrp);
call symput('unadjusted', 'Unadjusted '); /*for unadjusted table label*/
if file = 'psmatchfile' then do;
call symputx('ratio',upcase(ratio));
if upcase(ratio)='F' then call symputx("ratiolabel",'Fixed Ratio 1:'||strip(put(ceiling, 8.)));
if upcase(ratio)='V' then call symputx("ratiolabel",'Variable Ratio 1:'||strip(put(ceiling, 8.)));
call symputx("caliperlabel", cat(', Caliper: ', caliper));
end;
if file = 'stratificationfile' then do;
call symputx('pstrim', pstrim);
call symputx('percentiles', percentiles);
if missing(strataweight) =0 then call symputx('weightscheme', strataweight);
if upcase(strataweight)= 'ATE' or missing(strataweight) then call symputx("weightlabel","Average Treatment Effect (ATE)");
else if upcase(strataweight)= 'ATT' then call symputx("weightlabel","Average Treatment Effect in the Treated (ATT)");
end;
if file = 'iptwfile' then do;
if upcase(ipweight)= 'ATE' then call symputx("weightlabel","Average Treatment Effect (ATE)");
else if upcase(ipweight)= 'ATES' then call symputx("weightlabel","Average Treatment Effect, Stabilized (ATES)");
else if upcase(ipweight)= 'ATT' then call symputx("weightlabel","Average Treatment Effect in the Treated (ATT)");
call symputx('truncationlabel',strip(put(truncweight, best.)));
end;
run;
%end;
/*determine if only 1 baseline table and set &tablecount to 0. Will occur if all the following are true:
- 1 monitoring period
- DP stratification = N
- max(order) in baselinefile = 1
- if reporttype = T2L2, T4L2- then analysis must be covariate stratification*/
%if %eval(&b.=1) & %eval(&look_start.) = %eval(&look_end.) & &stratifybydp. = N & %eval(&numbaselinetablegrp.=1) %then %do;
%if %sysfunc(prxmatch(m/T2L2|T4L2/i,&reporttype.)) = 0 %then %do;
%let tablecount = 0;
%end;
%else %do;
%if &psfile. = covstratfile %then %let tablecount = 0;
%end;
%end;
/*Assign labels*/
%let baselinelabel = ;
%let grouplabel = &analysisgrp.;
%let psestimatelabel = &psestimategrp.;
%if %length(&baselinegroupnum.)>0 %then %do;
%let grouplabel2 = &analysisgrp2.;
%end;
%isdata(dataset=labelfile);
%if %eval(&nobs.>0) %then %do;
data _null_;
set labelfile(in=a where=(group="&analysisgrp" and runid = "&runid"))
%if %length(&baselinegroupnum.)>0 %then %do;
labelfile(in=b where=(group="&analysisgrp2" and runid = "&runid"))
%end;
%if %sysfunc(prxmatch(m/T2L2|T4L2/i,&reporttype.)) > 0 %then %do;
labelfile(in=c where=(group="&psestimategrp" and runid = "&runid"))
%end; ;
if a then do;
if labeltype = 'grouplabel' then call symputx('grouplabel',label);
if labeltype = 'baselinelabel' then call symputx('baselinelabel',cat(', ',strip(label), ','));
end;
%if %length(&baselinegroupnum.)>0 %then %do;
if b then do;
if labeltype = 'grouplabel' then call symputx('grouplabel2',label);
end;
%end;
%if %sysfunc(prxmatch(m/T2L2|T4L2/i,&reporttype.)) > 0 & &psfile. ne covstratfile %then %do;
if c then do;
if labeltype = 'grouplabel' then call symputx('psestimatelabel',label);
end;
%end;
run;
%end;
%let captionlabel = %bquote(&grouplabel.&pregnancylabel&baselinelabel.);
%if %length(&baselinegroupnum.)>0 %then %do;
%let captionlabel = %bquote(&grouplabel.&pregnancylabel and &grouplabel2.&pregnancylabel&baselinelabel.);
%end;
%if %sysfunc(prxmatch(m/T2L2|T4L2/i,&reporttype.)) >0 & &psfile. ne covstratfile %then %do;
%let captionlabel = %bquote(&psestimatelabel.);
%end;
/*1 block of code for both aggregate and DP tables*/
%macro baselinetoc(aggregated=, dpinparenthesis=, dpcomma=);
%if %eval(&unique_psestimate.) = 1 %then %do;
%tableletter();
%addtotoc(tabnum=Table 1&tableletter.,
caption=%quote(&aggregated.&unadjusted.Characteristics of &captionlabel. &dpinparenthesis.in the &database. from &startdateformatted. to &&enddate&periodid.formatted.));
%end;
/*For L2 tables - up to 2 additional adjusted tables*/
%if %sysfunc(prxmatch(m/T2L2|T4L2/i,&reporttype.)) > 0 %then %do;
/*PS Match Adjusted*/
%if &psfile. = psmatchfile %then %do;
%tableletter();
%addtotoc(tabnum=Table 1&tableletter.,
caption=%quote(&aggregated.Adjusted Characteristics of &grouplabel. (Propensity Score Matched&dpcomma., &ratiolabel.&caliperlabel.), in the &database. from &startdateformatted. to &&enddate&periodid.formatted.));
%end;
/*Unweighted - IPTW and PS Stratum*/
%if (&psfile. = iptwfile & %eval(&unique_psestimate.) = 1) | (&psfile. = stratificationfile & ("&weightscheme." = "ATE" | "&weightscheme." = "ATT") & %eval(&pstrim.>=0)) %then %do;
%tableletter();
%addtotoc(tabnum=Table 1&tableletter.,
caption=%quote(&aggregated.Unweighted Characteristics of &grouplabel. (Unweighted, Trimmed&dpcomma.) in the &database. from &startdateformatted. to &&enddate&periodid.formatted.));
%end;
/*Weighted - IPTW, PS Stratum, PS Stratification*/
%if &psfile. = iptwfile | &psfile. = stratificationfile %then %do;
%if &psfile. = iptwfile %then %let stratumtitle = Inverse Probability of Treatment Weighted, Trimmed&dpcomma., Weight: &weightlabel., Truncation: &truncationlabel.%nrbquote(%);
%else %if "&weightscheme." = "ATE" | "&weightscheme." = "ATT" %then
%let stratumtitle = Propensity Score Stratum Weighted, Trimmed&dpcomma., Percentiles: &percentiles., Weight: &weightlabel.;
%else %let stratumtitle =Propensity Score Stratified&dpcomma., Percentiles: &percentiles.;
%tableletter();
%addtotoc(tabnum=Table 1&tableletter.,
caption=%quote(&aggregated.Weighted Characteristics of &grouplabel. (&stratumtitle.), in the &database. from &startdateformatted. to &&enddate&periodid.formatted.));
%end;
%end; /*Additional L2 tables*/
%mend;
/*loop through each periodid*/
%do periodid = %eval(&look_start.) %to %eval(&look_end.);
/*Aggregated*/
%baselinetoc(%if %eval(&num_dp.)=1 %then %do;
aggregated=,
%end;
%else %do;
aggregated=%str(Aggregated ),
%end;
dpinparenthesis=, dpcomma=);
/*Output separate table for each Data Partner - loop through each DP*/
%if &stratifybydp. = Y %then %do;
%do dps = 1 %to %eval(&num_dp.);
%let maskedID = %scan(&masked_dplist,&dps);
%baselinetoc(aggregated = , dpinparenthesis=%str((&maskedid.) ), dpcomma=%str(, &maskedid.));
%end;
%end; /*DP stratification*/
%end; /*loop through each periodid*/
%end; /*loop through each row in baselinefile*/
%end; /*include baseline tables in toc*/
/*********************************************************************************************/
/* Covariate Profile Table */
/*********************************************************************************************/
%if &numprofilecovarstoinclude > 0 %then %do;
/* reset counter to reset table letter */
%let tablecount = 1;
%do periodid = %eval(&look_start.) %to %eval(&look_end.);
proc sql noprint ;
select 'order='||strip(put(order,8.))||' and runid='||quote(strip(runid))||' and group='||quote(strip(group))||' and cohort='||quote(strip(cohort))
into :whereexpr separated by '@'
from (select order, runid, group, case when(cohort is missing) then 'all' else cohort end as cohort
from baselinefile
where not missing(profilecovarstoinclude))
order by order;
quit;
%do wherenum = 1 %to %sysfunc(countw(&whereexpr, @));
%let where = %scan(&whereexpr,&wherenum, @);
data _temp_agg_order_profile;
set aggregate_profile(where=(periodid=&periodid and &where));
grouplabel='';
if cohort = 'mi' then group2=scan(group,1,'_');
else group2=group;
if cohort = 'switch' then switchlabel = ' ';
call symputx('runid',runid);
run;
%let profileswitches = 0;
%if &reporttype = T6 %then %do;
proc sql noprint;
select max(switchstep) into :profileswitches
from _temp_agg_order_profile;
quit;
%end;
%isdata(dataset=_temp_agg_order_profile);
%if &nobs > 0 %then %do;
%do s = 0 %to &profileswitches;
%if &reporttype = T6 %then %do;
data _temp_agg_profile;
set _temp_agg_order_profile (where=(switchstep = &s));
run;
/* Join treatment file onto profile table to obtain product group */
proc sql noprint undo_policy=none;
create table _temp_agg_profile as
select a.*, b.group as productswitchgroup
from _temp_agg_profile a
inner join infolder.&&&runid._treatmentpathways b
on a.group = b.analysisgrp and a.switchstep = b.switchevalstep;
quit;
%end;
%else %do;
proc datasets lib=work nolist;
change _temp_agg_order_profile = _temp_agg_profile;
run;
%end;
/* Check for existence of label file and join to profile dataset. Set grouplabel to missing if no labelfile */
%isdata(dataset=labelfile);
%if &nobs > 0 %then %do;
proc sql noprint undo_policy=none;
create table _temp_agg_profile as
select a.group, a.runid, a.order, a.periodid, b.label as grouplabel
%if %index(&where,%str(cohort="mi")) %then %do;
,c.label as grouplabel2, a.group2
%end;
%if %index(&where,%str(cohort="switch")) %then %do;
,d.label as switchlabel, a.productswitchgroup
%end;
from _temp_agg_profile(drop=grouplabel %if &reporttype = T6 %then %do; switchlabel %end;) a
left join labelfile(where=(lowcase(labeltype)='grouplabel')) b
on a.group = b.group and a.runid = b.runid
%if %index(&where,%str(cohort="mi")) %then %do;
left join labelfile(where=(lowcase(labeltype)='grouplabel')) c
on a.group2 = c.group and a.runid = c.runid
%end;
%if %index(&where,%str(cohort="switch")) %then %do;
left join labelfile(where=(lowcase(labeltype)='grouplabel')) d
on a.productswitchgroup = d.group and a.runid = d.runid
%end;
;
quit;
%end;
%else %do;
data _temp_agg_profile;
set _temp_agg_profile;
grouplabel2='';
switchlabel='';
run;
%end;
data _null_;
set _temp_agg_profile(keep=group grouplabel order
%if %index(&where,%str(cohort="mi")) %then %do;
group2 grouplabel2
%end;
%if %index(&where,%str(cohort="switch")) %then %do;
productswitchgroup switchlabel
%end;
);
if _n_ = 1;
if not missing(grouplabel) then call symputx('grouplabel',grouplabel);
else call symputx('grouplabel',group);
%if %index(&where,%str(cohort="nopreg")) %then %do;
if not missing(grouplabel) then call symputx('grouplabel',catx(' ',grouplabel,'Non-Pregnancy'));
else call symputx('grouplabel',catx(' ',group,'Non-Pregnancy'));
%end;
%else %if %index(&where,%str(cohort="preg")) %then %do;
if not missing(grouplabel) then call symputx('grouplabel',catx(' ',grouplabel,'Pregnancy'));
else call symputx('grouplabel',catx(' ',group,'Pregnancy'));
%end;
%else %if %index(&where,%str(cohort="mi")) %then %do;
if not missing(grouplabel) then do;
if not missing(grouplabel2) then call symputx('grouplabel',grouplabel2);
else call symputx('grouplabel',group2);
end;
else do;
call symputx('grouplabel',group2);
end;
%end;
%else %if &reporttype = T6 %then %do;
%if &s = 0 %then %do;
if not missing(grouplabel) then do;
call symputx('grouplabel',grouplabel);
end;
else do;
call symputx('grouplabel',group);
end;
%end;
%else %if &s = 1 %then %do;
if not missing(grouplabel) then do;
call symputx('grouplabel',grouplabel);
end;
else do;
call symputx('grouplabel',group);
end;
%end;
%else %if &s = 2 %then %do;
if not missing(grouplabel) then do;
call symputx('grouplabel',grouplabel);
end;
else do;
call symputx('grouplabel',group);
end;
%end;
%end;
run;
%tableletter();
%if &numprofilecovarstoinclude = 1 and &reporttype ^= T6 %then %let tableletter =;
%else %if &numprofilecovarstoinclude = 1 and &profileswitches = 0 and &reporttype = T6 %then %let tableletter =;
%addtotoc(tabnum=Table &tablenum.&tableletter.,
caption=%quote(Characteristic Profile of &grouplabel in the &database. from &startdateformatted. to &&enddate&periodid.formatted.));
%end; /* _temp_agg_order_profile */
%end; /* switch loop */
proc datasets library=work nowarn noprint;
delete _temp_agg_profile _temp_agg_order_profile;
quit;
%end; /* where loop */
%end; /* periodid loop */
%let tablenum = %eval(&tablenum + 1);
%end; /* &numprofilecovarstoinclude > 0 */
/*********************************************************************************************/
/* Effect estimate table */
/*********************************************************************************************/
%if &numl2comparisons > 0 %then %do;
/*loop through each baseline table*/
%do c = 1 %to &numl2comparisons;
/* reset counter to reset table letter */
%let tablecount = 1;
data _null_;
set l2comparisonfile(where=(order=&c.));
call symputx('analysisgrp', analysisgrp);
call symputx('runid', runid);
run;
/* Merge in group labels if they exist */
%let grouplabel = &analysisgrp;
%isdata(dataset=labelfile);
%if %eval(&nobs>0) %then %do;
data _null_;
set labelfile(in=a where=(group="&analysisgrp" and runid = "&runid")) ;
if labeltype = 'grouplabel' then call symputx('grouplabel',label);
run;
%end;
/* Store subgroup to determine subgroup labels */
proc sql noprint;
select distinct subgroup
into :subgrouplist
separated by ' '
from l2_effectestimates_&look_end.
where analysisgrp="&analysisgrp.";
quit;
%if %str(&subgrouplist.) = %str() %then %let tablecount = 0;
/* loop subgroup and assign subgroup label */
%do subgroupcount = 1 %to %sysfunc(countw(&subgrouplist));
%let subgroup= %scan(&subgrouplist,&subgroupcount);
%if %str(&subgroup.) = %str() %then %do;
%let titleend = %str();
%end;
%else %if &covarnum = 9000 %then %do;
%let titleend = %str(and Data Partner);
%end;
%else %do;
%if &covarnum < 1000 %then %do;
proc sql noprint;
select distinct strip(studyname) into: subgrouplabel
from infolder.&&&runid._covariatecodes
where covarnum = &covarnum.;
quit;
%end;
%if &covarnum = 1000 %then %let subgrouplabel = Sex;
%else %if &covarnum = 1001 %then %let subgrouplabel = Age Group;
%else %if &covarnum = 1002 %then %let subgrouplabel = Year;
%else %if &covarnum = 1003 %then %let subgrouplabel = Monitoring Period;
%else %if &covarnum = 1012 %then %let subgrouplabel = Race;
%else %if &covarnum = 1013 %then %let subgrouplabel = Hispanic Origin;
%else %if &covarnum = 1014 %then %let subgrouplabel = Delivery Status;
%else %if &covarnum = 2000 %then %let subgrouplabel = Match Method;
%else %if &covarnum = 2001 %then %let subgrouplabel = Birth Type;
%let titleend = %str(and &subgrouplabel);
%end;
%tableletter();
%addtotoc(tabnum=Table &tablenum.&tableletter.,
caption=%quote(Effect Estimates for &grouplabel. in the &database. from &startdateformatted. to &&enddate&look_end.formatted., by Analysis Type &titleend.));
%end; /* covarcount */
%let tablenum = %eval(&tablenum + 1);
%end; /* numl2comparison do loop */
%end; /* numl2comparison */
/*********************************************************************************************/
/* Type 1 and 2 summary tables */
/*********************************************************************************************/
%if %sysfunc(prxmatch(m/t1cida|t2cida|t2conc/i,&tdatasetlist.)) %then %do;
%do td = 1 %to &tdatasetlistnum.;
%let reporttable = %scan(&tdatasetlist, &td.);
%if ^%sysfunc(prxmatch(m/t1cida|t2cida|t2conc/i,&reporttable.)) %then %goto leavet1t2conc;
proc sql noprint;
%let tableobs = 0;
select max(stratificationorder)
into :tableobs trimmed
from tablefile
where dataset="&reporttable";
quit;
%do z = 1 %to %eval(&tableobs.);
data _null_;
set tablefile(where=(dataset="&reporttable" and stratificationorder=&z));
call symputx('tabletitle', tabletitle);
run;
%if &stratifybydp = Y %then %let tablecount=1;
%else %let tablecount=0;
%tableletter();
%addtotoc(tabnum=Table &tablenum.&tableletter.,
caption=%bquote(Summary of &reporttitle. in the &database. from &startdateformatted. to &enddateformatted.&tabletitle.));
%if &stratifybydp. = Y %then %do;
%do dps = 1 %to %eval(&num_dp.);
%let maskedID = %scan(&masked_dplist,&dps);
%tableletter();
%addtotoc(tabnum=Table &tablenum.&tableletter.,
caption=%bquote(Summary of &reporttitle. in the &database. for &maskedID. from &startdateformatted. to &enddateformatted.&tabletitle.));
%end;
%end;
%let tablenum = %eval(&tablenum + 1);
%end; /* z */
%leavet1t2conc:
%end; /* td */
%end; /* %sysfunc(prxmatch(m/t1cida|t2cida|t2conc/i,&tdatasetlist.)) */
/*****************************************************************************************/
/* Type 1 and 2 censor tables */
/*****************************************************************************************/
%if %sysfunc(prxmatch(m/t1censor|t2censor|t2followuptime/i,&tdatasetlist.)) > 0 %then %do;
%macro t1t2censortoc(tablename=, title=);
%let tableidlist=;
proc sql noprint;
select distinct table into: tableidlist separated by ' '
from tablefile(where=(dataset in ("&tablename.")));
quit;
%if %str("&tableidlist") ne %str("") %then %do;
%isdata(dataset=&tablename.);
%if %eval(&nobs.>0) %then %do;
%do t = 1 %to %sysfunc(countw(&tableidlist.));
%let tableid = %scan(&tableidlist., &t.);
%let stratificationorder = 0;
proc sql noprint;
select max(stratificationorder) into: stratificationorder
from tablefile(where=(dataset in ("&tablename.") and table = "&tableid"));
quit;
/*counter for determining table letter*/
%if %eval(&stratificationorder. = 1) & &stratifybydp. ne Y %then %let tablecount = 0;
%else %let tablecount = 1;
%do st = 1 %to &stratificationorder.;
data _null_;
set tablefile(where=(dataset in ("&tablename.") and table = "&tableid" and stratificationorder = &st.));
call symputx('tabletitle', tabletitle);
run;
%tableletter();
%if &tableid. = T1 %then %do;
%addtotoc(tabnum=Table &tablenum.&tableletter.,
caption=%quote(Summary of Time to End of &title. for &reporttitle. in the &database. from &startdateformatted. to &enddateformatted.&tabletitle.));
%if &stratifybydp. = Y & %eval(&st.=1) %then %do;
%tableletter();
%addtotoc(tabnum=Table &tablenum.&tableletter.,
caption=%quote(Summary of Time to End of &title. for &reporttitle. in the &database. from &startdateformatted. to &enddateformatted., by Data Partner));
%end;
%end;
%else %if &tableid. = T2 %then %do;
%addtotoc(tabnum=Table &tablenum.&tableletter.,
caption=%quote(Summary of Reasons for End of &title. for &reporttitle. in the &database. from &startdateformatted. to &enddateformatted.&tabletitle.));
%if &stratifybydp. = Y & %eval(&st.=1) %then %do;
%tableletter();
%addtotoc(tabnum=Table &tablenum.&tableletter.,
caption=%quote(Summary of Reasons for End of &title. for &reporttitle. in the &database. from &startdateformatted. to &enddateformatted., by Data Partner));
%end;
%end;
%else %if &tableid. = T3 & %eval(&st.=1) %then %do;
/*loop through each reason for censoring and within that - loop through stratificationorder*/
%do c = 1 %to %sysfunc(countw(&defaultcensororder., ' '));
%let reason = %scan(&defaultcensororder., &c.);
/*check if rows exist in table (censorreason parameter has already been applied in %censortables_createdata*/
data chktable;
set &tablename.(where=(table_name="&reason."));
run;
%isdata(dataset=chktable);
%if %eval(&nobs.>0) %then %do;
/*set table letter counter - need to check # of stratifications requested for censor reason*/
proc sql noprint;
select count(distinct stratificationorder) into: reasonstratificationorder
from tablefile
where dataset in ("&tablename.") and table = "&tableid" and findw(censorreason, "&reason.")>0;
quit;
%if %eval(&reasonstratificationorder. = 1) %then %let tablecount = 0;
%else %let tablecount = 1;
/*loop through each stratification*/
%do t3st = 1 %to &stratificationorder.;
%let censorreasontable = N;
data _null_;
set tablefile(where=(dataset in ("&tablename.") and table = "T3" and stratificationorder = &t3st.));
call symputx('tabletitle', tabletitle);
/*check if censoring reason requested*/
if findw(censorreason, "&reason.")>0 then call symputx('censorreasontable', 'Y');
run;
%if &censorreasontable. = Y %then %do;
%tableletter();
%addtotoc(tabnum=Table &tablenum.&tableletter.,
caption=%quote(Summary of Time to End of &title. due to %bquote(&&&reason._label) for &reporttitle. in the &database. from &startdateformatted. to &enddateformatted.&tabletitle.));
%end; /*censor reason requested*/
%end; /*loop through stratification*/
proc datasets nowarn noprint lib=work;
delete chktable;
quit;
/*after each censor reason upnumber table*/
%let tablenum = %eval(&tablenum + 1);
%end; /*dataset exists*/
%end; /*censor reason loop*/
%end; /*T3*/
%end; /*loop through stratifications*/
/*if table = T1 or T2 - upnumber table*/
%if %sysfunc(prxmatch(m/T1|T2/i,&tableid.)) > 0 %then %do;
%let tablenum = %eval(&tablenum + 1);
%end;
%end; /*underlying data exists*/
%end; /*loop through each table*/
%end; /*table requested*/
%mend;
%t1t2censortoc(tablename=t2followuptime, title=At-Risk Period);
%t1t2censortoc(tablename=t&typenum.censor, title=Observable Data);
%end; /*t1censor and t2censor tables*/
/*********************************************************************************************/
/* Type 4 summary tables */
/*********************************************************************************************/
%if %str("&reporttype") = %str("T4L1") & %str("&tablelist") ne %str("") %then %do;
%do tb = 1 %to %sysfunc(countw(&tablelist.));
%let table = %scan(&tablelist., &tb);
/*determine if table includes non-pregnant section*/;
%let nonpreg = %str( );
%let s=;
data _null_;
set tablefile(where=(table="&table"));
if tablesubstrat in ("t4nopreg", "t4nopreggestwk") then do;
call symput('nonpreg', " and Matched Non-Pregnant Episodes ");
call symputx('s', "s");
end;
run;
%if &stratifybydp = Y %then %let tablecount=1;
%else %let tablecount=0;
/*Overall*/
%tableletter();
%addtotoc(tabnum=Table &tablenum.&tableletter.,
%if &table. = T1 %then %do;
caption=%quote(Pregnancy Episodes&nonpreg.with &reporttitle. in the &database. from &startdateformatted. to &enddateformatted.));
%end;
%if &table. = T2 %then %do;
caption=%quote(&reporttitle. Episodes Among Pregnant&nonpreg.Cohort&s. in the &database. from &startdateformatted. to &enddateformatted.));
%end;
%if &table. = T3 %then %do;
caption=%quote(&reporttitle. Codes Among Pregnant&nonpreg.Cohort&s. in the &database. from &startdateformatted. to &enddateformatted., without Adjusting for Stockpiling));
%end;
%if &table. = T4 %then %do;
caption=%quote(&reporttitle. Codes Among Pregnant&nonpreg.Cohort&s. in the &database. from &startdateformatted. to &enddateformatted., Adjusting for Stockpiling));
%end;
%if &table. = T5 %then %do;
caption=%quote(Pregnancy Episodes&nonpreg.with &reporttitle. in the &database. from &startdateformatted. to &enddateformatted., by Gestational Week));
%end;
%if &table. = T6 %then %do;
caption=%quote(&reporttitle. Episodes Among Pregnant&nonpreg.Cohort&s. in the &database. from &startdateformatted. to &enddateformatted., by Gestational Week));
%end;
/*By DP*/
%if &stratifybydp. = Y %then %do;
%do dps = 1 %to %eval(&num_dp.);
%let maskedID = %scan(&masked_dplist,&dps);
%tableletter();
%addtotoc(tabnum=Table &tablenum.&tableletter.,
%if &table. = T1 %then %do;
caption=%quote(Pregnancy Episodes&nonpreg.with &reporttitle. in the &database. for &maskedid. from &startdateformatted. to &enddateformatted.));
%end;
%if &table. = T2 %then %do;
caption=%quote(&reporttitle. Episodes Among Pregnant&nonpreg.Cohort&s. in the &database. for &maskedid. from &startdateformatted. to &enddateformatted.));
%end;
%if &table. = T3 %then %do;
caption=%quote(&reporttitle. Codes Among Pregnant&nonpreg.Cohort&s. in the &database. for &maskedid. from &startdateformatted. to &enddateformatted., without Adjusting for Stockpiling));
%end;
%if &table. = T4 %then %do;
caption=%quote(&reporttitle. Codes Among Pregnant&nonpreg.Cohort&s. in the &database. for &maskedid. from &startdateformatted. to &enddateformatted., Adjusting for Stockpiling));
%end;
%if &table. = T5 %then %do;
caption=%quote(Pregnancy Episodes&nonpreg.with &reporttitle. in the &database. for &maskedid. from &startdateformatted. to &enddateformatted., by Gestational Week));
%end;
%if &table. = T6 %then %do;
caption=%quote(&reporttitle. Episodes Among Pregnant&nonpreg.Cohort&s. in the &database. for &maskedid. from &startdateformatted. to &enddateformatted., by Gestational Week));
%end;
%end;
%end;
%let tablenum = %eval(&tablenum + 1);
%end; /*loop through each table*/
%end; /*type 4 summary tables*/
/*********************************************************************************************/
/* Type 5 summary tables */
/*********************************************************************************************/
%if %str("&reporttype") = %str("T5") %then %do;
/*****************************************************************************************/
/* Type 5 Tables T1-T13, T18-T22 */
/*****************************************************************************************/
/*Example order of tables:
2a: Categorical - overall
2b: Continuous - all
2c: Categorical - by age group
2d: Continuous - by age group */
%macro t5toc(cattableid=, disttableid=, cattitle=, disttitle=);
/*if both categorical and continuous tables specified, then need to ascertain master order between both tables*/
%if %str("&cattableid.") ne %str("") & %str("&disttableid.") ne %str("") %then %do;
/*Because a user can select different stratifications for each table need to ascertain a master order from tablefile regardless of whether includeinreport = Y*/
/*if user excludes includeinreport = N from file, order may not match SOC standard order of operations */
proc sort data=input.&tablefile.(keep=table tablesub where=(table in ("&cattableid","&disttableid"))) out=_temptablefile;
by table;
run;
data _temptablefile;
set _temptablefile;
by table;
length order 3;
if first.table then order = 1;
else order = order+1;
retain order;
run;
proc sort data=_temptablefile nodupkey;
by tablesub;
run;
proc sort data=tablefile(keep=table tablesub stratificationorder tabletitle) out=_temptablefile1;
by tablesub;
run;
*create dataset that maps categorical and continuous tables;
data _tempmap;
merge _temptablefile
_temptablefile1(rename=table=cattable rename=stratificationorder=catstratificationorder where=(cattable="&cattableid"))
_temptablefile1(rename=table=disttable rename=stratificationorder=diststratificationorder where=(disttable="&disttableid"));
by tablesub;
if missing(catstratificationorder) & missing(diststratificationorder) then delete;
run;
proc sort data=_tempmap;
by order ;
run;
%end;
%else %do;
data _tempmap;
set tablefile(keep=table tablesub stratificationorder tabletitle
where=(table in (%if %str("&cattableid.") ne %str("") %then %do; "&cattableid" %end;
%if %str("&disttableid.") ne %str("") %then %do; "&disttableid" %end;)));
run;
%end;
/*Loop through each tablesub, determine whether to output categorical and/or continuous table*/
%isdata(dataset=_tempmap);
%let t5tableobs = &nobs.;
%let tablecount=1;
%do i = 1 %to %eval(&t5tableobs.);
%let cattablestratorder = 0;
%let disttablestratorder = 0;
data _null_;
set _tempmap;
if _n_ = &i. then do;
if tablesub = 'overall' and "&stratifybydp." = "Y" then call symputx('tabletitle', ', by Data Partner');
else call symputx('tabletitle', tabletitle);
/*Both requested - determine whether to print both tables*/
%if %str("&cattableid.") ne %str("") & %str("&disttableid.") ne %str("") %then %do;
if missing(cattable) | missing(disttable) then call symputx('numtables', 1);
else call symputx('numtables', 2);
if missing(cattable)=0 then call symputx('cattablestratorder', catstratificationorder);
if missing(disttable)=0 then call symputx('disttablestratorder', diststratificationorder);
%end;
%else %do;
call symputx('numtables', 1);
/*determine which table*/
if table = "&cattableid" then call symputx('cattablestratorder', stratificationorder);
if table = "&disttableid" then call symputx('disttablestratorder', stratificationorder);
%end;
end;
run;
/*reset table letter counter if only 1 table*/
%if %eval(&t5tableobs.=1) & %eval(&numtables.=1) %then %let tablecount=0;
%if %eval(&cattablestratorder.>0) %then %do;
%tableletter();
%addtotoc(tabnum=Table &tablenum.&tableletter.,
caption=%bquote(&cattitle. for &reporttitle. in the &database. from &startdateformatted. to &enddateformatted.&tabletitle.));
%end;
%if %eval(&disttablestratorder.>0) %then %do;
%tableletter();
%addtotoc(tabnum=Table &tablenum.&tableletter.,
caption=%bquote(&disttitle. for &reporttitle. in the &database. from &startdateformatted. to &enddateformatted.&tabletitle.));
%end;
%end;
/*Save the table of contents datasets for use during the Type 5 report output process*/
%isdata(dataset=t5_tempmap);
%if %eval(&nobs.>0) %then %do;
data t5_tempmap;
set t5_tempmap _tempmap (in=a);
%if %varexist(_tempmap,stratificationorder) = 1 %then %do;
if a and stratificationorder ne . then do;
%if %str("&cattableid.") ne %str("") %then %do;
cattable="&cattableid";
catstratificationorder = stratificationorder;
%end;
%else %if %str("&disttableid.") ne %str("") %then %do;
disttable="&disttableid";
diststratificationorder = stratificationorder;
%end;
end;
%end;
run;
%end;
%else %do;
/*dummy t5_tempmap file*/
data t5_tempmap;
set _tempmap;
%if %varexist(_tempmap,stratificationorder) = 1 %then %do;
if stratificationorder ne . then do;
%if %str("&cattableid.") ne %str("") %then %do;
length cattable $3;
cattable="&cattableid";
catstratificationorder = stratificationorder;
%end;
%else %if %str("&disttableid.") ne %str("") %then %do;
length disttable $3;
disttable="&disttableid";
diststratificationorder = stratificationorder;
%end;
end;
%end;
run;
%end;
proc datasets nowarn noprint lib=work;
delete _temp:;
quit;
%let tablenum = %eval(&tablenum+1);
%mend;
/*T1/T2 - Days Supplied per Dispensing*/
%if %sysfunc(prxmatch(m/T1\b|T2\b/i,&tablelist.)) > 0 %then %do;
%t5toc(cattableid=%if %sysfunc(prxmatch(m/T1\b/i,&tablelist.)) > 0 %then %do; T1 %end;,
disttableid=%if %sysfunc(prxmatch(m/T2\b/i,&tablelist.)) > 0 %then %do; T2 %end;,
cattitle=Categorical Summary of Days Supplied per Dispensing,
disttitle=Continuous Summary of Days Supplied per Dispensing);
%end;
/*T3/T4 - Cumulative episode duration*/
%if %sysfunc(prxmatch(m/T3\b|T4\b/i,&tablelist.)) > 0 %then %do;
%t5toc(cattableid=%if %sysfunc(prxmatch(m/T3\b/i,&tablelist.)) > 0 %then %do; T3 %end;,
disttableid=%if %sysfunc(prxmatch(m/T4\b/i,&tablelist.)) > 0 %then %do; T4 %end;,
cattitle=Categorical Summary of Patients%str(%') Cumulative Treatment Episode Durations,
disttitle=Continuous Summary of Patients%str(%') Cumulative Treatment Episode Durations);
%end;
/*T5/T6 - Episode duration - all episodes*/
%if %sysfunc(prxmatch(m/T5\b|T6\b/i,&tablelist.)) > 0 %then %do;
%t5toc(cattableid=%if %sysfunc(prxmatch(m/T5\b/i,&tablelist.)) > 0 %then %do; T5 %end;,
disttableid=%if %sysfunc(prxmatch(m/T6\b/i,&tablelist.)) > 0 %then %do; T6 %end;,
cattitle=Categorical Summary of All Treatment Episodes,
disttitle=Continuous Summary of All Treatment Episodes);
%end;
/*T7/T8 - Episode duration - first episode*/
%if %sysfunc(prxmatch(m/T7\b|T8\b/i,&tablelist.)) > 0 %then %do;
%t5toc(cattableid=%if %sysfunc(prxmatch(m/T7\b/i,&tablelist.)) > 0 %then %do; T7 %end;,
disttableid=%if %sysfunc(prxmatch(m/T8\b/i,&tablelist.)) > 0 %then %do; T8 %end;,
cattitle=Categorical Summary of First Treatment Episodes,
disttitle=Continuous Summary of First Treatment Episodes);
%end;
/*T9/T10 - Episode duration - second and subsequent episodes*/
%if %sysfunc(prxmatch(m/T9\b|T10\b/i,&tablelist.)) > 0 %then %do;
%t5toc(cattableid=%if %sysfunc(prxmatch(m/T9\b/i,&tablelist.)) > 0 %then %do; T9 %end;,
disttableid=%if %sysfunc(prxmatch(m/T10\b/i,&tablelist.)) > 0 %then %do; T10 %end;,
cattitle=Categorical Summary of Second and Subsequent Treatment Episodes,
disttitle=Continuous Summary of Second and Subsequent Treatment Episodes);
%end;
/*T11 - All episode gaps*/
%if %sysfunc(prxmatch(m/T11\b/i,&tablelist.)) > 0 %then %do;
%t5toc(cattableid=,
disttableid=T11,
cattitle=,
disttitle=Continuous Summary of All Treatment Episode Gaps);
%end;
/*T12 - First episode gap*/
%if %sysfunc(prxmatch(m/T12\b/i,&tablelist.)) > 0 %then %do;
%t5toc(cattableid=,
disttableid=T12,
cattitle=,
disttitle=Continuous Summary of First Treatment Episode Gaps);
%end;
/*T13 - Second and subequent episode gaps*/
%if %sysfunc(prxmatch(m/T13\b/i,&tablelist.)) > 0 %then %do;
%t5toc(cattableid=,
disttableid=T13,
cattitle=,
disttitle=Continuous Summary of Second and Subsequent Treatment Episode Gaps);
%end;
/*T18 - Filled daily dose in each dispensing*/
%if %sysfunc(prxmatch(m/T18\b/i,&tablelist.)) > 0 %then %do;
%t5toc(cattableid=T18,
disttableid=,
cattitle=Summary of Filled Daily Dose in Each Dispensing,
disttitle=);
%end;
/*T19 - Average filled daily dose in each episode*/
%if %sysfunc(prxmatch(m/T19\b/i,&tablelist.)) > 0 %then %do;
%t5toc(cattableid=T19,
disttableid=,
cattitle=Summary of Average Filled Daily Dose in Each Treatment Episode,
disttitle=);
%end;
/*T20 - Average filled daily dose in first episode*/
%if %sysfunc(prxmatch(m/T20\b/i,&tablelist.)) > 0 %then %do;
%t5toc(cattableid=T20,
disttableid=,
cattitle=Summary of Average Filled Daily Dose in Each Patient%str(%')s First Valid Episode,
disttitle=);
%end;
/*T21 - Cumulative filled dose in each episode*/
%if %sysfunc(prxmatch(m/T21\b/i,&tablelist.)) > 0 %then %do;
%t5toc(cattableid=T21,
disttableid=,
cattitle=Summary of Cumulative Filled Dose in All Treatment Episodes,
disttitle=);
%end;
/*T22 - Cumulative filled dose in first episode*/
%if %sysfunc(prxmatch(m/T22\b/i,&tablelist.)) > 0 %then %do;
%t5toc(cattableid=T22,
disttableid=,
cattitle=Summary of Cumulative Filled Dose in Each Patient%str(%')s First Treatment Episode,
disttitle=);
%end;
/*Additional variables for ordering Type 5 table report output*/
%isdata(dataset=t5_tempmap);
%if %eval(&nobs.>0) %then %do;
data t5_tempmap;
set t5_tempmap;
length t5order 3;
t5order=_n_;
run;
proc sort data = t5_tempmap;
by table t5order;
run;
data t5_tempmap;
set t5_tempmap;
by table;
length numtables tableorder 3;
if first.table and last.table
%if %varexist(t5_tempmap,cattable) = 1 & %varexist(t5_tempmap,disttable) = 1 %then %do; and (cattable = '' or disttable = '') %end;
then numtables=1;
else numtables=2;
retain tableorder;
if first.table then tableorder=0;
tableorder+1;
run;
proc sort data = t5_tempmap;
by t5order table;
run;
%end;
/*****************************************************************************************/
/* Type 5 censor tables (T14-T17) */
/*****************************************************************************************/
%macro t5censortoc(tableid=, first=, dataset=);
%if %sysfunc(prxmatch(m/T14\b|T16\b/i,&tableid.)) > 0 %then %do;
/*counter for determining table letter*/
%if &stratifybydp. = Y %then %let tablecount = 1;
%else %let tablecount = 0;
%tableletter();
%addtotoc(tabnum=Table &tablenum.&tableletter.,
caption=%quote(Summary of Reasons &first.Treatment Episodes Ended for &reporttitle. in the &database. from &startdateformatted. to &enddateformatted.));
%if &stratifybydp. = Y %then %do;
%tableletter();
%addtotoc(tabnum=Table &tablenum.&tableletter.,
caption=%quote(Summary of Reasons &first.Treatment Episodes Ended for &reporttitle. in the &database. from &startdateformatted. to &enddateformatted., by Data Partner));
%end;
%let tablenum = %eval(&tablenum + 1);
%end;
%if %sysfunc(prxmatch(m/T15\b|T17\b/i,&tableid.)) > 0 %then %do;
/*loop through each reason for censoring*/
%do c = 1 %to %sysfunc(countw(&defaultcensororder., ' '));
%let reason = %scan(&defaultcensororder., &c.);
%let censorreasontable = N;
data _null_;
set tablefile(where=(dataset in ("t5censor") and table = "&tableid."));
/*check if censoring reason requested*/
if findw(censorreason, "&reason.")>0 then call symputx('censorreasontable', 'Y');
run;
%if &censorreasontable. = Y %then %do;
/*check if rows exist in table (censorreason parameter has already been applied in %censortables_createdata*/
data chktable;
set &dataset.(where=(table_name="&reason."));
run;
%isdata(dataset=chktable);
%if %eval(&nobs.>0) %then %do;
/*note - table is not stratified by DP*/
%addtotoc(tabnum=Table &tablenum.,
caption=%quote(Summary of Episode Duration for &first.Treatment Episodes Ended due to %bquote(&&&reason._label) for &reporttitle. in the &database. from &startdateformatted. to &enddateformatted.));
%let tablenum = %eval(&tablenum + 1);
%end;
proc datasets nowarn noprint lib=work;
delete chktable;
quit;
%end;
%end;
%end;
%mend;
%if %sysfunc(prxmatch(m/T14\b/i,&tablelist.)) > 0 %then %do;
%t5censortoc(tableid=T14, first=%str(First ), dataset=);
%end;
%if %sysfunc(prxmatch(m/T15\b/i,&tablelist.)) > 0 %then %do;
%t5censortoc(tableid=T15, first=%str(First ), dataset=t5censor_first);
%end;
%if %sysfunc(prxmatch(m/T16\b/i,&tablelist.)) > 0 %then %do;
%t5censortoc(tableid=T16, first=, dataset=);
%end;
%if %sysfunc(prxmatch(m/T17\b/i,&tablelist.)) > 0 %then %do;
%t5censortoc(tableid=T17, first=, dataset=t5censor);
%end;
%end; /*type 5 tables*/
/*********************************************************************************************/
/* Type 6 tables */
/*********************************************************************************************/
%if %sysfunc(prxmatch(m/t6censor|t6plota|t6plotb/i,&tdatasetlist.)) > 0 %then %do;
%macro t6toc(tableid=, title=);
%isdata(dataset=table&tableid.);
%if %eval(&nobs.>0) %then %do;
%let stratificationorder = 0;
proc sql noprint;
select max(stratificationorder) into: stratificationorder
from tablefile(where=(table = "&tableid"));
quit;
/*counter for determining table letter*/
%if %eval(&stratificationorder. = 1) & &stratifybydp. ne Y %then %let tablecount = 0;
%else %let tablecount = 1;
%do st = 1 %to &stratificationorder.;
data _null_;
set tablefile(where=(table = "&tableid" and stratificationorder = &st.));
call symputx('tabletitle', tabletitle);
run;
%tableletter();
%addtotoc(tabnum=Table &tablenum.&tableletter.,
%if &tableid. eq T8 or &tableid. eq T9 or &tableid. eq T10 %then %do;
caption=%quote(Summary of &title. for &reporttitle. in the &database. from &startdateformatted. to &enddateformatted.&tabletitle.));
%end;
%if &stratifybydp. = Y & %eval(&st.=1) %then %do;
%tableletter();
%addtotoc(tabnum=Table &tablenum.&tableletter.,
%if &tableid. eq T8 or &tableid. eq T9 or &tableid. eq T10 %then %do;
caption=%quote(Summary of &title. for &reporttitle. in the &database. from &startdateformatted. to &enddateformatted., by Data Partner));
%end;
%end;
%end; /*loop through stratifications*/
%let tablenum = %eval(&tablenum + 1);
%end; /*underlying data exists*/
%mend t6toc;
%t6toc(tableid=T8, title=Episode Duration by Reason Episodes Ended);
%t6toc(tableid=T9, title=Time to First Switch or Episode End);
%t6toc(tableid=T10, title=Time to Second Switch or Episode End);
%end; /*type 6 tables*/
/*********************************************************************************************/
/* Code Distribution Tables */
/*********************************************************************************************/
%if &output_code_distribution. eq Y %then %do;
/* This macros output a specific distribution type (EXP or HOI) entries in the table of content */
%macro codedistribution_type_toc(distindextype=);
/* Compute group label to display in title */
%let grouplabel=;
%isdata(dataset=labelfile);
%if %eval(&nobs>0) %then %do;
proc sql noprint;
select label into :grouplabel trimmed from labelfile
where lower(group)="&group." and runid = "&runid" and
%if &distindextype. eq exp %then %do;
lower(labeltype)="grouplabel";
%end;
%else %do;
lower(labeltype)="outcomelabel";
%end;
quit;
%end;
%if %str("&grouplabel.") eq %str("") %then %let grouplabel = %trim(&group.);
/* Full Code Distribution Table */
%tableletter();
%addtotoc(tabnum=Table &tablenum.&tableletter.,
caption=%quote(Full Code Distribution of &grouplabel. in the &database. from &startdateformatted. to &enddateformatted.));
/* Total Code Counts Table */
%tableletter();
%addtotoc(tabnum=Table &tablenum.&tableletter.,
caption=%quote(Total Code Counts of &grouplabel. in the &database. from &startdateformatted. to &enddateformatted.));
%mend codedistribution_type_toc;
/* reset counter to reset table letter */
%let tablecount=1;
proc sql noprint;
select count(*) into :numgroupscodedist trimmed
from GroupsDist;
quit;
%do loopcount = 1 %to &numgroupscodedist.;
%let codedistexp = N;
%let codedisthoi = N;
data _null_;
set GroupsDist;
if &loopcount. = _N_;
call symputx('runid', runid);
call symputx('group', group);
if index(upcase(codedist), "EXP") > 0 then call symputx('codedistexp', 'Y');
if index(upcase(codedist), "HOI") > 0 then call symputx('codedisthoi', 'Y');
run;
%if &codedistexp. eq Y %then %do;
* Defensive: make sure the requested data is available;
%let obscount=0;
proc sql noprint;
select count(*) into :obscount from codedistdata
where lower(group) = "&group." and runid = "&runid" and lower(distindextype) = "exp";
quit;
%if %eval(&obscount. > 0) %then %codedistribution_type_toc(distindextype=exp);
%end;
%if &codedisthoi. eq Y %then %do;
* Defensive: make sure the requested data is available;
%let obscount=0;
proc sql noprint;
select count(*) into :obscount from codedistdata
where lower(group) = "&group." and runid = "&runid" and lower(distindextype) = "hoi";
quit;
%if %eval(&obscount. > 0) %then %codedistribution_type_toc(distindextype=hoi);
%end;
%end; *numgroupscodedist;
%let tablenum = %eval(&tablenum + 1);
%end;
/*********************************************************************************************/
/* Attrition table */
/*********************************************************************************************/
/* reset counter to reset table letter */
%let tablecount=1;
%do j = %eval(&look_start.) %to %eval(&look_end.);
%if %index(&reporttype,L2) %then %let attrperiodid = _&j;
%isdata(dataset=agg_patient_attrition&attrperiodid);
%let attrition_patient = &nobs;
%isdata(dataset=agg_episode_attrition&attrperiodid);
%let attrition_episode = &nobs;
%if &attrition_patient > 0 or &attrition_episode > 0 %then %do;
%if (&attrition_patient > 0 and &attrition_episode = 0) or (&attrition_patient = 0 and &attrition_episode > 0) %then %do;
%let tablecount = 0;
%end;
%if &attrition_episode > 0 %then %do;
%tableletter();
%addtotoc(tabnum=Table &tablenum.&tableletter.,
caption=%quote(Summary of Episode Level Cohort Attrition in the &database. from &startdateformatted. to &&enddate&j.formatted.));
%end;
%if &attrition_patient > 0 %then %do;
%tableletter();
%addtotoc(tabnum=Table &tablenum.&tableletter.,
caption=%quote(Summary of Patient Level Cohort Attrition in the &database. from &startdateformatted. to &&enddate&j.formatted.));
%end;
%let tablenum = %eval(&tablenum + 1);
%end;/* attrition_groups file */
%end;/*periodid */
/*** END TABLES **/
/*********************************************************************************************/
/* Figures */
/*********************************************************************************************/
%isdata(dataset=figurefile);
%if %eval(&nobs.>0) %then %do;
%let figurenum = 1; /* Add +1 for additional figure types that are requested */
%let tablecount = 1;
/***************************************************************************************/
/* L1 Figures */
/***************************************************************************************/
%if %sysfunc(prxmatch(m/T1|T2L1|T5|T6/i,&reporttype.)) > 0 %then %do;
/*utility macro to loop through groups*/
%macro figuretoc(figure=, title =, dataset_name =);
%isdata(dataset=&dataset_name.);
%if %eval(&nobs.>0) %then %do;
/*number of distinct groups in figure to loop through determine whether to add letter to figure #*/
proc sql noprint;
select distinct order
into :fgrouporderlist separated by ' '
from &dataset_name.
order by order;
select max(stratificationorder)
into :fstrataorder
from figurefile
where figure="&figure";
quit;
%if %sysfunc(countw(&fgrouporderlist.)) = 1 and &fstrataorder = 1 %then %let tablecount = 0;
%else %let tablecount = 1;
%do g = 1 %to %sysfunc(countw(&fgrouporderlist.));
%let order = %scan(&fgrouporderlist., &g.);
%let grouplabel = ;
%do f = 1 %to &fstrataorder;
%let figuretitle = "";
data _null_;
set figurefile(where=(figure = "&figure" and stratificationorder = &f));
call symputx('figuretitle', figuretitle);
run;
data _null_;
set &dataset_name.(where=(order = &order.));
if _n_ = 1 then do;
call symputx('grouplabel', grouplabel);
end;
run;
%tableletter();
%addtotoc(tabnum=Figure &figurenum.&tableletter.,
caption=%quote(&title. &grouplabel. in the &database. from &startdateformatted. to &enddateformatted.&figuretitle.));
%end;
%end; /*loop through each figure*/
%let figurenum = %eval(&figurenum.+1);
%end; /*figure dataset exists*/
%mend;
/**********************************************************************************************
T1: 1 figure:
1) F1: t1censor = Reasons for End of Observable Data by Group (1-CDF) - 1 figure per group
/**********************************************************************************************/
%if &reporttype. = T1 %then %do;
%figuretoc(figure=F1, title =Reasons for End of Observable Data Among, dataset_name = figureF1);
%end; /*T1*/
/**********************************************************************************************
T2L1: 3 figures:
1) F1: t2followuptime = Kaplan-Meier Estimate of Event of Interest Not Occurring
2) F2: t2followuptime = Reasons for End of Follow-Up by Group (1-CDF)
3) F3: t2censor = Reasons for End of Observable Data by Group (1-CDF)
/**********************************************************************************************/
%if &reporttype. = T2L1 %then %do;
/*F1: 1 figure per report*/
%isdata(dataset=figuref1);
%if %eval(&nobs.>0) %then %do;
%addtotoc(tabnum=Figure &figurenum.,
caption=%quote(Kaplan-Meier Estimate of Event of Interest Not Occurring in the &database. from &startdateformatted. to &enddateformatted.));
%let figurenum = %eval(&figurenum.+1);
%end;
/*F2: 1 figure per group*/
%if %sysfunc(prxmatch(m/F2/i,&figurelist.)) > 0 %then %do;
%figuretoc(figure=F2, title =Reasons for End of Follow-Up Among, dataset_name = figureF2);
%end; /*figuref2*/
/*F3: 1 figure per group*/
%if %sysfunc(prxmatch(m/F3/i,&figurelist.)) > 0 %then %do;
%figuretoc(figure=F3, title =Reasons for End of Observable Data Among, dataset_name = figureF3);
%end; /*figuref3*/
%end; /*T2L1*/
/**********************************************************************************************
T5: 5 figures:
1) F1: Patient Entry into Study by Month
2) F2: Number of Prescription Dispensings in Patients First Episodes by Month
3) F3: Total Days Supply in Patients' First Episodes by Month
4) F4: t5censor = Reasons for End of First Treatment Episode by Group
5) F5: t5censor = End of First Treatment Episode due to [Censoring Reason] by Group
/**********************************************************************************************/
%if &reporttype. = T5 %then %do;
/* F1 */
%if %sysfunc(prxmatch(m/\bF1\b/i,&figurelist.)) > 0 %then %do;
%figuretoc(figure=F1, title =Patient Entry into Study by Month for, dataset_name = figure123);
%end;
/* F2 */
%if %sysfunc(prxmatch(m/F2/i,&figurelist.)) > 0 %then %do;
%figuretoc(figure=F2, title =Number of Prescription Dispensings in Patients%str(%') First Episodes by Month Patient Entered into Study for,
dataset_name = figure123);
%end;
/* F3 */
%if %sysfunc(prxmatch(m/F3/i,&figurelist.)) > 0 %then %do;
%figuretoc(figure=F3, title =Total Days Supply in Patients%str(%') First Episodes by Month Patient Entered into Study for,
dataset_name = figure123);
%end;
/*F4: 1 figure per group*/
%if %sysfunc(prxmatch(m/F4/i,&figurelist.)) > 0 %then %do;
%figuretoc(figure=F4, title =Reasons for End of First Treatment Episode Among, dataset_name = figureF4);
%end; /*figuref4*/
/*F5: 1 figure per report*/
/*Censor reason*/
%if %sysfunc(prxmatch(m/F5/i,&figurelist.)) > 0 %then %do;
%isdata(dataset= figuref5);
%if %eval(&nobs.>0) %then %do;
data _null_;
set figurefile(where=(figure="F5"));
call symputx('censordisplay', censordisplay);
run;
%addtotoc(tabnum=Figure &figurenum,
caption =%quote(End of First Treatment Episode due to &&&censordisplay._label in the &database. from &startdateformatted. to &enddateformatted.));
%let figurenum = %eval(&figurenum.+1);
%end;
%end;
%end; /*T5*/
/**********************************************************************************************
T6: 7 figures:
1) F1 (not yet implemented)
2) F2 (not yet implemented)
3) F3 (not yet implemented)
4) F4: t6plota = Kaplan-Meier Estimate of First Switch Not Occurring
5) F5: t6plotb = Kaplan-Meier Estimate of Second Switch Not Occurring
6) F6: t6plota = Reasons for Censoring at First Switch Evaluation by Analysisgrp
7) F7: t6plotb = Reasons for Censoring at Second Switch Evaluation by Analysisgrp
/***********************************************************************************************/
%if &reporttype. = T6 %then %do;
/*F4 - F7: 1 figure per group*/
%if %sysfunc(prxmatch(m/F4/i,&figurelist.)) > 0 %then %do;
%figuretoc(figure=F4, title =Kaplan-Meier Estimate of First Switch Not Occurring Among, dataset_name = figureF4);
%end; /*figuref4*/
%if %sysfunc(prxmatch(m/F5/i,&figurelist.)) > 0 %then %do;
%figuretoc(figure=F5, title =Kaplan-Meier Estimate of Second Switch Not Occurring Among, dataset_name = figureF5);
%end; /*figuref5*/
%if %sysfunc(prxmatch(m/F6/i,&figurelist.)) > 0 %then %do;
%figuretoc(figure=F6, title =Reasons for Censoring at First Switch Evaluation Among, dataset_name = figureF6);
%end; /*figuref6*/
%if %sysfunc(prxmatch(m/F7/i,&figurelist.)) > 0 %then %do;
%figuretoc(figure=F7, title =Reasons for Censoring at Second Switch Evaluation Among, dataset_name = figureF7);
%end; /*figuref7*/
%end; /*T6*/
%end; /*L1 figures*/
/***************************************************************************************/
/* L2 Figures */
/***************************************************************************************/
%if %sysfunc(prxmatch(m/T2L2|T4L2/i,&reporttype.)) > 0 %then %do;
/*F1: PS distribution histograms*/
%if %sysfunc(prxmatch(m/F1/i,&figurelist.)) > 0 %then %do;
proc sql noprint;
select count(distinct AnalysisGrp) into: numPScomparisons
from l2comparisonfile(where=(OutputPSDistribution="Y"));
quit;
%do loopcount = 1 %to &numl2comparisons.;
data _NULL_;
set l2comparisonfile(where=(order=&loopcount.));
call symputx('runid', runid);
call symputx('analysisgrp', analysisgrp);
call symputx('OutputPSDistribution', OutputPSDistribution);
run;
%if &OutputPSDistribution. = Y %then %do;
%isdata(dataset=labelfile);
%let grouplabel=&analysisgrp.;
%if %eval(&nobs>0) %then %do;
data _NULL_;
set labelfile(where=(lowcase(labeltype)='grouplabel'));
if group="&analysisgrp." and runid = "&runid";
call symputx('grouplabel', Label);
run;
%put &grouplabel.;
%end;
%let andafter=;
proc sql noprint;
select strip(file) into: psfile
from pscs_masterinputs
where analysisgrp = "&analysisgrp." and missing(subgroup);
quit;
%if &psfile. = psmatchfile | &psfile. = stratificationfile | &psfile. = iptwfile %then %do;
data _null_;
set pscs_masterinputs (where=(lowcase(analysisgrp)="&analysisgrp." and missing(subgroup)));
call symputx("psestimategrp", lowcase(psestimategrp));
%if &psfile. = psmatchfile %then %do;
if upcase(ratio) = "F" then do;
call symput("andafter", " and After");
end;
%end;
%if &psfile = iptwfile %then %do;
call symput("andafter", " and After");
%end;
%else %if &psfile = stratificationfile %then %do;
if upcase(strataweight) in ("ATE", "ATT") then do;
call symput("andafter", " and After");
end;
%end;
run;
%do j = %eval(&look_start) %to %eval(&look_end);
%if &numPScomparisons.=1 and %eval(&look_end)=1 %then %do;
%let tablecount = 0;
%end;
%tableletter();
%addtotoc(tabnum=Figure &figurenum.&tableletter.,
caption=%quote(Histograms Depicting Propensity Score Distributions Before&andafter Adjustment for &grouplabel. in the &database. from &startdateformatted. to &&enddate&j.formatted.))
%end; /* loop periods */
%end; /*psfile*/
%end; /* OutputPSDistribution */
%end; /* loop comparisons */
%let figurenum = %eval(&figurenum.+1);
%end; /*Histograms*/
/*F2: Forest Plots*/
%if %sysfunc(prxmatch(m/F2/i,&figurelist.)) > 0 %then %do;
%if %sysfunc(prxmatch(m/T2L2/i,&reporttype.)) > 0 %then %let ForestRatioTitle = Hazard Ratios (HR);
%else %let ForestRatioTitle = Odds Ratios (OR);
%let tableletter=a;
%let tablecount = 1;
%do j = %eval(&look_start) %to %eval(&look_end);
%do plot = 1 %to 7;
%let forest_title = ;
data _null_;
set forest_&j(where=(plotorder=&plot));
call symputx("forest_title",forest_title);
run;
%if %length(&forest_title) > 0 %then %do;
%tableletter();
%addtotoc(tabnum=Figure &figurenum.&tableletter.,
caption=%quote(Forest Plot of &ForestRatioTitle and 95% Confidence Intervals (CI) for &forest_title in the &database. from &startdateformatted. to &&enddate&j.formatted.))
%end; /* Forest title exists */
%end; /* loop plots */
%end; /* loop periods */
%let figurenum = %eval(&figurenum.+1);
%end; /*Forest plots */
/*F3-F5: KM Plots - Type 2 only*/
%if &reporttype. = T2L2 & %sysfunc(prxmatch(m/F3|F4|F5/i,&figurelist.)) > 0 %then %do;
*reset tablecount;
%let tablecount = 1;
/*loop through each analysisgrp - dataset only exists if curve computed*/
%do loopcount = 1 %to &numl2comparisons.;
data _null_;
set l2comparisonfile(where=(order=&loopcount.));
call symputx('runid', runid);
call symputx('analysisgrp', analysisgrp);
run;
proc sql noprint;
select distinct strip(file) into: pscsfile trimmed
from pscs_masterinputs
where analysisgrp = "&analysisgrp." and runid = "&runid" and missing(subgroup);
quit;
%if &pscsfile. = psmatchfile | &pscsfile. = stratificationfile %then %do;
/*assign labels*/
data _null_;
set pscs_masterinputs(where=(analysisgrp="&analysisgrp." and missing(subgroup)));
call symputx("psestimategrp", lowcase(psestimategrp));
run;
data _null_;
set infolder.&&&runid._psestimationfile(where=(lowcase(psestimategrp)="&psestimategrp."));
call symputx('GRP1', eoi);
call symputx('GRP0', ref);
run;
%let outcomelabel = Event of Interest;
%let eoilabel = &grp1.;
%let reflabel = &grp0.;
%isdata(dataset=labelfile);
%if %eval(&nobs.>0) %then %do;
data _null_;
set labelfile(in=a where=(group="&analysisgrp" and runid = "&runid" and labeltype = "outcomelabel"))
labelfile(in=b where=(group="&grp1." and runid = "&runid." and labeltype = "grouplabel"))
labelfile(in=c where=(group="&grp0." and runid = "&runid." and labeltype = "grouplabel"));
if a then call symputx('outcomelabel', label);
if b then call symputx('eoilabel', label);
if c then call symputx('reflabel', label);
run;
%end;
/*loop through periodid*/
%do j = %eval(&look_start) %to %eval(&look_end);
/*F3*/
%isdata(dataset=figureF3_analysis&loopcount._&j.);
%if %eval(&nobs.>0) %then %do;
%tableletter();
%addtotoc(tabnum=Figure &figurenum.&tableletter.,
caption=%quote(Unadjusted Kaplan-Meier Estimate of &outcomelabel. Not Occurring Among &eoilabel. and &reflabel. in the &database. from &startdateformatted. to &&enddate&j.formatted.));
%end;
/*F4*/
%isdata(dataset=figureF4_analysis&loopcount._&j.);
%if %eval(&nobs.>0) %then %do;
%tableletter();
%addtotoc(tabnum=Figure &figurenum.&tableletter.,
caption=%quote(Conditional Kaplan-Meier Estimate of &outcomelabel. Not Occurring Among &eoilabel. and &reflabel. in the &database. from &startdateformatted. to &&enddate&j.formatted.));
%end;
/*F5*/
%isdata(dataset=figureF5_analysis&loopcount._&j.);
%if %eval(&nobs.>0) %then %do;
%tableletter();
%addtotoc(tabnum=Figure &figurenum.&tableletter.,
caption=%quote(Unconditional Kaplan-Meier Estimate of &outcomelabel. Not Occurring Among &eoilabel. and &reflabel. in the &database. from &startdateformatted. to &&enddate&j.formatted.));
%end;
%end; /*loop through periodid*/
%end; /*only PSmatch or stratification*/
%end;
/*if there is only 1 figure, rewrite figure # - this method is used instead of determining apriori b/c of
the numerous permutations of situations that can lead to 1 figure */
proc sql noprint;
select count(caption) into: countkm
from tableofcontents
where index(caption, 'Kaplan-Meier Estimate')>0;
quit;
%if %eval(&countkm.)=1 %then %do;
data tableofcontents;
set tableofcontents;
if index(caption, 'Kaplan-Meier Estimate')>0 then do;
tabnum = "Figure &figurenum.";
end;
run;
%end;
%let figurenum = %eval(&figurenum.+1);
%end; /*KM plots*/
%end; /*L2 figures*/
%end; /* Figure file */
%end; /*to be removed*/
/*****************/
/* Appendices */
/*****************/
/*Appendix A*/
%addtotoc(tabnum=Appendix A, caption=Dates of Available Data for Each Data Partner (DP) as of Request Distribution Date &datedistributed.);
/* The remaining appendices are created in appendix_driver.sas */
/*********************/
/* Remove empty rows */
/*********************/
data tableofcontents;
set tableofcontents;
if missing(tabnum)=0;
run;
%put =====> END MACRO: create_tableofcontents ;
%mend create_tableofcontents;