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Merge pull request #70 from dominodatalab/qc_t_saftey_01
Performed qc of saftey for 01
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‎qc/tfl/qc_t_saftey_01.sas‎

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/*****************************************************************************\
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* ____ _
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* | _ \ ___ _ __ ___ (_)_ __ ___
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* | | | |/ _ \| '_ ` _ \| | '_ \ / _ \
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* | |_| | (_) | | | | | | | | | | (_) |
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* |____/ \___/|_| |_| |_|_|_| |_|\___/
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* ____________________________________________________________________________
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* Sponsor : Domino
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* Study : CDISC01
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* Program : qc_t_pop.sas
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* Purpose : Create the QC Summary of Populations Table
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* ____________________________________________________________________________
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* DESCRIPTION
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*
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* Input files: ADaM.ADSL
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*
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* Output files: qc_t_pop.
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* t_pop.sas7bdat
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*
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* Macros: None vt
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*
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* Assumptions: Demo only - Second comment 20240311
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*
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* ____________________________________________________________________________
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* PROGRAM HISTORY
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* 10MAY2023 | Megan Harries | Original
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* 08DEC2023 | Petter Olsson | Demo Comment
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* ----------------------------------------------------------------------------
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\*****************************************************************************/
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*********;
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** Setup environment including libraries for this reporting effort;
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%include "/mnt/code/domino.sas";
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*********;
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ods path(prepend) work.templat(update);
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*Set the template for the output;
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proc template;
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define style newstyle;
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class Table /
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Rules = Groups
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Frame = void;
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style header
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/ just = c
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fontweight = medium;
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replace Body from Document /
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bottommargin = 1.54cm
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topmargin = 2.54cm
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rightmargin = 2.54cm
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leftmargin = 2.54cm;
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replace fonts /
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'TitleFont2' = ("Courier New",9pt)
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'TitleFont' = ("Courier New",9pt/*,Bold*/) /* titles */
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'StrongFont' = ("Courier New",9pt/*,Bold*/)
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'EmphasisFont' = ("Courier New",9pt,Italic)
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'FixedEmphasisFont' = ("Courier New, Courier",9pt,Italic)
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'FixedStrongFont' = ("Courier New, Courier",9pt/*,Bold*/)
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'FixedHeadingFont' = ("Courier New, Courier",9pt/*,Bold*/)
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'BatchFixedFont' = ("SAS Monospace, Courier New, Courier",9pt)
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'FixedFont' = ("Courier New, Courier",9pt)
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'headingEmphasisFont' = ("Courier New",9pt,Bold Italic)
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'headingFont' = ("Courier New",9pt/*,Bold*/) /* header block */
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'docFont' = ("Courier New",9pt); /* table cells */
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replace color_list
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"Colors used in the default style" /
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'link' = blue
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'bgH' = white /* header background */
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'fg' = black
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'bg' = _undef_;
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end;
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run ;
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options orientation = landscape nonumber nodate nobyline;
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** adsl and include required variables for table;
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data adsl_all (rename = (actarm = trta));
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length trtan agen sexn 8.;
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set adam.adsl;
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if actarm = "Placebo" then trtan = 1;
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else if actarm = "Xanomeline Low Dose" then trtan = 2;
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else if actarm = "Xanomeline High Dose" then trtan = 3;
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if age < 60 then agen = 1;
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else if 60 <= age < 65 then agen = 2;
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else if 65 <= age < 70 then agen = 3;
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else if 70 <= age < 75 then agen = 4;
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else if 75 <= age < 80 then agen = 5;
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else if 80 <= age then agen = 6;
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if sex = 'M' then sexn = 1;
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if sex = 'F' then sexn = 2;
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run;
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** observations in the population, and the parameters specified in SAP;
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data adsl (keep = usubjid trta trtan age agen sex sexn);
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set adsl_all(where = (trtan ne .));
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run;
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** create macro for counting number of placebo participants;
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proc sql noprint;
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select count(distinct usubjid)
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into :placebo_n
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from adsl(where = (trta = "Placebo"));
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quit;
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** create macro for counting number of Xanomeline Low Dose participants;
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proc sql noprint;
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select count(distinct usubjid)
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into :low_dose_n
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from adsl(where = (trta = "Xanomeline Low Dose"));
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quit;
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** create macro for counting number of Xanomeline High Dose participants;
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proc sql noprint;
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select count(distinct usubjid)
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into :high_dose_n
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from adsl(where = (trta = "Xanomeline High Dose"));
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quit;
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** create macro for each variable results;
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** calculate number of unique subjects with post-baseline results;
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proc sql;
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create table total_age as
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select trta, count(distinct usubjid) as count_age
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from adsl
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group by trta;
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quit;
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** calculate number of unique subjects for each age group;
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%macro age_data(agen = );
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data age&agen.;
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set adsl;
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where agen = &agen.;
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run;
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proc sql;
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create table total_age&agen. as
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select trta, count(distinct usubjid) as n&agen.
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from age&agen.
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group by trta;
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quit;
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%mend age_data;
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%age_data(agen = 1);
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%age_data(agen = 2);
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%age_data(agen = 3);
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%age_data(agen = 4);
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%age_data(agen = 5);
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%age_data(agen = 6);
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** merge the counts and calculate percentages;
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data results;
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merge total_age total_age1 total_age2 total_age3 total_age4 total_age5 total_age6;
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by trta;
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if n1 ne . then p1 = cats("(", put(100*n1/count_age, 6.1), ")");
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if n2 ne . then p2 = cats("(", put(100*n2/count_age, 6.1), ")");
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if n3 ne . then p3 = cats("(", put(100*n3/count_age, 6.1), ")");
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if n4 ne . then p4 = cats("(", put(100*n4/count_age, 6.1), ")");
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if n5 ne . then p5 = cats("(", put(100*n5/count_age, 6.1), ")");
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if n6 ne . then p6 = cats("(", put(100*n6/count_age, 6.1), ")");
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run;
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** concatenate results for any parameter data;
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data results_c;
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length results1 results2 results3 results4 results5 results6 $32;
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set results;
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** convert post baseline count to character;
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count_age_c = "";
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** if 100% then no decimal places;
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if p1 = "(100.0)" then p1 = "(100)";
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if p2 = "(100.0)" then p2 = "(100)";
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if p3 = "(100.0)" then p3 = "(100)";
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if p4 = "(100.0)" then p4 = "(100)";
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if p5 = "(100.0)" then p5 = "(100)";
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if p6 = "(100.0)" then p6 = "(100)";
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** if 0% then only n = 0 is displayed, no event or percentage;
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** concatenate n and p;
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if p1 = " " then results1 = "0";
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else results1 = catx(" ", put(n1, 8.), p1);
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if p2 = " " then results2 = "0";
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else results2 = catx(" ", put(n2, 8.), p2);
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if p3 = " " then results3 = "0";
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else results3 = catx(" ", put(n3, 8.), p3);
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if p4 = " " then results4 = "0";
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else results4 = catx(" ", put(n4, 8.), p4);
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if p5 = " " then results5 = "0";
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else results5 = catx(" ", put(n5, 8.), p5);
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if p6 = " " then results6 = "0";
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else results6 = catx(" ", put(n6, 8.), p6);
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run;
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** transpose any results dataset;
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options validvarname=v7;
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proc transpose data = results_c out = results_t name = agegroup;
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id trta;
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var count_age_c results1 results2 results3 results4 results5 results6;
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run;
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** add parameter identifier and order variable;
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data order_results(rename = (Xanomeline_Low_Dose = Low_Dose Xanomeline_High_Dose = High_Dose));
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length order1 8. ageresults $50 stat $8;
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set results_t;
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if agegroup = "count_age_c" then do;
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order1 = 1;
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ageresults = "";
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stat = "";
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end;
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else do;
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order1 = input(substr(agegroup, 8), 8.)+1;
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stat = "n (%)";
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end;
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if agegroup = "results1" then ageresults = "Less than 60 years old";
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else if agegroup = "results2" then ageresults = "60 years old <= age < 65 years old";
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else if agegroup = "results3" then ageresults = "65 years old <= age < 70 years old";
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else if agegroup = "results4" then ageresults = "70 years old <= age < 75 years old";
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else if agegroup = "results5" then ageresults = "75 years old <= age < 80 years old";
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else if agegroup = "results6" then ageresults = "80 years and older";
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run;
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** create the table output;
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ods pdf file = "/mnt/artifacts/TFL_QC/qc_t_pop.pdf"
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style = newstyle;
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ods noproctitle;
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ods escapechar = "^";
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** add titles to output;
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title1 justify = left "Domino" justify = right "Page ^{thispage} of ^{lastpage}";
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title2 "Table 14.3.4.1";
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title3 "Summary of Age for each Treatment";
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title4 "Analysis Set";
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** justify contents to decimal places;
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** if you want TFL to also be written to Dataset. proc report data = order_results headline split = "*" style(report) = {width = 100% cellpadding = 3} out = tflqc.t_pop;
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proc report data = order_results headline split = "*" style(report) = {width = 100% cellpadding = 3};
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column (order1 ageresults stat placebo low_dose high_dose);
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** order variables;
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define order1 / order noprint;
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define ageresults / "*Age Group" style(column) = {just = l asis = on width = 30%} style(header) = {just = l asis = on};
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define stat / "*Statistic" style(column) = {just = l width = 10%};
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define placebo / "Placebo* (N=%cmpres(&placebo_n))" style(column) = {just = d width = 18%};
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define low_dose / "Xanomeline Low Dose* (N=%cmpres(&low_dose_n))" style(column) = {just = d width = 20%};
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define high_dose / "Xanomeline High Dose* (N=%cmpres(&high_dose_n))" style(column) = {just = d width = 20%};
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** add footnotes describing the critical codes;
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footnote1 justify = left "Note: n = number of unique subjects in age group.";
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footnote2 justify = left "Note: percentages are based on the number of patients for each treatment.";
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footnote3 justify = left "Dataset(s): ADSL; Program: qc_t_pop.sas; Output: qc_t_pop.pdf; Generated on: &sysdate9 &systime";
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run;
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ods pdf close;
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