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Merge pull request #71 from dominodatalab/Interim_01
Final Interim 01
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‎prod/tfl/t_dm1.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 : t_ae_rel.sas
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* Purpose : Create the Treatment Emergent Adverse Events 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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* ADaM.ADAE
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*
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* Output files: t_ae_rel.pdf
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* t_ae_rel.sas7bdat
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*
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* Macros: tfl_metadata.sas
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*
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* Assumptions: test
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*
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* ____________________________________________________________________________
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* PROGRAM HISTORY
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* 24MAY2022 | Jake Tombeur | Original version
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* 10MAY2023 | Megan Harries | Updates for CDISC01 ADaMs
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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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proc format;
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picture pctmf (round default = 8) /* Picture format for percentages */
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. = ' ' (noedit)
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low-0.001 = ' ' (noedit)
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0.001-<0.1 = ' (<0.1%)' (noedit)
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0.1-<1 = ' (9.9%)' (prefix=' (')
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1-<99.90001 = ' (00.0%)' (prefix=' (')
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99.90001-<100 = '(>99.9%)' (noedit)
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100 = '(100%) ' (noedit)
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;
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run;
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data teae (rename = (actarm = trta));
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length relcat $20;
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set adam.adae;
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if aerel in ('POSSIBLE' 'PROBABLE' 'DEFINITE') then relcat = 'Related';
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else relcat = 'Not Related';
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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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run;
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** exclude non-treated subjects;
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data adsl1 (rename = (actarm = trta) where = (trtan ^= .));
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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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run;
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%let indat = teae;
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%let trtvarn = trtan;
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%let inadsl = adsl1;
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%let socvar = aesoc;
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%let ptvar = aedecod;
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%let totval = 99;
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%let trtnord = 99;
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%let pctfmt = pctmf.;
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%let byvar = relcat;
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/* Macro for creating #patients/#events counts */
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%macro ne_freq (indat =,outdat =, byvars =, anyvars = );
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%let byvars2 = %sysfunc(tranwrd(%quote(&byvars.) ,%str( ),%str( , )));
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%if &byvars ^= %then %let sep = %str( , );
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%else %let sep = ;
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proc sql;
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create table &outdat. as
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select count(distinct USUBJID) as stat_n,
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count(USUBJID) as stat_e
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&sep. &byvars2.
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%if &anyvars ^= %then %do i = 1 %to %sysfunc(countw(&anyvars));
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, 'ANY' as %scan(&anyvars, &i)
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%end;
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from &indat.
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%if &byvars. ^= %then group by &byvars2.;
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;
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quit;
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%mend;
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/* All aes (with total column if required) */
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data aes;
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set &indat
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&indat (in = intot);
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if intot then &trtvarn = &totval;
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run;
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/* Adsl with total column if required */
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data adslmod;
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set &inadsl
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&inadsl (in = intot );
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if intot then &trtvarn = &totval;
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run;
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/* Counts including totals (by Severity) */
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%ne_freq(indat = aes, outdat = out1, byvars = &byvar &trtvarn, anyvars = &socvar &ptvar);
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%ne_freq(indat = aes, outdat = out2, byvars = &byvar &trtvarn &socvar, anyvars = &ptvar);
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%ne_freq(indat = aes, outdat = out3, byvars = &byvar &trtvarn &socvar &ptvar, anyvars =);
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/* Counts including totals (Any Severity) */
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%ne_freq(indat = aes, outdat = out4, byvars = &trtvarn, anyvars = &byvar &socvar &ptvar);
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%ne_freq(indat = aes, outdat = out5, byvars = &trtvarn &socvar, anyvars = &byvar &ptvar);
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%ne_freq(indat = aes, outdat = out6, byvars = &trtvarn &socvar &ptvar, anyvars = &byvar);
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/* N counts for denominators */
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%ne_freq(indat = adslmod, outdat = Ncounts, byvars = &trtvarn, anyvars =);
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data Ncounts;
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set Ncounts (drop = stat_e rename = (stat_n = bigN));
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call symputx(cats('N_',&trtvarn), bigN, 'g');
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run;
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/* Set all ae counts together */
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data allcounts;
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length &socvar &ptvar $ 200;
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set out1-out6;
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run;
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/* Template dataset */
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proc sql;
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create table template as
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select *, 0 as stat_e, 0 as stat_n
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from (select distinct &socvar, &ptvar from &indat
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union
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select distinct &socvar, 'ANY' as &ptvar from &indat
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union
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select distinct 'ANY' as &ptvar, 'ANY' as &socvar from &indat),
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(select distinct &byvar from &indat
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union
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select distinct 'ANY' as &byvar from &indat),
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Ncounts
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order by &trtvarn, &socvar, &ptvar, &byvar;
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;
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quit;
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/* Merge on observed counts to template */
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proc sort data = allcounts out = allcounts_s;
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by &trtvarn &socvar &ptvar &byvar;
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run;
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data counts_w0;
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length &socvar &ptvar $ 200 statc_n statc_e statc_p $ 30;
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merge template allcounts_s;
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by &trtvarn &socvar &ptvar &byvar;
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/* Create character versions of counts */
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statc_n = strip(put(stat_n,5.));
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statc_e = strip(put(stat_e,5.));
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statc_p = put(stat_n/bigN * 100, &pctfmt);
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run;
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/* Concatenate n and percent*/
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data counts_cat (keep = &socvar &ptvar &trtvarn &byvar npp statc_e);
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length npp $ 50;
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set counts_w0;
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npp = cat(strip(statc_n), ' ', strip(statc_p));
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run;
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/* Create SOC and PT order variables based on # patients / frequency of event */
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proc rank data = counts_w0 (where = (&trtvarn = &trtnord & &ptvar = 'ANY' & &socvar ^= 'ANY' & &byvar = 'ANY')) out = socranks (keep = &socvar SOCord_NP SOCord_EV) ties = low descending;
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var stat_n stat_e;
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ranks SOCord_NP SOCord_EV;
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run;
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proc sort data = counts_w0 out = counts_w0s;
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by &socvar;
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run;
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proc rank data = counts_w0s (where = (&trtvarn = &trtnord & &ptvar ^= 'ANY' & &socvar ^= 'ANY' & &byvar = 'ANY')) out = ptranks (keep = &socvar &ptvar PTord_NP PTord_EV) ties = low descending;
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by &socvar;
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var stat_n stat_e;
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ranks PTord_NP PTord_EV;
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run;
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proc format;
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invalue relord 'ANY' = 1
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'Related' = 2
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'Not Related' = 3
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;
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run;
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proc sql;
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create table counts_word as
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select a.*,
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case when a.&socvar = 'ANY' then 1 else b.SOCord_NP + 1 end as SOCord_NP,
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case when a.&socvar = 'ANY' then 1 else b.SOCord_EV + 1 end as SOCord_EV,
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case when a.&ptvar = 'ANY' then 1 else c.PTord_NP + 1 end as PTord_NP,
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case when a.&ptvar = 'ANY' then 1 else c.PTord_EV + 1 end as PTord_EV,
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input(&byvar,relord.) as relord
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from counts_cat a left join socranks b
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on a.&socvar = b.&socvar
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left join ptranks c
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on a.&socvar = c.&socvar
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and a.&ptvar = c.&ptvar
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order by SOCord_NP, &socvar, PTord_NP, &ptvar, relord, &byvar, &trtvarn
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;
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quit;
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/* Transpose into long format */
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proc transpose data = counts_word out = counts_T (rename = (_NAME_ = statty COL1 = statval));
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by SOCord_NP &socvar PTord_NP &ptvar relord &byvar &trtvarn ;
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var npp statc_e;
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run;
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data counts_T;
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set counts_T;
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where &trtvarn ^= .;
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run;
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/* Transpose to trts are cols */
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proc transpose delim = _ prefix = trt_ data = counts_T out = counts_TT (drop = _NAME_);
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id &trtvarn statty;
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by SOCord_NP &socvar PTord_NP &ptvar relord &byvar;
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var statval;
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run;
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data extrow (keep = aesoc aedecod soc_pt_disp &byvar trt_99_npp);
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length soc_pt_disp $ 132;
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set counts_TT;
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by SOCord_NP aesoc;
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if first.aesoc & aesoc ^= 'ANY' then do;
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soc_pt_disp = aesoc;
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output;
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end;
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if aesoc = 'ANY' then do;
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soc_pt_disp = 'Subjects with at least one TEAE';
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output;
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end;
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if aedecod = 'ANY' then aedecod = 'Any event';
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soc_pt_disp = aedecod;
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if aesoc ^= 'ANY' then output;
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run;
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data final (drop = i);
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set extrow;
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array trtcounts $ trt_:;
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if aesoc = soc_pt_disp then do i = 1 to dim(trtcounts);
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trtcounts[i] = '';
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&byvar = ' ';
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end;
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if aedecod = soc_pt_disp then indent = 'Y';
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else indent = 'N';
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if &byvar = 'ANY' then &byvar = 'Total';
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&byvar = propcase(&byvar);
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soc_pt_disp = propcase(soc_pt_disp);
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aesoc = propcase(aesoc);
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aedecod = propcase(aedecod);
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soc_pt_disp = tranwrd(soc_pt_disp, "Teae", "TEAE");
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run;
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*include metadata;
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%tfl_metadata;
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** create the table output;
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ods pdf file = "/mnt/artifacts/TFL/&__prog_name..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 "&DisplayName.";
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title3 "&DisplayTitle.";
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title4 "&Title1.";
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** justify contents to decimal places;
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proc report data = final headline split = "*"
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style(report) = {width = 100%};
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** if you also want TFL written to Dataset out = tfl.&__prog_name.;
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column aesoc
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aedecod
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indent soc_pt_disp &byvar trt_99_npp;
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** order variables;
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define aesoc / order order = data noprint;
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define aedecod / order order = data noprint;
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define indent / order order = data noprint;
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define &byvar / display ''
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style(header) = {width = 8% just = l};
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define soc_pt_disp / order order = data "System Organ Class* Preferred Term"
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style(header) = {width = 60% asis = on just = l};
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define trt_99_npp / display "All Treatments*(N=&N_99)*n (%)"
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style(header) = {width = 30%} style(column) = {just = d};
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compute soc_pt_disp;
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if indent = 'Y' then call define(_COL_, "style", "style=[leftmargin = 0.3in]");
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endcomp;
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compute before aedecod;
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line '';
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endcomp;
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** add footnotes;
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footnote1 justify = left "&Footer1.";
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footnote2 justify = left "&Footer2.";
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footnote3 justify = left "&Footer3.";
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footnote4 justify = left "&Footer4.";
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footnote5 justify = left "&Footer5.";
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run;
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ods pdf close;
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