Create define.xml, SDTM, and ADaM expors for FDA submission
This code will not run in 32 bit SAS because you would need the pcfile server and recode the import of excel files.
Don not extract code from this readme, run section of cln_000makefile.sas instead.
Occasionally a download might fail. When this happens check you log and just rerun the download code.
Also you can download tne b64 coded file manually.
Download the makefile into the Classic 1980s SAS editor and highlight and submit sections of code.
You should be able to run the entire script but I suggest you do a piece at a time.
I have seen isues when I try to run 30 back to back programatic downloads.
After setup you could put together a short driver that just calls the macros.
But I think that is a little premature. Code is under development.
data;infile"./&pgm..sas";file".j.sas";input;_infile_=trim(_infile_);put _infile_;run;
*****************************************************************************************************************;
* *;
*; %let pgm=cln_000makefile; *;
* *;
*; %let purpose=An example of CDISC end to end processing of a clinical traial; *;
* *;
*; %put &=pgm; *;
*; %put &=purpose; *;
* *;
* I suggest you run sections of this code by highlighting and submitting. *;
* The entire script should run but I am not sure about all the dependecies. *;
* *;
* This code s still under development. *;
* *;
* ==============================================================================================================*;
* *;
* PROJECT TOKEN = cln *;
* *;
* WIN 10 64bit SAS 9.4M6(64bit) (This code will not run in lockdown an probaly not in EG. *;
* Best with Classic SAS *;
* *;
* Documentation *;
* ============== *;
* *;
* Origin (I have heavily modified this repository- for better or worse) *;
* https://github.com/wyp1125/SAS-Clinical-Trials-Toolkit *;
* Many thanks to the author. *;
* *;
* This is by no means a full and perfect clinical trial. *;
* Not all codelists, domains and values are present. *;
* This is just an example code. Maybe it can be educational. *;
* *;
* All input data ia in my github repository *;
* https://raw.githubusercontent.com/rogerjdeangelis/utl-end-to-end-cdisc-SDTM-ADaM-processing *;
* _ _ _ _ *;
* _____ _| |_ ___ _ __ _ __ __ _| | (_)_ __ _ __ _ _| |_ ___ *;
* / _ \ \/ / __/ _ \ `__| `_ \ / _` | | | | `_ \| `_ \| | | | __/ __| *;
* | __/> <| || __/ | | | | | (_| | | | | | | | |_) | |_| | |_\__ \ *;
* \___/_/\_\\__\___|_| |_| |_|\__,_|_| |_|_| |_| .__/ \__,_|\__|___/ *;
* |_| *;
* *;
* KEY EXTERNAL INPUT SAS EXCEL WORKBOOKS WITH DETAIL META DATA *;
* THES WORKBOOKS DRIVE ALL THE ANALYSIS EVEN THE CREATION OF THE DEFINE XML *;
* ========================================================================= *;
* _ _ _ _ *;
* _____ _____ ___| | _ __ ___ ___| |_ __ _ __| | __ _| |_ __ _ *;
* / _ \ \/ / __/ _ \ | | `_ ` _ \ / _ \ __/ _` | / _` |/ _` | __/ _` | *;
* | __/> < (_| __/ | | | | | | | __/ || (_| | | (_| | (_| | || (_| | *;
* \___/_/\_\___\___|_| |_| |_| |_|\___|\__\__,_| \__,_|\__,_|\__\__,_| *;
* *;
* GitHub (Workbooks are downloaded programatically) *;
* *;
* cln_sdtmMetadata.xlsx SDTM *;
* ====================== *;
* *;
* https://tinyurl.com/y2daeq4v *;
* *;
* *;
* cln_adamMetadata.xlsx ADaM *;
* ====================== *;
* *;
* https://tinyurl.com/y4kpeosh *;
* *;
* *;
* *;
* KEY EXTERNAL INPUT *;
* ================== *;
* *;
* GROUND TRUTH META DATA(Meta data driven processing) *;
* Below are the key sheets and tabs to produce ADAM and SDTM SAS datasets *;
* We start with two excel workbooks then create the define.xml from the workbooks. *;
* *;
* We use th meta data in the excel workbooks, not the define XML. *;
* The define XML is just excel output directed to ODM xlm sections. The ODM sections are *;
* concatenated to produce the SDTM an ADaM define XML files. *;
* _ _ _ *;
* ___ __| | |_ _ __ ___ _ __ ___ ___| |_ __ _ *;
* / __|/ _` | __| `_ ` _ \ | `_ ` _ \ / _ \ __/ _` | *;
* \__ \ (_| | |_| | | | | | | | | | | | __/ || (_| | *;
* |___/\__,_|\__|_| |_| |_| |_| |_| |_|\___|\__\__,_| *;
* *;
* All the input data is programatically downloaded from GiTHub *;
* *;
* &gbl_root/cln/xls/cln_sdtmMetadata.xlsx (excel image of sdtm_define.xml -download from Github ) *;
* *;
* SHEETS *;
* Member *;
* Name Type Vars *;
* *;
* DEFINE_HEADER_METADATA$ DATA 9 *;
* TOC_METADATA$ DATA 10 *;
* VARIABLE_METADATA$ DATA 16 *;
* VALUELEVEL_METADATA$ DATA 15 *;
* COMPUTATION_METHOD$ DATA 2 *;
* CODELISTS$ DATA 11 *;
* *;
* *;
* SHEET DEFINE_HEADER_METADATA *;
* ============================ *;
* *;
* Middle Observation(1 ) of DEFINE_HEADER_METADATA - Total Obs 1 *;
* *;
* Variable Type/Length Sample Value *;
* *;
* STUDYOID N8 123 *;
* *;
* FILEOID C6 XYZ123 *;
* STUDYNAME C6 XYZ123 *;
* STUDYDESCRIPTION C132 A PHASE IIB, DOU *;
* PROTOCOLNAME C6 XYZ123 *;
* STANDARD C4 SDTM *;
* VERSION C5 3.1.2 *;
* SCHEMALOCATION C48 http://www.cdisc *;
* STYLESHEET C15 define1-0-0.xsl *;
* CREATIONDATE C19 2021-01-23T11:48 *;
* TOTOBS C16 1 *;
* *;
* SHEET TOC_METADATA *;
* ================== *;
* *;
* Middle Observation(5 ) of TOC_METADATA - Total Obs 11 *;
* *;
* Variable Type/Length Middle Value *;
* *;
* DOMAIN C6 SUPPDM *;
* NAME C6 SUPPDM *;
* REPEATING C3 Yes *;
* ISREFERENCEDATA C3 No *;
* PURPOSE C12 Tabulation *;
* LABEL C34 DM - Supplementa *;
* STRUCTURE C51 Supplemental Qua *;
* DOMAINKEYS C48 STUDYID, RDOMAIN *;
* CLASS C22 Supplemental Qua *;
* ARCHIVELOCATIONID C8 ./suppdm *;
* TOTOBS C16 11 *;
* *;
* *;
* SHEET VARIABLE_METADATA *;
* ======================= *;
* *;
* Middle Observation(64 ) of VARIABLE_METADATA - Total Obs 128 *;
* *;
* Variable Type/Length Sample Value *;
* *;
* DOMAIN C6 LB ** DOMAIN (eleven domains) *;
* VARIABLE C8 LBDTC *;
* VARNUM N8 21 *;
* LENGTH N8 16 *;
* TYPE C7 date *;
* LABEL C40 Date/Time of Spe *;
* SIGNIFICANTDIGITS C1 *;
* ORIGIN C18 Central laborato *;
* DISPLAYFORMAT C3 *;
* COMPUTATIONMETHODOID C14 *;
* CODELISTNAME C8 *;
* MANDATORY C3 No *;
* ROLE C18 Timing *;
* ROLECODELIST C8 ROLECODE *;
* VALUELISTOID C13 *;
* ITEMOID C40 LB.LBDTC *;
* TOTOBS C16 128 *;
* COMMENT C2000 *;
* *;
* *;
* SHEET VALUELEVEL_METADATA *;
* ========================= *;
* *;
* Middle Observation(5 ) of VALUELEVEL_METADATA - Total Obs 10 *;
* *;
* Variable Type/Length Sample Value *;
* *;
* VALUELISTOID C13 LBTESTCDVALUE *;
* VALUENAME C6 BILDIR * LAB TEST *;
* TYPE C5 float *;
* LENGTH N8 8 *;
* LABEL C32 Direct Bilirubin *;
* SIGNIFICANTDIGITS C1 1 *;
* ORIGIN C18 Central laborato *;
* DISPLAYFORMAT C3 4.2 *;
* COMPUTATIONMETHODOID C1 *;
* CODELISTNAME C1 *;
* MANDATORY C2 No *;
* ROLE C1 *;
* ROLECODELIST C1 *;
* ITEMOID C200 LBTESTCDVALUE.BI *;
* TOTOBS C16 10 *;
* COMMENT C2000 *;
* *;
* *;
* SHEET COMPUTATION_METHOD *;
* ========================= *;
* *;
* Middle Observation(1 ) of COMPMETHOD - Total Obs 1 *;
* *;
* Variable Type/Length Sample Value *;
* *;
* COMPUTATIONMETHODOID C14 AGECALCULATION *;
* COMPUTATIONMETHOD C42 integer value of (BRTHDT - RFSTDTC)/365.25 *;
* *;
* *;
* SHEET CODELISTS *;
* =============== *;
* *;
* Middle Observation(67 ) of CODELISTS - Total Obs 135 *;
* *;
* Variable Type/Length Sample Value *;
* *;
* CODELISTNAME C8 SEX *;
* CODEDVALUE C36 F *;
* RANK N 8 3 *;
* TRANSLATED C46 FEMALE *;
* TYPE C4 TEXT *;
* CODELISTDICTIONARY C6 *;
* CODELISTVERSION C3 *;
* SOURCEDATASET C11 demographic *;
* SOURCEVARIABLE C8 gender *;
* SOURCEVALUE C11 . *;
* SOURCETYPE C9 number *;
* TOTOBS C16 135 *;
* *;
* _ _ *;
* __ _ __| | __ _ _ __ ___ _ __ ___ ___| |_ __ _ *;
* / _` |/ _` |/ _` | `_ ` _ \ | `_ ` _ \ / _ \ __/ _` | *;
* | (_| | (_| | (_| | | | | | | | | | | | | __/ || (_| | *;
* \__,_|\__,_|\__,_|_| |_| |_| |_| |_| |_|\___|\__\__,_| *;
* *;
* ADAM has the sheets above and two additional sheets (excel image of adam_define.xml-download from Github ) *;
* *;
* &gbl_root/cln/xls/cln_adamMetadata.xlsx *;
* *;
* *;
* SHEET ANALYSIS_RESULTS *;
* ====================== *;
* *;
* Middle Observation(2 ) of ANALYSISRESULTS - Total Obs 5 *;
* *;
* Variable Type/Length Sample Value *;
* *;
* ANALYSISDATASET C5 ADEF *;
* DISPLAYID C13 Table_14.2.1 *;
* DISPLAYNAME C47 Responder Analysis by Visit *;
/* PROGRAMMINGCODE C800 procfreq;data=adef;bycrit1avisitn;tablestrtpn*crit1fl;run */;
* DOCLEAFID C40 SAP_Section_9.2. *;
* RESULTID C43 Responder Analysis by Visit *;
* REASON C58 Efficacy endpoint pre-specified in SAP *;
* PARAMLIST C41 XPPAIN/Pain Scor *;
* ANALYSISVARIABLES C22 CRIT1FL *;
* SELECTIONCRITERIA C54 Where ITTFL='Y' and ABLFL ^= 'Y' and PARAMCD='XPPAIN' *;
* DOCUMENTATION C24 SAP_Section_9.2. *;
* PROGRAM *;
* *;
* SHEET EXTERNALLINKS *;
* =================== *;
* *;
* Middle Observation(3 ) of externallinks - Total Obs 6 *;
* *;
* LEAFID C17 SAP_Section_9.2. *;
* LEAFRELPATH C130 .\studyxyz123\studyxyz123_csr.pdf#nameddest=SAP_SEC_9.2.2 *;
* TITLE C17 SAP Section 9.2. *;
* *;
* ____ ____ _____ _ _ *;
* _ __ __ ___ __ / ___| _ \| ___| __| | __ _| |_ __ _ *;
* | `__/ _` \ \ /\ / / | | | |_) | |_ / _` |/ _` | __/ _` | *;
* | | | (_| |\ V V / | |___| _ <| _| | (_| | (_| | || (_| | *;
* |_| \__,_| \_/\_/ \____|_| \_\_| \__,_|\__,_|\__\__,_| *;
* *;
* *;
* RAW CRF SOURCE SAS DATASETS (DOWNLOAD) *;
* --------------------------------------- *;
* *;
* Base64 encoded SAS raw for programatic downloads *;
* Downloading binary data is problematic so I provide *;
* encoded text files and SAS tools to covert to decode into binary SAS datasets. *;
* *;
* CLN_RAWADVERSE.B64 *;
* CLN_RAWDEMOGRAPHIC.B64 *;
* CLN_RAWDOSING.B64 *;
* CLN_RAWLABS.B64 *;
* CLN_RAWPAIN.B64 *;
* *;
* I aslo provide SAS datasets however I do use these, You can download and eliminate the b64 decode/ *;
* *;
* SAS V9 datasets *;
* CLN_RAWADVERSE.SAS7BDAT *;
* CLN_RAWDEMOGRAPHIC.SAS7BDAT *;
* CLN_RAWDOSING.SAS7BDAT *;
* CLN_RAWLABS.SAS7BDAT *;
* CLN_RAWPAIN.SAS7BDAT *;
* *;
* ___ _ ____ _ _ *;
* / ___| / \ / ___| | |_ ___ ___ | |___ *;
* \___ \ / _ \ \___ \ | __/ _ \ / _ \| / __| *;
* ___) / ___ \ ___) | | || (_) | (_) | \__ \ *;
* |____/_/ \_\____/ \__\___/ \___/|_|___/ *;
* *;
* https://raw.githubusercontent.com/rogerjdeangelis/CostReports/master/cst_010.sas *;
* *;
* Package cst_010.sas *;
* *;
* Collection of abour 40 tools (sas macros) *;
* *;
* *;
* ==============================================================================================================*;
* *;
* INTERNAL MACROS *;
* =============== *;
* *;
* cln_100makedefine make define.xml *;
* *;
* cln_110mkesdtmdy cdisc tools *;
* cln_120mkesrtodr *;
* cln_130cfb *;
* cln_140mkeMtyTbl *;
* cln_150domainx *;
* cln_160dtc2dt *;
* cln_170mrgsup *;
* *;
* cln_500sdtmDm create stdm datasets *;
* cln_525sdtmAe *;
* cln_550sdtmEx *;
* cln_575sdtmLb *;
* cln_600sdtmXp *;
* *;
* cln_615adamAdsl create aam datasets *;
* cln_625adamAdae *;
* cln_650adamAdef *;
* cln_675adamAdTte *;
* *;
* *;
* EXTERNAL MACROS IN AUTOCALL LIBRARY *;
* ==================================== *;
* Utility and performance macros in *;
* *;
* cln_010.sas (package of 40+ utilties) *;
* *;
* *;
* PINNACLE (You can test the v5 xport files with pinnacle - interatively) *;
* ============================================================ *;
* Download Pinnacle 21 *
* *;
* https://www.c.com/projects/installing-opencdisc-community *;
* *;
* Create parent folder and subfolders *;
* *;
* global_root/pin (set up for Pinnacle ) *;
* *;
* Cfg * for pinnacle config files *;
* Txt * for pinnacle report file *;
* Xml * for pinnacle xml files *;
* *;
* SAS Proc CDISC *;
* ============== *;
* *;
* There is proc cdisc code you can run to check the SDTM DM sas Dataset *;
* *;
/* PROC CDISC MODEL = SDTM; */;
/* SDTM SDTMVersion = "3.1"; */;
/* DOMAINDATA data = cln.Dm */;
/* domain = DM */;
/* category = SPECIAL; */;
/* run;quit; */;
* *;
* _ __ _ __ ___ ___ ___ ___ ___ *;
* | `_ \| `__/ _ \ / __/ _ \/ __/ __| *;
* | |_) | | | (_) | (_| __/\__ \__ \ *;
* | .__/|_| \___/ \___\___||___/___/ *;
* |_| *;
* *;
* 1. define root directory *;
* *;
* 2. assign libname to root directory *;
* *;
* 3. create autocall subdirectory *;
* *;
* 4. create directory structure *;
* *;
* 5. copy sas tools from the GitHub into OTO(autocall) subdirectory *;
* *;
* 6. compile tools into work.sasmacr *;
* *;
* 7. create formats *;
* *;
* 8. copy excel workbooks from the GiHub (key step) *;
* *;
* 9. create stdmDefine.xml and adamDefine.xml *;
* *;
* 10. copy raw crf sas datasets from the GitHub *;
* *;
* 11. ceate sdtm datasets and associated V5 export files *;
* *;
* ae.sas7bdat cln_sdtmAe.xpt *;
* dm.sas7bdat cln_sdtmdm.xpt *;
* ex.sas7bdat cln_sdtmLb.xpt *;
* lb.sas7bdat cln_sdtmsEx.xpt *;
* suppdm.sas7bdat cln_sdtmsuppdm.xpt *;
* xp.sas7bdat cln_sdtmsXp.xpt *;
* *;
* 12. ceate adam datasets and associated V5 export files *;
* *;
* adae.sas7bdat cln_adamadae.xpt *;
* adef.sas7bdat cln_adamadef.xpt *;
* adsl.sas7bdat cln_adamadsl.xpt *;
* adtte.sas7bdat cln_adamadtte.xpt *;
* *;
* _ _ *;
* ___ _ _| |_ _ __ _ _| |_ *;
* / _ \| | | | __| `_ \| | | | __| *;
* | (_) | |_| | |_| |_) | |_| | |_ *;
* \___/ \__,_|\__| .__/ \__,_|\__| *;
* |_| *;
* *;
* THE PRIMARY OUTPUTS ARE THE ADaM and SDTM, DEFINE.XMLs, DATASETS, AND XPORT FILES *;
* *;
* FINAL STATE OF DIRECTORIES *;
* *;
* I-INPUT FROM GITHUB O= OUTPUT *;
* *;
* Directory of &gbl_root/cln *;
* *;
* O cln_fmt.sas7bcat * formats *;
* *;
* I cln_rawadverse.sas7bdat * raw data *;
* I cln_rawdemographic.sas7bdat *;
* I cln_rawdosing.sas7bdat *;
* I cln_rawlabs.sas7bdat *;
* I cln_rawpain.sas7bdat *;
* *;
* O adae.sas7bdat * adams; *;
* O adef.sas7bdat *;
* O adsl.sas7bdat *;
* O adtte.sas7bdat *;
* *;
* O ae.sas7bdat *sdtms; *;
* O dm.sas7bdat *;
* O ex.sas7bdat *;
* O lb.sas7bdat *;
* O suppdm.sas7bdat *;
* O xp.sas7bdat *;
* *;
* <DIR> b64 *;
* I cln_adamMetadata.b64 *base 64 of excel mata data for adam datasets; *;
* I cln_sdtmMetadata.b64 *base 64 of excel mata data for sdtm datasets; *;
* *;
* I cln_rawadverse.b64 * base 64 encoded raw sas datasets; *;
* I cln_rawdemographic.b64 *;
* I cln_rawdosing.b64 *;
* I cln_rawlabs.b64 *;
* I cln_rawpain.b64 *;
* <DIR> log *;
* <DIR> oto *;
* I cln_010.sas * many macro tools; *;
* *;
* I cln_100makedefine.sas * CDISC utilities ( extract meta data from excel tabs; *;
* I cln_110mkesdtmdy.sas *;
* I cln_120mkesrtodr.sas *;
* I cln_130cfb.sas *;
* I cln_140mkeMtyTbl.sas *;
* I cln_150domainx.sas *;
* I cln_160dtc2dt.sas *;
* I cln_170mrgsup.sas *;
* *;
* I cln_500sdtmDm.sas * create sdtm datasets DM; *;
* I cln_525sdtmAe.sas * AE *;
* I cln_550sdtmEx.sas * EX *;
* I cln_575sdtmLb.sas * LB *;
* I cln_600sdtmXp.sas * XP *;
* *;
* I cln_615adamAdsl.sas * create adam datasets ADSL *;
* I cln_625adamAdae.sas * ADSL *;
* I cln_650adamAdef.sas * ADAE *;
* I cln_675adamAdTte.sas * ADEF *;
* *;
* <DIR> pdf *;
* <DIR> pin *;
* <DIR> png *;
* <DIR> rtf *;
* <DIR> sas *;
* *;
* <DIR> xls *;
* O cln_adamMetadata.xlsx * excel mata data for adam datasets; *;
* O cln_sdtmMetadata.xlsx * excel mata data for sdtm datasets; *;
* *;
* <DIR> xml *;
* *;
* O cln_adamDefine.xml * concatenation of all odm sections below *;
* *;
* O cln_adamdefine_header.xml * excel odm sections created from excel tab header *;
* O cln_adamanalysisresults.xml .. *;
* O cln_adamcompmethod.xml *;
* O cln_adamitemdef.xml *;
* O cln_adamitemdef_value.xml *;
* O cln_adamitemgroupdef.xml *;
* O cln_adamleaves.xml *;
* O cln_adamvaluelist.xml *;
* O cln_sdtmcompmethod.xml *;
* *;
* O cln_sdtmDefine.xml * concatenation of all stdm sections below *;
* *;
* O cln_sdtmdefine_header.xml * excel odm section created from excel tab header *;
* O cln_sdtmitemdef.xml .. *;
* O cln_sdtmitemdef_value.xml *;
* O cln_sdtmitemgroupdef.xml *;
* O cln_sdtmvaluelist.xml *;
* <DIR> xpt *;
* O cln_adamadtte.xpt *;
* O cln_adamadae.xpt *;
* O cln_adamadef.xpt *;
* O cln_adamadsl.xpt *;
* *;
* O cln_sdtmAe.xpt *;
* O cln_sdtmdm.xpt *;
* O cln_sdtmsEx.xpt *;
* O cln_sdtmsuppdm.xpt *;
* O cln_sdtmsXp.xpt *;
* *;
* *;
*******************************************************************************************************************;
* *;
* Version History *;
* *;
* Version Date Programmer Description *;
* ------- --------- ---------- ----------- *;
* 1.0 24JAN2021 rdeangel creation *;
* *;
* *;
*******************************************************************************************************************;
/*___ _____ _____ _ _ ____
/ ___|| ____|_ _| | | | _ \
\___ \| _| | | | | | | |_) |
___) | |___ | | | |_| | __/
|____/|_____| |_| \___/|_|
*/
%symdel
gbl_root
gbl_tools;
%let gbl_root =d:/cln; * autocall library;
%let gbl_tools=https://raw.githubusercontent.com/rogerjdeangelis/CostReports/master/cst_010.sas;
%put &=gbl_root;
%put &=gbl_tools;
* create folder even if it does not exist;
options dlcreatedir;
libname cln "&gbl_root";
options nodlcreatedir;
/* Just in case you rerun */
proc datasets lib=work kill;
run;quit;
proc catalog cat=work.sasmacr et=macro;
delete
cln_100makedefine
cln_110mkesdtmdy
cln_120mkesrtodr
cln_130cfb
cln_140mkeMtyTbl
cln_150domainx
cln_160dtc2dt
cln_170mrgsup
cln_500sdtmDm
cln_525sdtmAe
cln_550sdtmEx
cln_575sdtmLb
cln_600sdtmXp
cln_615adamAdsl
cln_625adamAdae
cln_650adamAdef
cln_675adamAdTte
;run;quit;
%utlfkil(&gbl_root/oto/cln_100makedefine.sas);
%utlfkil(&gbl_root/oto/cln_110mkesdtmdy.sas);
%utlfkil(&gbl_root/oto/cln_120mkesrtodr.sas);
%utlfkil(&gbl_root/oto/cln_130cfb.sas);
%utlfkil(&gbl_root/oto/cln_140mkeMtyTbl.sas);
%utlfkil(&gbl_root/oto/cln_150domainx.sas);
%utlfkil(&gbl_root/oto/cln_160dtc2dt.sas);
%utlfkil(&gbl_root/oto/cln_170mrgsup.sas);
%utlfkil(&gbl_root/oto/cln_500sdtmDm.sas);
%utlfkil(&gbl_root/oto/cln_525sdtmAe.sas);
%utlfkil(&gbl_root/oto/cln_550sdtmEx.sas);
%utlfkil(&gbl_root/oto/cln_575sdtmLb.sas);
%utlfkil(&gbl_root/oto/cln_600sdtmXp.sas);
%utlfkil(&gbl_root/oto/cln_615adamAdsl.sas);
%utlfkil(&gbl_root/oto/cln_625adamAdae.sas);
%utlfkil(&gbl_root/oto/cln_650adamAdef.sas);
%utlfkil(&gbl_root/oto/cln_675adamAdTte.sas);
proc datasets lib=cln nolist;
delete
adae
adef
adsl
adtte
ae
cln_rawadverse
cln_rawdemographic
cln_rawdosing
cln_rawlabs
cln_rawpain
dm
ex
lb;
run;quit;
libname sdtm "&gbl_root";
libname adam "&gbl_root";
data _null_;
length newdir $64;
newdir=dcreate('oto',"&gbl_root"); /* autocall folder */
run;quit;
options fmtsearch=(cln.cln_fmt work.formats) xwait xsync
sasautos=("&gbl_root./oto", sasautos) ;
/*
Folders so far
Directory of d:\cln
<DIR> oto * autocall library
/* _ __ _ _
___ _ __ ___ __ _| |_ ___ / _| ___ | | __| | ___ _ __ ___
/ __| `__/ _ \/ _` | __/ _ \ | |_ / _ \| |/ _` |/ _ \ `__/ __|
| (__| | | __/ (_| | || __/ | _| (_) | | (_| | __/ | \__ \
\___|_| \___|\__,_|\__\___| |_| \___/|_|\__,_|\___|_| |___/
*/
* create root folder for sas datasets;
* create subfolders;
data _null_;
length newdir $64;
newdir=dcreate('oto',"&gbl_root"); /* autocall folder */
newdir=dcreate('xls',"&gbl_root"); /* input excel image of define xml - key metatdata */
newdir=dcreate('pdf',"&gbl_root"); /* documentation */
newdir=dcreate('zip',"&gbl_root"); /* zipped saves */
newdir=dcreate('rtf',"&gbl_root"); /* tables and listings */
newdir=dcreate('png',"&gbl_root"); /* figures */
newdir=dcreate('log',"&gbl_root"); /* batch logs */
newdir=dcreate('b64',"&gbl_root"); /* base 64 binaries from github - github does not support auto downloads */
newdir=dcreate('sas',"&gbl_root"); /* base 64 binaries from github - github does not support auto downloads */
newdir=dcreate('xml',"&gbl_root"); /* define xml and define.xml odm sections */
newdir=dcreate('xpt',"&gbl_root"); /* SAS V5 export */
newdir=dcreate('pin',"&gbl_root"); /* pinacle 21 */
run;quit;
/* OUTPUT DIRECTORY STRUCTURE
Directory of &gbl_root
<DIR> b64
<DIR> log
<DIR> oto ** autocall library
<DIR> pdf
<DIR> pin
<DIR> png
<DIR> rtf
<DIR> sas
<DIR> xls
<DIR> xml
<DIR> xpt
<DIR> zip
*/
/* _ _ _
__ _ ___| |_ | |_ ___ ___ | |___
/ _` |/ _ \ __| | __/ _ \ / _ \| / __|
| (_| | __/ |_ | || (_) | (_) | \__ \
\__, |\___|\__| \__\___/ \___/|_|___/
|___/
*/
filename _bcot "&gbl_root/oto/cln_010.sas";
proc http
method='get'
url="&gbl_tools"
out= _bcot;
run;quit;
/* OUTPUT
Directory of &gbl_root
<DIR> b64
<DIR> log
<DIR> oto
cln_010.sas * many macro tools;
<DIR> pdf
<DIR> pin
<DIR> png
<DIR> rtf
<DIR> xls
<DIR> xml
<DIR> xpt
<DIR> zip
*/
/* _ _ _ _
___ ___ _ __ ___ _ __ (_) | ___ | |_ ___ ___ | |___
/ __/ _ \| `_ ` _ \| `_ \| | |/ _ \ | __/ _ \ / _ \| / __|
| (_| (_) | | | | | | |_) | | | __/ | || (_) | (_) | \__ \
\___\___/|_| |_| |_| .__/|_|_|\___| \__\___/ \___/|_|___/
|_|
*/
* compile utility macros;
filename cin "&gbl_root./oto/cln_010.sas" lrecl=4096 recfm=v;
%inc cin / nosource;
/*__ _
/ _| ___ _ __ _ __ ___ __ _| |_ ___
| |_ / _ \| `__| `_ ` _ \ / _` | __/ __|
| _| (_) | | | | | | | | (_| | |_\__ \
|_| \___/|_| |_| |_| |_|\__,_|\__|___/
*/
proc format lib=cln.cln_fmt;
value visit_labs_month
0=baseline
1=3 months
2=6 months;
value _0n1y 0 = 'N'
1 = 'Y'
;
value avisitn 1 = '3'
2 = '6'
;
value popfl 0 - high = 'Y'
other = 'N'
;
value $trt01pn 'Analgezia HCL 30 mg' = '1'
'Placebo' = '0'
;
value agegr1n 0 - 54 = "1"
55-high= "2"
;
value agegr1_ 1 = "<55 YEARS"
2 = ">=55 YEARS"
;
value $aereln 'NOT' = '0'
'POSSIBLY' = '1'
'PROBABLY' = '2'
;
value $aesevn 'MILD' = '1'
'MODERATE' = '2'
'SEVERE' = '3'
;
value relgr1n 0 = 'NOT RELATED'
1 = 'RELATED'
;
value evntdesc 0 = 'PAIN RELIEF'
1 = 'PAIN WORSENING PRIOR TO RELIEF'
2 = 'PAIN ADVERSE EVENT PRIOR TO RELIEF'
3 = 'COMPLETED STUDY PRIOR TO RELIEF'
;
run;
/*
Note: Formatds are not sent to FDA we provide code/decode pairs
proc catalog cat=cln.cln_fmt;
contents;
run;quit;
Contents of Catalog CLN.CLN_FMT
# Name Type
------------------------------------
1 AGEGR1N FORMAT
2 AGEGR1_ FORMAT
3 AVISITN FORMAT
4 EVNTDESC FORMAT
5 POPFL FORMAT
6 RELGR1N FORMAT
7 VISIT_LABS_MONTH FORMAT
8 _0N1Y FORMAT
9 AERELN FORMATC
10 AESEVN FORMATC
11 TRT01PN FORMATC
*/
/* _ _ _ _ _
__ _ ___| |_ __ _| |_ __ __ ___ __| | _| |__ ___ ___ | | _____
/ _` |/ _ \ __| \ \/ / \ \/ / \ \ /\ / / `__| |/ / `_ \ / _ \ / _ \| |/ / __|
| (_| | __/ |_ > <| |> < \ V V /| | | <| |_) | (_) | (_) | <\__ \
\__, |\___|\__| /_/\_\_/_/\_\ \_/\_/ |_| |_|\_\_.__/ \___/ \___/|_|\_\___/
|___/
*/
* DOWNLOAD EXCEL WOOKBOOKS WITH META DATA;
* you can download the workbooks manually and place in /cln/xls or run these scripts;
* The code below downloads the base64 text and converts the text to binary zipped xml ;
* Only if you need to encode the excel workbooks in bas64 for upload/download from GitHub. Bas64 is text;
%*utl_b64encode(&gbl_root/xls/cln_adamMetadata.xlsx,&gbl_root/b64/cln_adamMetadata.b64); /*only if I need to upload another newer version of the data */
%*utl_b64encode(&gbl_root/xls/cln_sdtmMetadata.xlsx,&gbl_root/b64/cln_sdtmMetadata.b64); /*only if I need to upload another newer version of the data */
* download cln.sdtmMetadata.b64 and convert to sdtmMetadata.xlsx;
filename download clear;
filename download "&gbl_root/b64/cln_sdtmMetadata.b64";
proc http
method='GET'
url="https://raw.githubusercontent.com/rogerjdeangelis/utl-end-to-end-cdisc-SDTM-ADaM-processing/master/cln_sdtmMetadata.b64"
out=download;
run;quit;
filename download clear;
%utl_b64decode(&gbl_root/b64/cln_sdtmMetadata.b64,&gbl_root/xls/cln_sdtmMetadata.xlsx);
* download cln.adamMetadata.b64 and convert to adamMetadata.xlsx;
filename download clear;
filename download "&gbl_root/b64/cln_adamMetadata.b64";
proc http
method='GET'
url="https://raw.githubusercontent.com/rogerjdeangelis/utl-end-to-end-cdisc-SDTM-ADaM-processing/master/cln_adamMetadata.b64"
out=download;
run;quit;
filename download clear;
%utl_b64decode(&gbl_root/b64/cln_adamMetadata.b64,&gbl_root/xls/cln_adamMetadata.xlsx);
run;quit;
/* structure
- added files
Directory of &gbl_root/cln
cln_fmt.sas7bcat
* formats
<DIR> b64
- cln_adamMetadata.b64 *base 64 of excel mata data for adam datasets;
- cln_sdtmMetadata.b64 *base 64 of excel mata data for sdtm datasets;
<DIR> log
<DIR> oto
cln_010.sas * many macro tools;
<DIR> pdf
<DIR> pin
<DIR> png
<DIR> rtf
<DIR> sas
<DIR> xls
- cln_adamMetadata.xlsx * excel mata data for adam datasets;
- cln_sdtmMetadata.xlsx * excel mata data for sdtm datasets;
<DIR> xml
<DIR> xpt
<DIR> zip
*/
/* _ __ _ _
__| | ___ / _(_)_ __ ___ __ ___ __ ___ | |
/ _` |/ _ \ |_| | `_ \ / _ \ \ \/ / `_ ` _ \| |
| (_| | __/ _| | | | | __/ > <| | | | | | |
\__,_|\___|_| |_|_| |_|\___| /_/\_\_| |_| |_|_|
*/
filename ft15f001 "&gbl_root/oto/cln_100makedefine.sas";
parmcards4;
%macro cln_100makedefine(path=,metadata=,out=);
/*---------------------------------------------------------------*;
* %make_define generates parts of the define.xml file for the SDTM and ADaM.
* The parts can be concatenated into the define.xml file using shell scripts.
*
* PARAMETERS:
* path = System path to where the SDTM or ADaM metadata
* file exists as well as where the define.xml
* file will be stored.
* metadata = The name of the metadata spreadsheet.
*
* It requires that the following tabs exist in the metadata file:
* DEFINE_HEADER_METADATA = define file header metadata
* TOC_METADATA = "table of contents" dataset metadata
* VARIABLE_METADATA = variable/column level metadata
* VALUELEVEL_METADATA = value/parameter level metadata
* COMPUTATIONAL_MKETHOD = computational methods
* CODELISTS = controlled terminology metadata
* ANALYSIS_RESULTS = ADaM analysis metadata. [Only for ADaM define]
* EXTERNAL_LINKS = ADaM results file pointers. [Only for ADaM define]
INPUT
=====
TWO EXECL WORKBOOKS WITH THE SHEETD THAT MAP TO THE DEFINE XLM ODM SECTIONS
cln_sdtmMetadata.xlsx
sheets
DEFINE_HEADER_METADATA
TOC_METADATA
VARIABLE_METADATA
VALUELEVEL_METADATA
COMPUTATIONAL_MKETHOD
CODELISTS
cln_adamMetadata.xlsx
sheets
DEFINE_HEADER_METADATA
TOC_METADATA
VARIABLE_METADATA
VALUELEVEL_METADATA
COMPUTATIONAL_MKETHOD
CODELISTS
ANALYSIS_RESULTS
EXTERNAL_LINKS
OUTPUT
======
Directory of d:\cln\xml
-----------------------
cln_sdtmDefine.xml 62,255 SDTM DEFINE XLM
cln_adamDefine.xml 47,905 ADAM DEFILE XML
cln_adamanalysisresults.xml 8,700 concatenate these 8 xlm sections into cln_adamDefine.xml
cln_adamcompmethod.xml 385
cln_adamdefine_header.xml 1,738
cln_adamitemdef.xml 21,165
cln_adamitemdef_value.xml 1,118
cln_adamitemgroupdef.xml 12,744
cln_adamleaves.xml 1,463
cln_adamvaluelist.xml 592
cln_sdtmcompmethod.xml 290 concatenate these 6 xlm sections into cln_sdtmDefine.xml
cln_sdtmdefine_header.xml 1,677
cln_sdtmitemdef.xml 27,026
cln_sdtmitemdef_value.xml 2,778
cln_sdtmitemgroupdef.xml 29,536
cln_sdtmvaluelist.xml 948
*/
**** GET DEFINE FILE HEADER INFORMATION METADATA;
proc import
out = define_header
datafile = "&path\&metadata"
dbms=xlsx
replace;
sheet="DEFINE_HEADER_METADATA";
run;
**** DETERMINE IF THIS IS A SDTM DEFINE FILE OR AN ADAM DEFINE FILE
**** AND SET THE STANDARD MACRO VARIABLE FOR THE REST OF THE PROGRAM;
data _null_;
set define_header;
if upcase(standard) = 'ADAM' then
call symput('standard','ADAM');
else if upcase(standard) = 'SDTM' then
call symput('standard','SDTM');
else
put "ERR" "OR: CDISC standard undefined in define_header_metadata";
run;
**** GET "TABLE OF CONTENTS" LEVEL DATASET METADATA;
proc import
out = toc_metadata
datafile = "&path\&metadata"
dbms=xlsx
replace;
sheet = "TOC_METADATA" ;
run;
**** GET THE VARIABLE METADATA;
proc import
out = VARIABLE_METADATA
datafile = "&path\&metadata"
dbms=xlsx
replace;
sheet = "VARIABLE_METADATA";
run;
**** GET THE CODELIST METADATA;
proc import
out = codelists
datafile = "&path\&metadata"
dbms=xlsx
replace;
sheet = "CODELISTS" ;
run;
**** GET THE COMPUTATIONAL METHOD METADATA;
proc import
out = compmethod
datafile = "&path\&metadata"
dbms=xlsx
replace;
sheet = "COMPUTATION_METHOD" ;
run;
**** GET THE VALUE LEVEL METADATA;
proc import
out = valuelevel
datafile = "&path\&metadata"
dbms=xlsx
replace;
sheet = "VALUELEVEL_METADATA" ;
run;
%if "&standard" = "ADAM" %then
%do;
**** GET THE ANALYSIS RESULTS METADATA;
proc import
out = analysisresults
datafile = "&path\&metadata"
dbms=xlsx
replace;
sheet = "ANALYSIS_RESULTS" ;
run;
**** GET THE ANALYSIS RESULTS METADATA;
proc import
out = externallinks
datafile = "&path\&metadata"
dbms=xlsx
replace;
sheet = "EXTERNAL_LINKS" ;
run;
%end;
**** USE HTMLENCODE ON SOURCE TEXT THAT NEEDS ENCODING FOR PROPER BROWSER REPRESENTATIION;
%if &standard=ADAM %then
%do;
data toc_metadata;
length documentation $ 800;
set toc_metadata;
documentation = htmlencode(documentation);
** convert single quotes to double quotes;
documentation = tranwrd(documentation, "'", '"');
** convert double quotes to html quote;
documentation = tranwrd(trim(documentation), '"', '"');
format documentation $800.;
run;
%end;
data variable_metadata;
length comment $ 2000;
set variable_metadata;
format comment;
informat comment;
origin = htmlencode(origin);
label = htmlencode(label);
comment = htmlencode(comment);
**** FOR ADAM, JOIN ORIGIN/"SOURCE" AND COMMENT
**** TO FORM "SOURCE/DERIVATION" METADATA;
if "&standard" = "ADAM" and origin ne '' and
comment ne '' then
comment = "SOURCE: " || left(trim(origin)) ||
" DERIVATION: " || left(trim(comment));
else if "&standard" = "ADAM" and origin ne '' and
comment = '' then
comment = "SOURCE: " || left(trim(origin));
if "&standard" = "ADAM" and origin = '' and
comment ne '' then
comment = "DERIVATION: " || left(trim(comment));
run;
data codelists;
set codelists;
codedvalue = htmlencode(codedvalue);
translated = htmlencode(translated);
run;
data compmethod;
set compmethod;
computationmethod = htmlencode(computationmethod);
run;
data valuelevel;
length comment $ 2000;
set valuelevel;
format comment;
informat comment;
origin = htmlencode(origin);
label = htmlencode(label);
comment = htmlencode(comment);
**** FOR ADAM, JOIN ORIGIN/"SOURCE" AND COMMENT
**** TO FORM "SOURCE/DERIVATION" METADATA;
if "&standard" = "ADAM" and origin ne '' and
comment ne '' then
comment = "SOURCE: " || left(trim(origin)) ||
" DERIVATION: " || left(trim(comment));
else if "&standard" = "ADAM" and origin ne '' and
comment = '' then
comment = "SOURCE: " || left(trim(origin));
if "&standard" = "ADAM" and origin = '' and
comment ne '' then
comment = "DERIVATION: " || left(trim(comment));
run;
%if "&standard" = "ADAM" %then
%do;
data analysisresults;
length programmingcode $800. docleafid $40.;
set analysisresults;
where displayid ne '';
arrow + 1;
selectioncriteria = htmlencode(selectioncriteria);
paramlist = htmlencode(paramlist);
reason = htmlencode(reason);
documentation = htmlencode(documentation);
if index(documentation, '[r]')>0 then
docleafid = substr(documentation, index(documentation,'[r]')+3, index(documentation,'[\r]')-index(documentation,'[r]')-3);
else
docleafid = '.';
programmingcode = htmlencode(programmingcode);
** convert single quotes to double quotes;
programmingcode = tranwrd(programmingcode, "'", '"');
** convert double quotes to html quote;
programmingcode = tranwrd(programmingcode, '"', '"');
format programmingcode $800.;
run;
** ENSURE UNIQUENESS ON DISPLAYID AND RESULTID AND CREATE A COMBO ID;
data analysisresults;
set analysisresults;
by displayid notsorted;
drop resultnum;
retain resultnum;
if first.displayid then
resultnum = 0;
resultnum + 1;
if not(first.displayid and last.displayid) then
arid = trim(displayid) || ".R." || put(resultnum,z2.);
else
arid = displayid;
run;
** IF DOCLEAFID IS NON-MISSING, MERGE IN THE TITLE FROM EXTERNAL_LINKS;
proc sort
data = analysisresults;
by docleafid;
run;
proc sort
data = externallinks (keep = leafid title rename=(leafid=docleafid title=doctitle))
out = doc_links;
by docleafid;
run;
data analysisresults;
merge analysisresults (in = inar) doc_links (in = indoc_links);
by docleafid;
if inar;
** if the leaf ID exists, then the title of the leaf ID will be printed and can be removed from DOCUMENTIATION;
if indoc_links then
documentation = tranwrd(documentation, '[r]' || trim(docleafid) || '[\r]', " ");
run;
proc sort
data = analysisresults;
by arrow;
run;
%end;
**** CREATE DEFINE FILE HEADER SECTION;
filename dheader "&out.define_header.xml";
data define_header;
set define_header;
file dheader notitles;
creationdate = compress(put(datetime(), IS8601DT.));
put @1 '<?xml version="1.0" encoding="ISO-8859-1" ?>' /
@1 '<?xml-stylesheet type="text/xsl" href="' stylesheet +(-1) '"?>' /
@1 '<!-- ******************************************************************************* -->' /
@1 '<!-- File: define.xml -->' /
@1 "<!-- Date: &sysdate9. -->" /
@1 '<!-- Description: Define.xml file for ' studyname +(-1) ' -->' /
@1 '<!-- ******************************************************************************* -->' /
@1 '<ODM' /
@3 'xmlns="http://www.cdisc.org/ns/odm/v1.2"' /
@3 'xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"' /
@3 'xmlns:xlink="http://www.w3.org/1999/xlink"' /
@3 'xmlns:def="http://www.cdisc.org/ns/def/v1.0"' /
%if "&standard" = "ADAM" %then
@3 'xmlns:adamref="http://www.cdisc.org/ns/ADaMRes/DRAFT"' /
;
@3 'xsi:schemaLocation="' schemalocation +(-1) '"' /
@3 'FileOID="' fileoid +(-1) '"' /
@3 'ODMVersion="1.2"' /
@3 'FileType="Snapshot"' /
@3 'CreationDateTime="' creationdate +(-1) '">' /
@1 '<Study OID="' studyoid +(-1) '">' /
@3 '<GlobalVariables>' /
@5 '<StudyName>' studyname +(-1) '</StudyName>' /
@5 '<StudyDescription>' studydescription +(-1) '</StudyDescription>' /
@5 '<ProtocolName>' protocolname +(-1) '</ProtocolName>' /
@3 '</GlobalVariables>' /
@3 '<MetaDataVersion OID="CDISC.' standard +(-1) '.' version +(-1) '"' /
@5 'Name="' studyname +(-1) ',Data Definitions"' /
@5 'Description="' studyname +(-1) ',Data Definitions"' /
@5 'def:DefineVersion="1.0.0"' /
@5 'def:StandardName="CDISC ' standard +(-1) '"' /
@5 'def:StandardVersion="' version +(-1) '">' /
%if "&standard" = "ADAM" %then
%do;
@5 '<def:SupplementalDoc>' /
@7 '<def:DocumentRef leafID="Suppdoc"/>' /
@5 '</def:SupplementalDoc>' /
@5 '<def:leaf ID="Suppdoc" xlink:href="dataguide.pdf">' /
@7 '<def:title>Data Guide</def:title>' /
%end;
%else %if "&standard" = "SDTM" %then
%do;
@5 '<def:AnnotatedCRF>' /
@7 '<def:DocumentRef leafID="blankcrf"/>' /
@5 '</def:AnnotatedCRF>' /
@5 '<def:leaf ID="blankcrf" xlink:href="blankcrf.pdf">' /
@7 '<def:title>Annotated Case Report Form</def:title>' /
%end;
@5 '</def:leaf>';
run;
**** ADD OTHER ADAM EXTERNAL LINKS;
%if "&standard" = "ADAM" %then
%do;
filename leaves "&out.leaves.xml";
data _null_;
set externallinks;
file leaves notitles;
put @5 '<def:leaf ID="' leafid +(-1) '"' /
@7 'xlink:href="' leafrelpath +(-1) '">' /
@7 '<def:title>' title '</def:title>' /
@5 '</def:leaf>'
;
run;
%end;
**** ADD ITEMOID TO VARIABLE METADATA;
data variable_metadata;
set variable_metadata(rename=(domain = oid));
length itemoid $ 40;
if variable in ("STUDYID","DOMAIN","USUBJID","SUBJID") then
itemoid = variable;
else
itemoid = compress(oid || "." || variable);
run;
**** ADD ITEMOID TO VALUE LEVEL METADATA;
data valuelevel;
set valuelevel;
length itemoid $ 200;
itemoid = compress(valuelistoid || "." || valuename);
run;
**** CREATE COMPUTATION METHOD SECTION;
filename comp "&out.compmethod.xml";
data compmethods;
set compmethod;
file comp notitles;
if _n_ = 1 then
put @5 "<!-- ******************************************* -->" /
@5 "<!-- COMPUTATIONAL METHOD INFORMATION *** -->" /
@5 "<!-- ******************************************* -->";
put @5 '<def:ComputationMethod OID="' computationmethodoid +(-1) '">' computationmethod +(-1) '</def:ComputationMethod>';
run;
**** CREATE VALUE LEVEL LIST DEFINITION SECTION;
proc sort
data=valuelevel;
where valuelistoid ne '';
by valuelistoid;
run;
filename vallist "&out.valuelist.xml";
data valuelevel;
set valuelevel;
by valuelistoid;
file vallist notitles;
if _n_ = 1 then
put @5 "<!-- ******************************************* -->" /
@5 "<!-- VALUE LEVEL LIST DEFINITION INFORMATION ** -->" /
@5 "<!-- ******************************************* -->";
if first.valuelistoid then
put @5 '<def:ValueListDef OID="' valuelistoid +(-1) '">';
put @7 '<ItemRef ItemOID="' itemoid +(-1) '"' /
@9 'Mandatory="' mandatory +(-1) '"/>';
if last.valuelistoid then
put @5 '</def:ValueListDef>';
run;
**** CREATE "ITEMGROUPDEF" SECTION;
proc sort
data=VARIABLE_METADATA;
where oid ne '';
by oid varnum;
run;
proc sort
data=toc_metadata;
where oid ne '';
by oid;
run;
filename igdef "&out.itemgroupdef.xml";
data itemgroupdef;
length label $ 40;
merge toc_metadata VARIABLE_METADATA(drop=label);
by oid;
file igdef notitles;
if first.oid then
do;
put @5 "<!-- ******************************************* -->" /
@5 "<!-- " oid @25 "ItemGroupDef INFORMATION *** -->" /
@5 "<!-- ******************************************* -->" /
@5 '<ItemGroupDef OID="' oid +(-1) '"' /
@7 'Name="' name +(-1) '"' /
@7 'Repeating="' repeating +(-1) '"' /
@7 'Purpose="' purpose +(-1) '"' /
@7 'IsReferenceData="' isreferencedata +(-1) '"' /
@7 'def:Label="' label +(-1) '"' /
@7 'def:Structure="' structure +(-1) '"' /
@7 'def:DomainKeys="' domainkeys +(-1) '"' /
@7 'def:Class="' class +(-1) '"' ;
%if &standard=ADAM %then
put @7 'def:ArchiveLocationID="Location.' archivelocationid +(-1) '"' /
@7 'Comment="' documentation +(-1) '">'
;
%else
put @7 'def:ArchiveLocationID="Location.' archivelocationid +(-1) '">';
;
end;
put @7 '<ItemRef ItemOID="' itemoid +(-1) '"' /
@9 'OrderNumber="' varnum +(-1) '"' /
@9 'Mandatory="' mandatory +(-1) @;
if role ne '' and "&standard" = "SDTM" then
put '"' /
@9 'Role="' role +(-1) '"' /
@9 'RoleCodeListOID="CodeList.' rolecodelist +(-1) '"/>';
else
put '"/>';
if last.oid then
put @7 "<!-- **************************************************** -->" /
@7 "<!-- def:leaf details for hypertext linking the dataset -->" /
@7 "<!-- **************************************************** -->" /
@7 '<def:leaf ID="Location.' oid +(-1) '" xlink:href="' archivelocationid +(-1) '.xpt">' /
@9 '<def:title>' archivelocationid +(-1) '.xpt </def:title>' /
@7 '</def:leaf>' /
@5 '</ItemGroupDef>';
run;
**** CREATE "ITEMDEF" SECTION;
filename idef "&out.itemdef.xml";
data itemdef;
set VARIABLE_METADATA end=eof;
by oid;
file idef notitles;
if _n_ = 1 then
put @5 "<!-- ************************************************************ -->" /
@5 "<!-- The details of each variable is here for all domains -->" /
@5 "<!-- ************************************************************ -->" ;
put @5 '<ItemDef OID="' itemoid +(-1) '"' /
@7 'Name="' variable +(-1) '"' /
@7 'DataType="' type +(-1) '"' /
@7 'Length="' length +(-1) '"';
if significantdigits ne '' then
put @7 'SignificantDigitis="' significantdigits +(-1) '"';
if displayformat ne '' then
put @7 'def:DisplayFormat="' displayformat +(-1) '"';
if computationmethodoid ne '' then
put @7 'def:ComputationMethodOID="' computationmethodoid +(-1) '"';
put %if "&standard" = "SDTM" %then
@7 'Origin="' origin +(-1) '"' / ;
@7 'Comment="' comment +(-1) '"' /
@7 'def:Label="' label +(-1) '">';
if codelistname ne '' then
put @7 '<CodeListRef CodeListOID="CodeList.' codelistname +(-1) '"/>';
if valuelistoid ne '' then
put @7 '<def:ValueListRef ValueListOID="' valuelistoid +(-1) '"/>';
put @5 '</ItemDef>';
run;
**** ADD ITEMDEFS FOR VALUE LEVEL ITEMS TO "ITEMDEF" SECTION;
filename idefvl "&out.itemdef_value.xml";
data itemdefvalue;
set valuelevel end=eof;
by valuelistoid;
file idefvl notitles;
if _n_ = 1 then
put @5 "<!-- ************************************************************ -->" /
@5 "<!-- The details of value level items are here -->" /
@5 "<!-- ************************************************************ -->" ;
put @5 '<ItemDef OID="' itemoid +(-1) '"' /
@7 'Name="' valuename +(-1) '"' /
@7 'DataType="' type +(-1) '"' /
@7 'Length="' length +(-1) '"';
if significantdigits ne '' then
put @7 'SignificantDigitis="' significantdigits +(-1) '"';
if displayformat ne '' then
put @7 'def:DisplayFormat="' displayformat +(-1) '"';
if computationmethodoid ne '' then
put @7 'def:ComputationMethodOID="' computationmethodoid +(-1) '"';
put %if "&standard" = "SDTM" %then
@7 'Origin="' origin +(-1) '"' / ;
@7 'Comment="' comment +(-1) '"' /
@7 'def:Label="' label +(-1) '">';
if codelistname ne '' then
put @7 '<CodeListRef CodeListOID="CodeList.' codelistname +(-1) '"/>';
put @5 '</ItemDef>';
run;
**** ADD ANALYSIS RESULTS METADATA SECTION FOR ADAM;
%if "&standard" = "ADAM" %then
%do;
filename ar "&out.analysisresults.xml";
data _null_;
set analysisresults;
** note that it is required that identical display IDs be adjacent to
** each other in the metadata spreadsheet;
by displayid notsorted;
file ar notitles;
if _n_ = 1 then
put @5 "<!-- ************************************************************ -->" /
@5 "<!-- Analysis Results MetaData are Presented Below -->" /
@5 "<!-- ************************************************************ -->"
;
if first.displayid then
put @5 '<adamref:AnalysisResultDisplays>' /
@7 '<adamref:ResultDisplay DisplayIdentifier="' displayid +(-1)
'" OID="' displayid +(-1) '" DisplayLabel="' displayname +(-1)
'" leafID="' displayid +(-1) '">' ;
put @9 '<adamref:AnalysisResults ' /
@9 'OID="' arid +(-1) '"' /
@9 'ResultIdentifier="' resultid +(-1) '"' /
@9 'Reason="' reason +(-1) '">' /
@9 '<!-- List the parameters and parameter codes -->' /
@9 '<adamref:ParameterList>'
;
** loop through PARAMCD/PARAM sets;
set = 1;
do while(scan(paramlist,set,'|') ne '');
paramset = scan(paramlist,set,'|');
paramcd = scan(paramset,1,'/\');
param = trim(scan(paramset,2,'/\'));
put @11 '<adamref:Parameter ParamCD="' paramcd +(-1)
'" Param="' param +(-1) '"/>' ;
set = set + 1;
end;
put @9 '</adamref:ParameterList>';
** loop through the analysis variables;
set = 1;
do while(scan(analysisvariables,set,',') ne '');
analysisvar = scan(analysisvariables,set,',');
put @11 '<adamref:AnalysisVariable ItemOID="' analysisdataset +(-1)
'.' analysisvar +(-1) '"/>';
set = set + 1;
end;
put @9 '<!-- AnalysisDatasets are pairs of dataset references and selection criteria. Dataset references are ItemGroupRefs. The label in the xsl is the def:label for the ItemGroup -
put @9 '<adamref:AnalysisDataset>' /
@11 '<ItemGroupRef ItemGroupOID="' analysisdataset +(-1) '" Mandatory="No"/>' /
@11 '<adamref:SelectionCriteria>' /
@13 '<def:ComputationMethod OID="SC' _n_ z3.
'" Name="Selection Criteria ' _n_ z3. '"> [' selectioncriteria ' ]</def:ComputationMethod> '/
@11 '</adamref:SelectionCriteria> ' /
@9 '</adamref:AnalysisDataset> ' /
@9 '<adamref:Documentation leafID="' docleafid +(-1) '">' /
@11 '<TranslatedText xml:lang="en">' Documentation /
@11 '</TranslatedText>' /
@9 '</adamref:Documentation>' /
@9 '<adamref:ProgrammingCode>' /
@9 '<def:ComputationMethod OID="' displayid +(-1) '">' /
@1 ProgrammingCode /
@9 '</def:ComputationMethod>' /
@9 '</adamref:ProgrammingCode>' /
@7 '</adamref:AnalysisResults>' ;
if last.displayid then
put @5 '</adamref:ResultDisplay>' /
@5 '</adamref:AnalysisResultDisplays>'
;
run;
%end;
**** CREATE CODELIST SECTION;
filename codes "&xml.codelist.xml";
proc sort
data=codelists
nodupkey;
by codelistname codedvalue translated;
run;
**** MAKE SURE CODELIST IS UNIQUE;
data _null_;
set codelists;
by codelistname codedvalue;
if not (first.codedvalue and last.codedvalue) then
put "ERR" "OR: multiple versions of the same coded value "
codelistname= codedvalue=;
run;
proc sort
data=codelists;
by codelistname rank;
run;
data codelists;
set codelists end=eof;
by codelistname rank;
file codes notitles;
if _n_ = 1 then
put @5 "<!-- ************************************************************ -->" /
@5 "<!-- Codelists are presented below -->" /
@5 "<!-- ************************************************************ -->" ;
if first.codelistname then
put @5 '<CodeList OID="CodeList.' codelistname +(-1) '"' /
@7 'Name="' codelistname +(-1) '"' /
@7 'DataType="' type +(-1) '">';
**** output codelists that are not external dictionaries;
if codelistdictionary = '' then
do;
put @7 '<CodeListItem CodedValue="' codedvalue +(-1) '"' @;
if rank ne . then
put ' def:Rank="' rank +(-1) '">';
else
put '>';
put @9 '<Decode>' /
@11 '<TranslatedText>' translated +(-1) '</TranslatedText>' /
@9 '</Decode>' /
@7 '</CodeListItem>';
end;
**** output codelists that are pointers to external codelists;
if codelistdictionary ne '' then
put @7 '<ExternalCodeList Dictionary="' codelistdictionary +(-1)
'" Version="' codelistversion +(-1) '"/>';
if last.codelistname then
put @5 '</CodeList>';
if eof then
put @3 '</MetaDataVersion>' /
@1 '</Study>' /
@1 '</ODM>';
run;
%mend cln_100makedefine;
;;;;
run;quit;
* put the xml pieces together;
* ADAM XML;
%cln_100makedefine(path=&gbl_root/xls/,metadata=cln_adammetadata.xlsx,out=&gbl_root/xml/cln_adam);
filename def (
"d:/cln/xml/cln_adamanalysisresults.xml"
"d:/cln/xml/cln_adamcompmethod.xml"
"d:/cln/xml/cln_adamdefine_header.xml"
"d:/cln/xml/cln_adamitemdef.xml"
"d:/cln/xml/cln_adamitemdef_value.xml"
"d:/cln/xml/cln_adamitemgroupdef.xml"
"d:/cln/xml/cln_adamleaves.xml"
"d:/cln/xml/cln_adamvaluelist.xml"
);
data _null_;
infile def lrecl=384 recfm=v;
file "d:/cln/xml/cln_adamDefine.xml";
input;
put _infile_;
run;quit;
* SDTM XML;
%cln_100makedefine(path=&gbl_root/xls/,metadata=cln_sdtmmetadata.xlsx,out=&gbl_root/xml/cln_sdtm);
filename def (
"d:/cln/xml/cln_sdtmcompmethod.xml"
"d:/cln/xml/cln_sdtmdefine_header.xml"
"d:/cln/xml/cln_sdtmitemdef.xml"
"d:/cln/xml/cln_sdtmitemdef_value.xml"
"d:/cln/xml/cln_sdtmitemgroupdef.xml"
"d:/cln/xml/cln_sdtmvaluelist.xml"
);
data _null_;
infile def lrecl=384 recfm=v;
file "d:/cln/xml/cln_sdtmDefine.xml";
input;
put _infile_;
run;quit;
/*
CURRENT STATE OF DIRECTORIES
Directory of &gbl_root/cln
- added files
cln_fmt.sas7bcat
* formats
<DIR> b64
cln_adamMetadata.b64 *base 64 of excel mata data for adam datasets;
cln_sdtmMetadata.b64 *base 64 of excel mata data for sdtm datasets;
<DIR> log
<DIR> oto
cln_010.sas * many macro tools;
<DIR> pdf
<DIR> pin
<DIR> png
<DIR> rtf
<DIR> xls
cln_adamMetadata.xlsx * excel mata data for adam datasets;
cln_sdtmMetadata.xlsx * excel mata data for sdtm datasets;
<DIR> xml
- cln_adamDefine.xml * concatenation of all odm sections below
- cln_adamdefine_header.xml * excel odm section created from excel tab header
- cln_adamanalysisresults.xml ..
- cln_adamcompmethod.xml
- cln_adamitemdef.xml
- cln_adamitemdef_value.xml
- cln_adamitemgroupdef.xml
- cln_adamleaves.xml
- cln_adamvaluelist.xml
- cln_sdtmcompmethod.xml
- cln_sdtmDefine.xml * concatenation of all stdm sections below
- cln_sdtmdefine_header.xml * excel odm section created from excel tab header
- cln_sdtmitemdef.xml ..
- cln_sdtmitemdef_value.xml
- cln_sdtmitemgroupdef.xml
- cln_sdtmvaluelist.xml
*/
/* _ _ __ _ _
___ _ __ __| | __| | ___ / _(_)_ __ ___ __ ___ __ ___ | |
/ _ \ `_ \ / _` | / _` |/ _ \ |_| | `_ \ / _ \ \ \/ / `_ ` _ \| |
| __/ | | | (_| | | (_| | __/ _| | | | | __/ > <| | | | | | |
\___|_| |_|\__,_| \__,_|\___|_| |_|_| |_|\___| /_/\_\_| |_| |_|_|
_ _
___ __| (_)___ ___ _ __ ___ __ _ ___ _ __ ___ ___
/ __/ _` | / __|/ __| | `_ ` _ \ / _` |/ __| `__/ _ \/ __|
| (_| (_| | \__ \ (__ | | | | | | (_| | (__| | | (_) \__ \
\___\__,_|_|___/\___| |_| |_| |_|\__,_|\___|_| \___/|___/
___ ___ _ ____ _ _ ____
/ / |/ _ \ _ __ ___ | | _____/ ___| __| | |_ _ __ ___ | _ \ _ _
| | | | | | `_ ` _ \| |/ / _ \___ \ / _` | __| `_ ` _ \| | | | | | |
| | | |_| | | | | | | < __/___) | (_| | |_| | | | | | |_| | |_| |
|_|_|\___/|_| |_| |_|_|\_\___|____/ \__,_|\__|_| |_| |_|____/ \__, |
|___/
*/
filename ft15f001 "&gbl_root/oto/cln_110mkesdtmdy.sas";
parmcards4;
*---------------------------------------------------------------*;
* make_sdtm_dy.sas is a SAS macro that takes two SDTM --DTC dates
* and calculates a SDTM study day (--DY) variable. It must be used
* in a datastep that has both the REFDATE and DATE variables
* specified in the macro parameters below.
* MACRO PARAMETERS:
* refdate = --DTC baseline date to calculate the --DY from.
* Generally RFSTDTC.
* date = --DTC date to calculate the --DY to. The variable
* associated with the --DY variable.
*---------------------------------------------------------------*;
%macro cln_110mkesdtmdy(refdate=,date=);
if length(&date) >= 10 and length(&refdate) >= 10 then
do;
if input(&date,yymmdd10.) >=
input(&refdate,yymmdd10.) then
%upcase(%substr(&date,1,%length(&date)-3))DY = input(&date,yymmdd10.)- input(&refdate,yymmdd10.)+ 1;
else
%upcase(%substr(&date,1,%length(&date)-3))DY = input(&date,yymmdd10.)- input(&refdate,yymmdd10.);
end;
%mend cln_110mkesdtmdy;
;;;;
run;quit;
/* ____ ___ _ _ _
/ |___ \ / _ \ _ __ ___ | | _____ ___ _ __| |_ ___ __| |_ __
| | __) | | | | `_ ` _ \| |/ / _ \/ __| `__| __/ _ \ / _` | `__|
| |/ __/| |_| | | | | | | < __/\__ \ | | || (_) | (_| | |
|_|_____|\___/|_| |_| |_|_|\_\___||___/_| \__\___/ \__,_|_|
*/
filename ft15f001 "&gbl_root/oto/cln_120mkesrtodr.sas";
parmcards4;
*----------------------------------------------------------------*;
* make_sort_order.sas creates a global macro variable called
* **SORTSTRING where ** is the name of the dataset that contains
* the metadata specified sort order for a given dataset.
*
* MACRO PARAMETERS:
* metadatafile = the file containing the dataset metadata
* dataset = the dataset or domain name
*----------------------------------------------------------------*;
%macro cln_120mkesrtodr(metadatafile=,dataset=);
proc import
datafile="&metadatafile"
out=_temp
dbms=xlsx
replace;
sheet="TOC_METADATA";
run;
** create **SORTSTRING macro variable;
%global &dataset.SORTSTRING;
data _null_;
set _temp;
where name = "&dataset";
call symputx(compress("&dataset" || "SORTSTRING"),
translate(domainkeys," ",","));
run;
%mend cln_120mkesrtodr;
;;;;
run;quit;
/* _____ ___ __ _
/ |___ / / _ \ ___ / _| |__
| | |_ \| | | |/ __| |_| `_ \
| |___) | |_| | (__| _| |_) |
|_|____/ \___/ \___|_| |_.__/
*/
filename ft15f001 "&gbl_root/oto/cln_130cfb.sas";
parmcards4;
*---------------------------------------------------------;
* Macro for deriving ABLFL, BASE, CHG, and PCHG for a BDS
* formatted ADaM data set;
* Assumes baseline is the last non-missing value on or before
* study day 1 and that the INDDATA is an SDTM data set with
* variables USUBJID and VISITNUM
*---------------------------------------------------------;
%macro cln_130cfb(indata= ,outdata= ,avalvar= ,dayvar= ,keepvars= );
proc sort
data = &indata
out = &outdata (rename = (&avalvar = aval));
by usubjid visitnum;
run;
* Baseline is defined as the last non-missing value prior to study day 1 first dose;
* (note, values on Day 1 are assumed to occur before the first dose);
data base1 (keep = usubjid visitnum) base2 (keep = usubjid base);
set &outdata;
where &dayvar<=1 and aval > .z;
by usubjid visitnum;
rename aval = base;
if last.usubjid;
run;
* Do one merge to identify the baseline record;
data &outdata;
merge &outdata base1 (in = inbase);
by usubjid visitnum;
if inbase then
ablfl = 'Y';
run;
* Do another merge to merge in the baseline value;
data &outdata;
merge &outdata base2;
by usubjid;
%if &keepvars^= %then
keep &keepvars;
;
chg = aval - base;
pchg = divide(chg,base*100);
run;
%mend cln_130cfb;
;;;;
run;quit;
/* _ _ ___ _ __ __ _ _____ _ _
/ | || | / _ \ _ __ ___ | | _____| \/ | |_ _ |_ _| |__ | |
| | || |_| | | | `_ ` _ \| |/ / _ \ |\/| | __| | | || | | `_ \| |
| |__ _| |_| | | | | | | < __/ | | | |_| |_| || | | |_) | |
|_| |_| \___/|_| |_| |_|_|\_\___|_| |_|\__|\__, ||_| |_.__/|_|
|___/
*/
filename ft15f001 "&gbl_root/oto/cln_140mkeMtyTbl.sas";
parmcards4;
*---------------------------------------------------------------*;
* make_empty_dataset.sas creates a zero record dataset based on a
* dataset metadata spreadsheet. The dataset created is called
* EMPTY_** where "**" is the name of the dataset. This macro also
* creates a global macro variable called **KEEPSTRING that holds
* the dataset variables desired and listed in the order they
* should appear. [The variable order is dictated by VARNUM in the
* metadata spreadsheet.]
*
* MACRO PARAMETERS:
* metadatafile = the MS Excel file containing the dataset metadata
* dataset = the dataset or domain name you want to extract
*---------------------------------------------------------------*;
%macro cln_140mkeMtyTbl(metadatafile=,dataset=);
/*
%let metadatafile=&gbl_root.:/cln/xls/cln_sdtmMetadata.xlsx;
%let dataset=DM;
*/
%global keepstring;
%local i;
proc import
datafile="&metadatafile"
out=_temp
dbms=xlsx
replace;
sheet="VARIABLE_METADATA";
run;
** sort the dataset by expected specified variable order;
proc sort
data=_temp;
where domain = "&dataset";
by varnum;
run;
** create keepstring macro variable and load metadata
** information into macro variables;
%global &dataset.KEEPSTRING;
data _null_;
set _temp nobs=nobs end=eof;
if _n_=1 then
call symput("vars", compress(put(nobs,3.)));
call symputx('var' || compress(put(_n_, 3.)), variable);
call symputx('label' || compress(put(_n_, 3.)), label);
call symputx('length' || compress(put(_n_, 3.)), put(length, 3.));
** valid ODM types include TEXT, INTEGER, FLOAT, DATETIME,
** DATE, TIME and map to SAS numeric or character;
if upcase(type) in ("INTEGER", "FLOAT") then
call symputx('type' || compress(put(_n_, 3.)), "");
else if upcase(type) in ("TEXT", "DATE", "DATETIME",
"DATE", "TIME") then
call symputx('type' || compress(put(_n_, 3.)), "$");
else
put "ERR" "OR: not using a valid ODM type. " type=;
** create **KEEPSTRING macro variable;
length keepstring $ 32767;
retain keepstring;
keepstring = compress(keepstring) || "|" || left(variable);
if eof then
call symputx(upcase(compress("&dataset" || 'KEEPSTRING')),
left(trim(translate(keepstring," ","|"))));
run;
** create a 0-observation template data set used for assigning
** variable attributes to the actual data sets;
data EMPTY_&dataset;
%do i=1 %to &vars;
attrib &&var&i label="&&label&i" length=&&type&i.&&length&i...;
%if &&type&i=$ %then
retain &&var&i '';
%else
retain &&var&i .;
;
%end;
if 0;
run;
%mend cln_140mkeMtyTbl;
;;;;
run;quit;
/* ____ ___ _ _
/ | ___| / _ \ __| | ___ _ __ ___ __ _(_)_ __ __ __
| |___ \| | | |/ _` |/ _ \| `_ ` _ \ / _` | | `_ \\ \/ /
| |___) | |_| | (_| | (_) | | | | | | (_| | | | | |> <
|_|____/ \___/ \__,_|\___/|_| |_| |_|\__,_|_|_| |_/_/\_\
*/
filename ft15f001 "&gbl_root/oto/cln_150domainx.sas";
parmcards4;
%macro cln_150domainx(domain= ,suppqual=0);
/*
%let domain=DM;
%let subqual=0;
%let outlib=work;
*/
%local suppdata idvar varlist nvars;
%if &suppqual %then
%let suppdata=suppqual;
%else
%let suppdata=supp&domain;
;
%* count the number of supplemental qualifiers for the given domain;
proc sort
data = &sourcelib..&suppdata
out = nvars
nodupkey;
where rdomain=upcase("&domain");
by qnam idvar;
run;
/*
Up to 40 obs WORK.NVARS total obs=2
STUDYID RDOMAIN USUBJID IDVAR IDVARVAL QNAM QLABEL QVAL QORIG QEVAL
XYZ123 DM UNI101 RACEOTH Race, Other BRAZILIA CRF
XYZ123 DM UNI101 RANDDTC Randomization Date 2010-04-02 CRF
*/
data _null_;
set nvars end=eof;
by qnam idvar;
length varlist $200;
retain varlist;
if not first.qnam then
put 'PROB' 'LEM: More than one IDVAR for the domain-- '
rdomain= qnam=
idvar= ;
else
do;
nvars + 1;
varlist = trim(varlist) || " " || trim(qnam);
end;
if eof then
do;
call symput("nvars", put(nvars, 2.));
call symput("varlist", trim(left(varlist)));
call symput("idvar", trim(idvar));
end;
run;
%put domain=&domain idvar=&idvar nvars=&nvars varlist=&varlist;
proc sort
data = &sourcelib..&suppdata
out = supp&domain;
where rdomain=upcase("&domain");
by usubjid idvar idvarval;
run;
/*
Up to 40 obs WORK.SUPPDM total obs=66
Obs STUDYID RDOMAIN USUBJID IDVAR IDVARVAL QNAM QLABEL QVAL QORIG QEVAL
1 XYZ123 DM UNI101 RACEOTH Race, Other BRAZILIA CRF
2 XYZ123 DM UNI101 RANDDTC Randomization Date 2010-04-02 CRF
3 XYZ123 DM UNI102 RANDDTC Randomization Date 2010-02-13 CRF
*/
%* determine whether IDVAR in the parent domain is character or numeric;
%if &idvar^= %then
%do;
%let dsetnum=%sysfunc(open(&sourcelib..&domain));
%let varnum=%sysfunc(varnum(&dsetnum,&idvar));
%let idtype=%sysfunc(vartype(&dsetnum,&varnum));
%let rc=%sysfunc(close(&dsetnum));
%end;
%else
%let idtype= ;
data supp&domain.x;
set supp&domain;
by usubjid idvar idvarval;
drop q: idvarval idvar i rdomain;
length &varlist $200.;
retain &varlist;
array vars{*} &varlist;
if first.idvarval then
do i = 1 to dim(vars);
vars{i} = '';
end;
do i = 1 to dim(vars);
if upcase(qnam)=upcase(vname(vars{i})) then
vars{i} = qval;
end;
/*
%** convert to numeric if numeric in the parent domain;
%if &idvar^= and &idtype=N %then
&idvar = input(idvarval, best.);
%else %if &idvar^= %then
&idvar = idvarval;
;
*/
if last.idvarval;
run;
proc sort
data = supp&domain.x;
by usubjid &idvar;
run;quit;
proc sort
data = &sourcelib..&domain
out = __tmp;
by usubjid &idvar;
run;quit;
data &outlib..&domain;
merge __tmp supp&domain ;
by usubjid &idvar;
run;
/*
Middle Observation(33 ) of work.DM - Total Obs 66
-- CHARACTER --
STUDYID C15 XYZ123 Study Identifier
DOMAIN C2 DM Domain Abbreviation
USUBJID C25 UNI504 Unique Subject Identifier
SUBJID C7 504 Subject Identifier for the Study
RFSTDTC C16 2010-06-19 Subject Reference Start Date/Time
RFENDTC C16 2010-12-20 Subject Reference End Date/Time
SITEID C7 500 Study Site Identifier
BRTHDTC C16 1977-02-01 Date/Time of Birth
AGEU C5 YEARS Age Units
SEX C2 Wh Sex
RACE C40 Other Race
ARMCD C8 0 Planned Arm Code
ARM C40 Placebo Description of Planned Arm
COUNTRY C3 USA Country
RDOMAIN C2 DM Related Domain Abbreviation
IDVAR C8 Identifying Variable
IDVARVAL C200 Identifying Variable Value
QNAM C8 RANDDTC Qualifier Variable Name
QLABEL C40 Randomization Da Qualifier Variable Label
QVAL C200 2010-06-19 Data Value
QORIG C8 CRF Origin
QEVAL C8 Evaluator
TOTOBS C16 66 TOTOBS
-- NUMERIC --
AGE N8 33 Age
*/
%mend cln_150domainx;
;;;;
run;quit;
/* __ ___ _ _ ____ _ _
/ |/ /_ / _ \ __| | |_ ___|___ \ __| | |_
| | `_ \| | | |/ _` | __/ __| __) / _` | __|
| | (_) | |_| | (_| | || (__ / __/ (_| | |_
|_|\___/ \___/ \__,_|\__\___|_____\__,_|\__|
*/
filename ft15f001 "&gbl_root/oto/cln_160dtc2dt.sas";
parmcards4;
%macro cln_160dtc2dt (dtcvar , prefix=a, refdt= );
if length(trim(&dtcvar))=10 and index(&dtcvar,'--')=0 then
&prefix.dt = input(&dtcvar, yymmdd10.);
else if length(&dtcvar)=16 and index(&dtcvar,'--')=0 and index(&dtcvar,'-:')=0 then
do;
&prefix.dtm = input(trim(&dtcvar)||":00", e8601dt19.);
&prefix.dt = datepart(&prefix.dtm);
* optionally add formats: ;
* format &prefix.dtm datetime16.;
end;
%if &refdt^= %then
%do;
if .<&prefix.dt<&refdt then
&prefix.dy = &prefix.dt - &refdt;
else if &prefix.dt>=&refdt then
&prefix.dy = &prefix.dt - &refdt + 1;
%end;
* optionally add formats: ;
* format &prefix.dt yymmdd10. ;
%mend cln_160dtc2dt;
;;;;
run;quit;
/* _____ ___
/ |___ / _ \ _ __ ___ _ __ __ _ ___ _ _ _ __
| | / / | | | `_ ` _ \| `__/ _` / __| | | | `_ \
| | / /| |_| | | | | | | | | (_| \__ \ |_| | |_) |
|_|/_/ \___/|_| |_| |_|_| \__, |___/\__,_| .__/
|___/ |_|
*/
filename ft15f001 "&gbl_root/oto/cln_170mrgsup.sas";
parmcards4;
*------------------------------------------------------------;
* Merge supplemental qualifiers into the parent SDTM domain;
* This can either be for an entire library or for specified
* domains;
*------------------------------------------------------------;
%macro cln_170mrgsup(sourcelib=library, outlib=WORK, domains= , suppqual=0);
%local domain;
/*
libname cln "d:/cln";
%let sourcelib=cln;
%let domains=DM;
%let domain=DM;
*/
%** de-normalize suppqual and merge into the given domain;
%*-------------------------------------------------------;
%* If DOMAINS parameter specified, then loop through those
%* domains;
%* otherwise, dynamically identify the SUPPxx data sets and
%* go through them all;
%*-------------------------------------------------------;
%let _wrd=1;
%if &DOMAINS^= %then
%do %while(%scan(&domains,&_wrd)^= );
%let domain=%scan(&domains,&_wrd);
%cln_150domainx(domain=&domain,suppqual=0);
%let _wrd=%eval(&_wrd+1);
%end;
%else
%do;
%** find all of the SUPPxx datasets and loop through each one;
ods output members=members;
proc contents
data = &sourcelib.._all_ memtype=data nods ;
run;
data membersx;
set members;
if upcase(name)=:'SUPP' and upcase(name)^=:'SUPPQUAL' then
do;
rdomain = substr(name,5,2);
put name= rdomain= ;
output;
end;
else if upcase(name)=:'SUPPQUAL' then
call symput("suppqual","1");
run;
%** loop through each domain;
proc sql /* noprint */;
select count(distinct rdomain)
into :domn
from %if &suppqual %then &sourcelib..suppqual; %else
membersx;
quit;
proc sql;
select distinct rdomain
into :domain1 - :domain%left(&domn)
from %if &suppqual %then &sourcelib..suppqual; %else
membersx;
;
%do _i=1 %to &domn;
%cln_150domainx(domain=&&domain&_i,suppqual=&suppqual);
%end;
%end; %* if domains not specified explicitly...;
%mend cln_170mrgsup;
;;;;
run;quit;
/*
CURRENT STATE OF DIRECTORIES
- added files
Directory of &gbl_root/cln
cln_fmt.sas7bcat
* formats
<DIR> b64
cln_adamMetadata.b64 *base 64 of excel mata data for adam datasets;
cln_sdtmMetadata.b64 *base 64 of excel mata data for sdtm datasets;
<DIR> log
<DIR> oto
cln_010.sas * many macro tools;
<DIR> pdf
<DIR> pin
<DIR> png
<DIR> rtf
<DIR> sas
cln_010.sas * SAS Tools
- cln_100makedefine.sas * CDISC utilities ( extract meta data from excel tabs;
- cln_110mkesdtmdy.sas
- cln_120mkesrtodr.sas
- cln_130cfb.sas
- cln_140mkeMtyTbl.sas
- cln_150domainx.sas
- cln_160dtc2dt.sas
- cln_170mrgsup.sas
<DIR> xls
cln_adamMetadata.xlsx * excel mata data for adam datasets;
cln_sdtmMetadata.xlsx * excel mata data for sdtm datasets;
<DIR> xml
cln_adamDefine.xml * concatenation of all odm sections below
cln_adamdefine_header.xml * excel odm section created from excel tab header
cln_adamanalysisresults.xml ..
cln_adamcompmethod.xml
cln_adamitemdef.xml
cln_adamitemdef_value.xml
cln_adamitemgroupdef.xml
cln_adamleaves.xml
cln_adamvaluelist.xml
cln_sdtmcompmethod.xml
cln_sdtmDefine.xml * concatenation of all stdm sections below
cln_sdtmdefine_header.xml * excel odm section created from excel tab header
cln_sdtmitemdef.xml ..
cln_sdtmitemdef_value.xml
cln_sdtmitemgroupdef.xml
cln_sdtmvaluelist.xml
<DIR> xpt
<DIR> zip
*/
/* _ _ _
___ _ __ __| | ___ __| (_)___ ___ _ __ ___ __ _ ___ _ __ ___ ___
/ _ \ `_ \ / _` | / __/ _` | / __|/ __| | `_ ` _ \ / _` |/ __| `__/ _ \/ __|
| __/ | | | (_| | | (_| (_| | \__ \ (__ | | | | | | (_| | (__| | | (_) \__ \
\___|_| |_|\__,_| \___\__,_|_|___/\___| |_| |_| |_|\__,_|\___|_| \___/|___/
_ _ _ _
__ _ ___| |_ _ __ __ ___ __ __| | __ _| |_ __ _ ___ ___| |_ ___
/ _` |/ _ \ __| | `__/ _` \ \ /\ / / / _` |/ _` | __/ _` / __|/ _ \ __/ __|
| (_| | __/ |_ | | | (_| |\ V V / | (_| | (_| | || (_| \__ \ __/ |_\__ \
\__, |\___|\__| |_| \__,_| \_/\_/ \__,_|\__,_|\__\__,_|___/\___|\__|___/
|___/
you can download the individual raw sas datases into the folder below or run this script
./cln/cln_rawadverse.sas7bdat
./cln/cln_rawdemographic.sas7bdat
./cln/cln_rawdosing.sas7bdat
./cln/cln_rawlabs.sas7bdat
./cln/cln_rawpain.sas7bdat
There are warning whem trying to clear a file when it is not defined. This is a precaution because in any section of code fails
a difficult conflict may arise and you may not be able to use the fileref.
*/
filename download clear;
filename download "&gbl_root/b64/cln_rawdemographic.b64";
%*utl_b64encode(&gbl_root/sd1/cln_rawdemographic.sas7bdat,&gbl_root/b64/cln_rawdemographic.b64); /*only if I need to upload another newer version of the data */
proc http
method='GET'
url="https://raw.githubusercontent.com/rogerjdeangelis/utl-end-to-end-cdisc-SDTM-ADaM-processing/master/cln_rawdemographic.b64"
out=download;
run;quit;
filename download clear;
%utl_b64decode(&gbl_root/b64/cln_rawdemographic.b64,&gbl_root/cln_rawdemographic.sas7bdat);
filename download clear;
filename download "&gbl_root/b64/cln_rawadverse.b64";
%*utl_b64encode(&gbl_root/sd1/cln_rawadverse.sas7bdat,&gbl_root/b64/cln_rawadverse.b64);/* not needed */
proc http
method='GET'
url="https://raw.githubusercontent.com/rogerjdeangelis/utl-end-to-end-cdisc-SDTM-ADaM-processing/master/cln_rawadverse.b64"
out=download;
run;quit;
filename download clear;
%utl_b64decode(&gbl_root/b64/cln_rawadverse.b64,&gbl_root/cln_rawadverse.sas7bdat);
filename download clear;
filename download "&gbl_root/b64/cln_rawdosing.b64";
%*utl_b64encode(&gbl_root/sd1/cln_rawdosing.sas7bdat,&gbl_root/b64/cln_rawdosing.b64);/* not needed */
proc http
method='GET'
url="https://raw.githubusercontent.com/rogerjdeangelis/utl-end-to-end-cdisc-SDTM-ADaM-processing/master/cln_rawdosing.b64"
out=download;
run;quit;
filename download clear;
%utl_b64decode(&gbl_root/b64/cln_rawdosing.b64,&gbl_root/cln_rawdosing.sas7bdat);
filename download clear;
filename download "&gbl_root/b64/cln_rawlabs.b64";
%*utl_b64encode(&gbl_root/sd1/cln_rawlabs.sas7bdat,&gbl_root/b64/cln_rawlabs.b64);/* not needed */
proc http
method='GET'
url="https://raw.githubusercontent.com/rogerjdeangelis/utl-end-to-end-cdisc-SDTM-ADaM-processing/master/cln_rawlabs.b64"
out=download;
run;quit;
filename download clear;
%utl_b64decode(&gbl_root/b64/cln_rawlabs.b64,&gbl_root/cln_rawlabs.sas7bdat);
filename download clear;
filename download "&gbl_root/b64/cln_rawpain.b64";
%*utl_b64encode(&gbl_root/sd1/cln_rawpain.sas7bdat,&gbl_root/b64/cln_rawpain.b64); /* not needed */
proc http
method='GET'
url="https://raw.githubusercontent.com/rogerjdeangelis/utl-end-to-end-cdisc-SDTM-ADaM-processing/master/cln_rawpain.b64"
out=download;
run;quit;
filename download clear;
%utl_b64decode(&gbl_root/b64/cln_rawpain.b64,&gbl_root/cln_rawpain.sas7bdat);
/*
/*
CURRENT STATE OF DIRECTORIES
- added files
Directory of &gbl_root/cln
cln_fmt.sas7bcat * formats
- cln_rawadverse.sas7bdat * raw data
- cln_rawdemographic.sas7bdat
- cln_rawdosing.sas7bdat
- cln_rawlabs.sas7bdat
- cln_rawpain.sas7bdat
* formats
<DIR> b64
cln_adamMetadata.b64 *base 64 of excel mata data for adam datasets;
cln_sdtmMetadata.b64 *base 64 of excel mata data for sdtm datasets;
- cln_rawadverse.b64 * base 64 encoded raw sas datasets;
- cln_rawdemographic.b64
- cln_rawdosing.b64
- cln_rawlabs.b64
- cln_rawpain.b64
<DIR> log
<DIR> oto
cln_010.sas * many macro tools;
<DIR> pdf
<DIR> pin
<DIR> png
<DIR> rtf
<DIR> sas
cln_010.sas * SAS Tools
cln_100makedefine.sas * CDISC utilities ( extract meta data from excel tabs;
cln_110mkesdtmdy.sas
cln_120mkesrtodr.sas
cln_130cfb.sas
cln_140mkeMtyTbl.sas
cln_150domainx.sas
cln_160dtc2dt.sas
cln_170mrgsup.sas
<DIR> xls
cln_adamMetadata.xlsx * excel mata data for adam datasets;
cln_sdtmMetadata.xlsx * excel mata data for sdtm datasets;
<DIR> xml
cln_adamDefine.xml * concatenation of all odm sections below
cln_adamdefine_header.xml * excel odm section created from excel tab header
cln_adamanalysisresults.xml ..
cln_adamcompmethod.xml
cln_adamitemdef.xml
cln_adamitemdef_value.xml
cln_adamitemgroupdef.xml
cln_adamleaves.xml
cln_adamvaluelist.xml
cln_sdtmcompmethod.xml
cln_sdtmDefine.xml * concatenation of all stdm sections below
cln_sdtmdefine_header.xml * excel odm section created from excel tab header
cln_sdtmitemdef.xml ..
cln_sdtmitemdef_value.xml
cln_sdtmitemgroupdef.xml
cln_sdtmvaluelist.xml
<DIR> xpt
<DIR> zip
_ _ _ _
___ _ __ __| | __ _ ___| |_ _ __ __ ___ __ __| | __ _| |_ __ _
/ _ \ `_ \ / _` | / _` |/ _ \ __| | `__/ _` \ \ /\ / / / _` |/ _` | __/ _` |
| __/ | | | (_| | | (_| | __/ |_ | | | (_| |\ V V / | (_| | (_| | || (_| |
\___|_| |_|\__,_| \__, |\___|\__| |_| \__,_| \_/\_/ \__,_|\__,_|\__\__,_|
|___/
_ _
___ _ __ __| | ___ ___| |_ _ _ _ __
/ _ \ `_ \ / _` | / __|/ _ \ __| | | | `_ \
| __/ | | | (_| | \__ \ __/ |_| |_| | |_) |
\___|_| |_|\__,_| |___/\___|\__|\__,_| .__/
|_|
*/
/* _ _ _ _
___| |_ __ _ _ __| |_ ___ __| (_)___ ___
/ __| __/ _` | `__| __| / __/ _` | / __|/ __|
\__ \ || (_| | | | |_ | (_| (_| | \__ \ (__
|___/\__\__,_|_| \__| \___\__,_|_|___/\___|
_ __ _ __ ___ ___ ___ ___ ___
| `_ \| `__/ _ \ / __/ _ \/ __/ __|
| |_) | | | (_) | (_| __/\__ \__ \
| .__/|_| \___/ \___\___||___/___/
|_|
*/
/*___ ____ _____ __ __
/ ___|| _ \_ _| \/ |___
\___ \| | | || | | |\/| / __|
___) | |_| || | | | | \__ \
|____/|____/ |_| |_| |_|___/
___ ___ ___ _ _ ____
| ___| / _ \ / _ \ ___ __| | |_ _ __ ___ | _ \ _ __ ___
|___ \| | | | | | / __|/ _` | __| `_ ` _ \| | | | `_ ` _ \
___) | |_| | |_| \__ \ (_| | |_| | | | | | |_| | | | | | |
|____/ \___/ \___/|___/\__,_|\__|_| |_| |_|____/|_| |_| |_|
_ ____ __ __
_ __ ___ __ _| | _____ | _ \| \/ |
| `_ ` _ \ / _` | |/ / _ \ | | | | |\/| |
| | | | | | (_| | < __/ | |_| | | | |
|_| |_| |_|\__,_|_|\_\___| |____/|_| |_|
*/
filename ft15f001 "&gbl_root/oto/cln_500sdtmDm.sas";
parmcards4;
%macro cln_500sdtmDm ;
*---------------------------------------------------------------*;
* STDM_DM.sas creates the SDTM DM and SUPPDM datasets and saves them
* as permanent SAS datasets to the sdtm libref.
*---------------------------------------------------------------*;
libname cln "&gbl_root";
**** GET FIRST AND LAST DOSE DATE FOR RFSTDTC AND RFENDTC;
proc sort
data=cln.cln_rawdosing(keep=subject startdt enddt)
out=dosing;
by subject startdt;
run;
/*
DOSING total obs=84
Obs SUBJECT STARTDT ENDDT
1 101 04/02/2010 07/26/2010 1st dose
2 101 07/31/2010 10/10/2010 last dose
3 102 02/13/2010 03/20/2010
4 102 03/25/2010 08/10/2010
5 103 05/16/2010 11/14/2010
6 104 01/02/2010 01/10/2010
7 104 01/15/2010 05/25/2010
*/
**** FIRSTDOSE=FIRST DOSING AND LASTDOSE=LAST DOSING;
data dosing1st;
set dosing;
by subject;
format firstdose lastdose mmddyy10.;
retain firstdose lastdose;
if first.subject then
do;
firstdose = .;
lastdose = .;
end;
firstdose = min(firstdose,startdt,enddt);
lastdose = max(lastdose,startdt,enddt);
drop startdt enddt;
if last.subject;
run;
/*
Unique Patent first and last dose
DOSING1ST total obs=60
Obs SUBJECT FIRSTDOSE LASTDOSE
1 101 04/02/2010 10/10/2010
2 102 02/13/2010 08/10/2010
3 103 05/16/2010 11/14/2010
4 104 01/02/2010 07/04/2010
5 105 04/20/2010 10/19/2010
6 106 04/01/2010 10/10/2010
*/
**** GET DEMOGRAPHICS DATA;
proc sort
data=cln.cln_rawdemographic
out=demographic;
by subject;
run;
* ADD FIRST AND LAST DOSE TO PATIENT DEMOGRAPHICS;
data demog_dose;
merge demographic
dosing1st;
by subject;
run;
/*
Middle Observation(30 ) of demog_dose - Total Obs 60
-- CHARACTER --
ORACE C8 Oher Race Specify
UNIQUEID C6 UNI506 Company Wide Subject ID
GENDER C5 White GENDER
RACE C5 White RACE
TRT1 C7 Placebo TRT1
-- NUMERIC --
SUBJECT N8 506 Subject Number
TRT N8 0 Treatment
DOB N8 1664 Date of Birth
RANDDT N8 18282 Randomization Date
FIRSTDOSE N8 18282 FIRSTDOSE *** Added to unique patient record
LASTDOSE N8 18463 LASTDOSE
*/
**** CREATE EMPTY DM DATASET SHELL CALLED EMPTY_DM (MATCH FDA VARIABLES ;
%cln_140mkeMtyTbl(metadatafile=&gbl_root/xls/cln_sdtmMetadata.xlsx,dataset=DM);
**** DERIVE THE MAJORITY OF SDTM DM VARIABLES;
data dm;
set EMPTY_DM
demog_dose;
studyid = 'XYZ123';
domain = 'DM';
usubjid = left(uniqueid);
subjid = put(subject,3.);
rfstdtc = put(firstdose,yymmdd10.);
rfendtc = put(lastdose,yymmdd10.);
siteid = substr(subjid,1,1) || "00";
brthdtc = put(dob,yymmdd10.);
age = floor ((intck('month',dob,firstdose) -
(day(firstdose) < day(dob))) / 12);
if age ne . then
ageu = 'YEARS';
country = "USA";
sex=gender;
arm=trt1;
armcd=put(trt,3.);
drop gender trt trt1;
run;
/*
The CONTENTS Procedure
WORK.EMPTY_DM Observations 0
Variables in Creation Order
# Variable Type Len Label
1 STUDYID Char 15 Study Identifier
2 DOMAIN Char 2 Domain Abbreviation
3 USUBJID Char 25 Unique Subject Identifier
4 SUBJID Char 7 Subject Identifier for the Study
5 RFSTDTC Char 16 Subject Reference Start Date/Time
6 RFENDTC Char 16 Subject Reference End Date/Time
7 SITEID Char 7 Study Site Identifier
8 BRTHDTC Char 16 Date/Time of Birth
9 AGE Num 8 Age
10 AGEU Char 5 Age Units
11 SEX Char 2 Sex
12 RACE Char 40 Race
13 ARMCD Char 8 Planned Arm Code
14 ARM Char 40 Description of Planned Arm
15 COUNTRY Char 3 Country
*/
%cln_120mkesrtodr(metadatafile=&gbl_root/xls/cln_sdtmMetadata.xlsx,dataset=DM);
%put &=dmkeepstring;
%put &=dmsortstring;
/* FDA variables to keep based on define xml (in excel)
DMKEEPSTRING=STUDYID DOMAIN USUBJID SUBJID RFSTDTC RFENDTC SITEID BRTHDTC AGE AGEU SEX RACE ARMCD ARM COUNTRY
DMSORTSTRING=STUDYID USUBJID
*/
* SORT AND KEEP;
proc sort
data=dm(keep = &DMKEEPSTRING)
out=cln.dm;
by &DMSORTSTRING;
run;
/*
Final SDTN DM dataset
Middle Observation(30 ) of cln.dm - Total Obs 60
-- CHARACTER --
STUDYID C15 XYZ123 Study Identifier
DOMAIN C2 DM Domain Abbreviation
USUBJID C25 UNI506 Unique Subject Identifier
SUBJID C7 506 Subject Identifier for the Study
RFSTDTC C16 2010-01-20 Subject Reference Start Date/Time
RFENDTC C16 2010-07-20 Subject Reference End Date/Time
SITEID C7 500 Study Site Identifier
BRTHDTC C16 1964-07-22 Date/Time of Birth
AGEU C5 YEARS Age Units
SEX ** issue C2 Wh Sex
RACE C40 White Race
ARMCD C8 0 Planned Arm Code
ARM C40 Placebo Description of Planned Arm
COUNTRY C3 USA Country
TOTOBS C16 60 TOTOBS
-- NUMERIC --
AGE N8 45 Age
*/
* SUPLEMENTA DM DATA;
**** CREATE EMPTY SUPPDM DATASET CALLED EMPTY_DM;
%cln_140mkeMtyTbl(metadatafile=&gbl_root/xls/cln_sdtmMetadata.xlsx,dataset=SUPPDM);
/*
We do use the excel mete (same as XML) to set correct variable names, types and lengths
Middle Observation(33 ) of SUPPDM - Total Obs 66
-- CHARACTER --
STUDYID C15 XYZ123 Study Identifier
RDOMAIN C2 DM Related Domain Abbreviation
USUBJID C25 UNI504 Unique Subject Identifier
IDVAR C8 Identifying Variable
IDVARVAL C200 Identifying Variable Value
QNAM C8 RANDDTC Qualifier Variable Name
QLABEL C40 Randomization Da Qualifier Variable Label
QVAL C200 2010-06-19 Data Value
QORIG C8 CRF Origin
QEVAL C8 Evaluator
TOTOBS C16 66 TOTOBS
*/
%put &=SUPPDMKEEPSTRING;
* SUPPDMKEEPSTRING = STUDYID RDOMAIN USUBJID IDVAR IDVARVAL QNAM QLABEL QVAL QORIG QEVAL;
* FILL IN AND USE SUPPDMKEEPSTRING TO KEEP FDA VARIABLES FROM MACRO CLN_140MKEMTYTBL;
data suppdm;
set EMPTY_SUPPDM
dm;
keep &SUPPDMKEEPSTRING;
**** OUTPUT OTHER RACE AS A SUPPDM VALUE;
if orace ne '' then
do;
rdomain = 'DM';
qnam = 'RACEOTH';
qlabel = 'Race, Other';
qval = left(orace);
qorig = 'CRF';
output;
end;
**** OUTPUT RANDOMIZATION DATE AS SUPPDM VALUE;
if randdt ne . then
do;
rdomain = 'DM';
qnam = 'RANDDTC';
qlabel = 'Randomization Date';
qval = left(put(randdt,yymmdd10.));
qorig = 'CRF';
output;
end;
run;
%cln_120mkesrtodr(metadatafile=&gbl_root/xls/cln_sdtmMetadata.xlsx,dataset=SUPPDM);
%put &=SUPPDMSORTSTRING;
* SUPPDMSORTSTRING = STUDYID RDOMAIN USUBJID IDVAR IDVARVAL QNAM;
proc sort
data=suppdm
out=cln.suppdm;
by &SUPPDMSORTSTRING;
run;
* SORT USING SORTSTRING FROM META DATA;
* create v5 export files;
libname xpt xport "&gbl_root/xpt/cln_sdtmdm.xpt";
data xpt.dm;
set cln.dm;
run;quit;
libname xpt clear;
libname xpt xport "&gbl_root/xpt/cln_sdtmsuppdm.xpt";
data xpt.suppdm;
set cln.suppdm;
run;quit;
libname xpt clear;
%mend cln_500sdtmDm;
;;;;
run;quit;
/*
PROC CDISC MODEL = SDTM;
SDTM SDTMVersion = "3.1";
DOMAINDATA data = cln.Dm
domain = DM
category = SPECIAL;
run;quit;
*/
/*
%inc "&gbl_root/oto/cln_500sdtmDm.sas";
%cln_500sdtmDm;
*/
/* _ _ ____ __ __
___ _ __ __| | _ __ ___ __ _| | _____ | _ \| \/ |
/ _ \ `_ \ / _` | | `_ ` _ \ / _` | |/ / _ \ | | | | |\/| |
| __/ | | | (_| | | | | | | | (_| | < __/ | |_| | | | |
\___|_| |_|\__,_| |_| |_| |_|\__,_|_|\_\___| |____/|_| |_|
____ ____ ____ _ _ _
| ___|___ \| ___| ___ __| | |_ _ __ ___ / \ ___
|___ \ __) |___ \/ __|/ _` | __| `_ ` _ \ / _ \ / _ \
___) / __/ ___) \__ \ (_| | |_| | | | | |/ ___ \ __/
|____/_____|____/|___/\__,_|\__|_| |_| |_/_/ \_\___|
*/
filename ft15f001 "&gbl_root/oto/cln_525sdtmAe.sas";
parmcards4;
%macro cln_525sdtmAe;
%cln_140mkeMtyTbl(metadatafile=&gbl_root/xls/cln_sdtmMetadata.xlsx,dataset=AE);
%put &AEKEEPSTRING;
**** DERIVE THE MAJORITY OF SDTM AE VARIABLES;
options missing = ' ';
data ae;
set EMPTY_AE
cln.cln_rawadverse;
studyid = 'XYZ123';
domain = 'AE';
usubjid = left(uniqueid);
run;
proc sort
data=ae;
by usubjid;
run;
data ae;
merge ae(in=inae) cln.cln_dm(keep=usubjid rfstdtc);
by usubjid;
if inae;
%cln_110mkesdtmdy(refdate=rfstdtc,date=aestdtc);
%cln_110mkesdtmdy(refdate=rfstdtc,date=aeendtc);
run;
**** CREATE SEQ VARIABLE;
proc sort
data=ae;
by studyid usubjid aedecod aestdtc aeendtc;
run;
data ae;
retain STUDYID DOMAIN USUBJID AESEQ AETERM AEDECOD AEBODSYS AESEV AESER AEACN AEREL AESTDTC
AEENDTC AESTDY AEENDY;
set ae(drop=aeseq);
by studyid usubjid aedecod aestdtc aeendtc;
if not (first.aeendtc and last.aeendtc) then
put "WARN" "ING: key variables do not define an unique record. " usubjid=;
retain aeseq;
if first.usubjid then
aeseq = 1;
else
aeseq = aeseq + 1;
label aeseq = "Sequence Number";
run;
**** SORT AE ACCORDING TO METADATA AND SAVE PERMANENT DATASET;
%cln_120mkesrtodr(metadatafile=&gbl_root/xls/cln_sdtmMetadata.xlsx,dataset=AE);
proc sort
data=ae(keep = &AEKEEPSTRING)
out=cln.ae;
by &AESORTSTRING;
run;
libname xpt xport "&gbl_root/xpt/cln_sdtmAe.xpt";
data xpt.AE;
set cln.ae;
run;quit;
libname xpt clear;
/*
Middle Observation(20 ) of cln.ae - Total Obs 40
-- CHARACTER --
STUDYID C15 XYZ123 Study Identifier
DOMAIN C2 AE Domain Abbreviation
USUBJID C25 UNI305 Unique Subject Identifier
AETERM C200 POUNDING HEART Reported Term for the Adverse Event
AEDECOD C200 PALPITATIONS Dictionary-Derived Term
AEBODSYS C200 CARDIAC DISORDER Body System or Organ Class
AESEV C40 severe Severity/Intensity
AESER C40 N Serious Event
AEACN C40 no dose change Action Taken with Study Treatment
AEREL C40 not Causality
AESTDTC C16 2010-10-05 Start Date/Time of Adverse Event
AEENDTC C16 2010-10-05 End Date/Time of Adverse Event
TOTOBS C16 40 TOTOBS
-- NUMERIC --
AESEQ N8 1 Sequence Number
AESTDY N8 Study Day of Start of Adverse Event
AEENDY N8 Study Day of End of Adverse Event
*/
%mend cln_525sdtmAe;
;;;;
run;quit;
/*
%inc "&gbl_root/oto/cln_525sdtmAe.sas";
%cln_525sdtmAe;
*/
/*___ ____ ___ _ _ _____
| ___| ___| / _ \ ___ __| | |_ _ __ ___ | ____|_ __
|___ \___ \| | | / __|/ _` | __| `_ ` _ \| _| \ \/ /
___) |__) | |_| \__ \ (_| | |_| | | | | | |___ > <
|____/____/ \___/|___/\__,_|\__|_| |_| |_|_____/_/\_\
*/
filename ft15f001 "&gbl_root/oto/cln_550sdtmEx.sas";
parmcards4;
%macro cln_550sdtmEx ;
%cln_140mkeMtyTbl(metadatafile=&gbl_root/xls/cln_sdtmMetadata.xlsx,dataset=EX);
**** DERIVE THE MAJORITY OF SDTM EX VARIABLES;
data ex;
set EMPTY_EX
cln.cln_rawdosing;
studyid = 'XYZ123';
domain = 'EX';
usubjid = left(uniqueid);
exdose = dailydose;
exdostot = dailydose;
exdosu = 'mg';
exdosfrm = 'TABLET, COATED';
exstdtc=put(startdt,yymmdd10.);
exendtc=put(enddt,yymmdd10.);
run;
proc sort
data=ex;
by usubjid;
run;
**** CREATE SDTM STUDYDAY VARIABLES AND INSERT EXTRT;
data ex;
merge ex(in=inex) cln.dm(keep=usubjid rfstdtc arm);
by usubjid;
if inex;
%cln_110mkesdtmdy(refdate=rfstdtc,date=exstdtc);
%cln_110mkesdtmdy(refdate=rfstdtc,date=exendtc);
**** in this simplistic case all subjects received the treatment they were randomized to;
extrt = arm;
run;
**** CREATE SEQ VARIABLE;
proc sort
data=ex;
by studyid usubjid extrt exstdtc;
run;
OPTIONS MISSING = ' ';
data ex;
retain STUDYID DOMAIN USUBJID EXSEQ EXTRT EXDOSE EXDOSU EXDOSFRM EXDOSTOT
EXSTDTC EXENDTC EXSTDY EXENDY;
set ex(drop=exseq);
by studyid usubjid extrt exstdtc;
if not (first.exstdtc and last.exstdtc) then
put "WARN" "ING: key variables do not define an unique record. " usubjid=;
retain exseq;
if first.usubjid then
exseq = 1;
else
exseq = exseq + 1;
label exseq = "Sequence Number";
run;
**** SORT EX ACCORDING TO METADATA AND SAVE PERMANENT DATASET;
%cln_120mkesrtodr(metadatafile=&gbl_root/xls/cln_sdtmMetadata.xlsx,dataset=EX);
proc sort
data=ex(keep = &EXKEEPSTRING)
out=cln.ex;
by &EXSORTSTRING;
run;
libname xpt xport "&gbl_root/xpt/cln_sdtmsEx.xpt";
data xpt.Ex;
set cln.Ex;
run;quit;
libname xpt clear;
/*
Middle Observation(42 ) of cln.ex - Total Obs 84
-- CHARACTER --
STUDYID C15 XYZ123 Study Identifier
DOMAIN C2 EX Domain Abbreviation
USUBJID C25 UNI505 Unique Subject Identifier
EXTRT C40 Name of Actual Treatment
EXDOSU C40 mg Dose Units
EXDOSFRM C40 TABLET, COATED Dose Form
EXSTDTC C16 2010-03-13 Start Date/Time of Treatment
EXENDTC C16 2010-06-15 End Date/Time of Treatment
-- NUMERIC --
EXSEQ N8 1 Sequence Number
EXDOSE N8 2 Dose per Administration
EXDOSTOT N8 2 Total Daily Dose
EXSTDY N8 Study Day of Start of Treatment
EXENDY N8 Study Day of End of Treatment
*/
%mend cln_550sdtmEx;
;;;;
run;quit;
/*
%inc "&gbl_root/oto/cln_550sdtmEx.sas";
%cln_550sdtmEx;
*/
/*___ _____ ____ _ _ _ _
| ___|___ | ___| ___ __| | |_ _ __ ___ | | | |__
|___ \ / /|___ \/ __|/ _` | __| `_ ` _ \| | | `_ \
___) |/ / ___) \__ \ (_| | |_| | | | | | |___| |_) |
|____//_/ |____/|___/\__,_|\__|_| |_| |_|_____|_.__/
*/
filename ft15f001 "&gbl_root/oto/cln_575sdtmLb.sas";
parmcards4;
%macro cln_575sdtmLb ;
%cln_140mkeMtyTbl(metadatafile=&gbl_root/xls/cln_sdtmMetadata.xlsx,dataset=LB);
proc format;
value visit_labs_month
0=baseline
1=3 months
2=6 months;
run;
data lb;
set EMPTY_LB
cln.cln_rawlabs;
studyid = 'XYZ123';
domain = 'LB';
usubjid = left(uniqueid);
lborres = left(put(nresult,best.));
lborresu = left(colunits);
lbornrlo = left(put(lownorm,best.));
lbornrhi = left(put(highnorm,best.));
lbcat = labcat;
lbtest = labtest;
lbtestcd = labtest;
**** create standardized results;
lbstresc = lborres;
lbstresn = nresult;
lbstresu = lborresu;
lbstnrlo = lownorm;
lbstnrhi = highnorm;
if lbstnrlo ne . and lbstresn ne . and
round(lbstresn,.0000001) < round(lbstnrlo,.0000001) then
lbnrind = 'LOW';
else if lbstnrhi ne . and lbstresn ne . and
round(lbstresn,.0000001) > round(lbstnrhi,.0000001) then
lbnrind = 'HIGH';
else if lbstnrhi ne . and lbstresn ne . then
lbnrind = 'NORMAL';
visitnum = month;
visit = put(month,visit_labs_month.);
if visit = 'baseline' then
lbblfl = 'Y';
else
lbblfl = ' ';
lbdtc = put(labdate,yymmdd10.);
run;
proc sort
data=lb;
by usubjid;
run;
**** CREATE SDTM STUDYDAY VARIABLES;
data lb;
merge lb(in=inlb) cln.dm(keep=usubjid rfstdtc);
by usubjid;
if inlb;
%cln_110mkesdtmdy(refdate=rfstdtc,date=lbdtc)
run;
**** CREATE SEQ VARIABLE;
proc sort
data=lb;
by studyid usubjid lbtestcd visitnum;
run;
data lb;
retain STUDYID DOMAIN USUBJID LBSEQ LBTESTCD LBTEST LBCAT LBORRES LBORRESU LBORNRLO LBORNRHI
LBSTRESC LBSTRESN LBSTRESU LBSTNRLO LBSTNRHI LBNRIND LBBLFL VISITNUM VISIT LBDTC LBDY;
set lb(drop=lbseq);
by studyid usubjid lbtestcd visitnum;
if not (first.visitnum and last.visitnum) then
put "WARN" "ING: key variables do not define an unique record. " usubjid=;
retain lbseq;
if first.usubjid then
lbseq = 1;
else
lbseq = lbseq + 1;
label lbseq = "Sequence Number";
run;
**** SORT LB ACCORDING TO METADATA AND SAVE PERMANENT DATASET;
%cln_120mkesrtodr(metadatafile=&gbl_root/xls/cln_sdtmMetadata.xlsx,dataset=LB);
proc sort
data=lb(keep = &LBKEEPSTRING)
out=cln.lb;
by &LBSORTSTRING;
run;
libname xpt xport "&gbl_root/xpt/cln_sdtmLb.xpt";
data xpt.Lb;
set cln.Lb;
run;quit;
libname xpt clear;
%mend cln_575sdtmLb;
;;;;
run;quit;
/*
%inc "&gbl_root/oto/cln_575sdtmLb.sas";
%cln_575sdtmLb;
*/
/*__ ___ ___ _ _ __ __
/ /_ / _ \ / _ \ ___ __| | |_ _ __ ___ \ \/ /_ __
| `_ \| | | | | | / __|/ _` | __| `_ ` _ \ \ /| `_ \
| (_) | |_| | |_| \__ \ (_| | |_| | | | | |/ \| |_) |
\___/ \___/ \___/|___/\__,_|\__|_| |_| |_/_/\_\ .__/
|_|
*/
filename ft15f001 "&gbl_root/oto/cln_600sdtmXp.sas";
parmcards4;
%macro cln_600sdtmXp ;
*---------------------------------------------------------------*;
* XP.sas creates the SDTM XP dataset and saves it
* as a permanent SAS datasets to the sdtm libref.
*---------------------------------------------------------------*;
%cln_140mkeMtyTbl(metadatafile=&gbl_root/xls/cln_sdtmMetadata.xlsx,dataset=XP);
proc format;
value pain
0='None'
1='Mild'
2='Moderate'
3='Severe';
value visit_labs_month
0='Baseline visit'
1='Month 3 visit'
2='Month 6 visit';
run;
**** DERIVE THE MAJORITY OF SDTM XP VARIABLES;
data xp;
set empty_xp cln.cln_rawpain;
studyid = 'XYZ123';
domain = 'XP';
usubjid = left(uniqueid);
xptest = 'Pain Score';
xptestcd = 'XPPAIN';
**** transpose pain data;
array dates {3} randomizedt month3dt month6dt;
array scores {3} painbase pain3mo pain6mo;
do i = 1 to 3;
visitnum = i - 1;
visit = put(visitnum,visit_labs_month.);
if scores{i} ne . then
do;
xporres = left(put(scores{i},pain.));
xpstresc = xporres;
xpstresn = scores{i};
xpdtc = put(dates{i},yymmdd10.);
output;
end;
end;
*drop randomizedt month3dt month6dt painbase pain3mo pain6mo i;
run;
proc sort
data=xp;
by usubjid;
run;
**** CREATE SDTM STUDYDAY VARIABLES;
data xp;
merge xp(in=inxp) cln.dm(keep=usubjid rfstdtc);
by usubjid;
if inxp;
%cln_110mkesdtmdy(refdate=rfstdtc,date=xpdtc);
run;
**** CREATE SEQ VARIABLE;
proc sort
data=xp;
by studyid usubjid xptestcd visitnum;
run;
data xp;
retain STUDYID DOMAIN USUBJID XPSEQ XPTESTCD XPTEST XPORRES VISITNUM VISIT XPDTC XPDY;
set xp(drop=xpseq);
by studyid usubjid xptestcd visitnum;
if not (first.visitnum and last.visitnum) then
put "WARN" "ING: key variables do not define an unique record. " usubjid=;
retain xpseq;
if first.usubjid then
xpseq = 1;
else
xpseq = xpseq + 1;
label xpseq = "Sequence Number";
run;
**** SORT XP ACCORDING TO METADATA AND SAVE PERMANENT DATASET;
%cln_120mkesrtodr(metadatafile=&gbl_root/xls/cln_sdtmMetadata.xlsx,dataset=XP);
proc sort
data=xp(keep = &XPKEEPSTRING)
out=cln.xp;
by &XPSORTSTRING;
run;
libname xpt xport "&gbl_root/xpt/cln_sdtmsXp.xpt";
data xpt.Xp;
set cln.Xp;
run;quit;
libname xpt clear;
/*
Middle Observation(88 ) of cln.xp - Total Obs 177
-- CHARACTER --
STUDYID C15 XYZ123 Study Identifier
DOMAIN C2 XP Domain Abbreviation
USUBJID C25 UNI507 Unique Subject Identifier
XPTESTCD C8 XPPAIN Pain Test Short Name
XPTEST C40 Pain Score Pain Test Name
XPORRES C200 Severe Result or Finding in Original Units
VISIT C200 baseline Visit Name
XPDTC C16 2010-04-06 Date/Time of Collection
XPSTRESC C200 Severe Result or Finding in Standard Format
TOTOBS C16 177 TOTOBS
-- NUMERIC --
XPSEQ N8 1 Sequence Number
VISITNUM N8 0 Visit Number
XPDY N8 1 Study Day of Collection
XPSTRESN N8 3 Numeric Result/Finding in Standard Units
*/
%mend cln_600sdtmXp;
;;;;
run;quit;
/*
%inc "&gbl_root/oto/cln_600sdtmXp.sas";
%cln_600sdtmXp;
*/
/*
FINAL STATE OF DIRECTORIES
- added files
Directory of &gbl_root/cln
cln_fmt.sas7bcat * formats
cln_rawadverse.sas7bdat * raw data
cln_rawdemographic.sas7bdat
cln_rawdosing.sas7bdat
cln_rawlabs.sas7bdat
cln_rawpain.sas7bdat
ae.sas7bdat *sdtms;
dm.sas7bdat
ex.sas7bdat
lb.sas7bdat
suppdm.sas7bdat
xp.sas7bdat
<DIR> b64
cln_adamMetadata.b64 *base 64 of excel mata data for adam datasets;
cln_sdtmMetadata.b64 *base 64 of excel mata data for sdtm datasets;
cln_rawadverse.b64 * base 64 encoded raw sas datasets;
cln_rawdemographic.b64
cln_rawdosing.b64
cln_rawlabs.b64
cln_rawpain.b64
<DIR> log
<DIR> oto
cln_010.sas * many macro tools;
cln_010.sas * SAS Tools
cln_100makedefine.sas * CDISC utilities ( extract meta data from excel tabs;
cln_110mkesdtmdy.sas
cln_120mkesrtodr.sas
cln_130cfb.sas
cln_140mkeMtyTbl.sas
cln_150domainx.sas
cln_160dtc2dt.sas
cln_170mrgsup.sas
- cln_500sdtmDm.sas * create sdtm datasets DM;
- cln_525sdtmAe.sas * AE
- cln_550sdtmEx.sas * EX
- cln_575sdtmLb.sas * LB
- cln_600sdtmXp.sas * XP
<DIR> pdf
<DIR> pin
<DIR> png
<DIR> rtf
<DIR> sas
<DIR> xls
cln_adamMetadata.xlsx * excel mata data for adam datasets;
cln_sdtmMetadata.xlsx * excel mata data for sdtm datasets;
<DIR> xml
cln_adamDefine.xml * concatenation of all odm sections below
cln_adamdefine_header.xml * excel odm section created from excel tab header
cln_adamanalysisresults.xml ..
cln_adamcompmethod.xml
cln_adamitemdef.xml
cln_adamitemdef_value.xml
cln_adamitemgroupdef.xml
cln_adamleaves.xml
cln_adamvaluelist.xml
cln_sdtmcompmethod.xml
cln_sdtmDefine.xml * concatenation of all stdm sections below
cln_sdtmdefine_header.xml * excel odm section created from excel tab header
cln_sdtmitemdef.xml ..
cln_sdtmitemdef_value.xml
cln_sdtmitemgroupdef.xml
cln_sdtmvaluelist.xml
<DIR> xpt
- cln_sdtmDm.xpt
- cln_sdtmAe.xpt
- cln_sdtmsEx.xpt
- cln_sdtmsuppdm.xpt
- cln_sdtmsXp.xpt
*/
/* _ ____ __ __
/ \ | _ \ __ _| \/ |
/ _ \ | | | |/ _` | |\/| |
/ ___ \| |_| | (_| | | | |
/_/ \_\____/ \__,_|_| |_|
__ _ ____ _ _ _ _
/ /_ / | ___| __ _ __| | __ _ _ __ ___ / \ __| |___| |
| `_ \| |___ \ / _` |/ _` |/ _` | `_ ` _ \ / _ \ / _` / __| |
| (_) | |___) | (_| | (_| | (_| | | | | | |/ ___ \ (_| \__ \ |
\___/|_|____/ \__,_|\__,_|\__,_|_| |_| |_/_/ \_\__,_|___/_|
*/
filename ft15f001 "&GBL_ROOT/OTO/CLN_615ADAMADSl.SAS";
parmcards4;
%macro cln_615adamAdsl ;
*------------------------------------------------------------*;
* ADSL.sas creates the ADaM ADSL data set
* as permanent SAS datasets to the ADaM libref.
*------------------------------------------------------------*;
**** CREATE EMPTY ADSL DATASET CALLED EMPTY_ADSL;
%cln_140mkeMtyTbl(metadatafile=&gbl_root/xls/cln_adamMetadata.xlsx,dataset=ADSL);
%cln_170mrgsup(sourcelib=cln, domains=DM);
** find the change from baseline so that responders can be flagged ;
** (2-point improvement in pain at 6 months);
%cln_130cfb(indata=cln.xp, outdata=responders, dayvar=xpdy, avalvar= xpstresn,
keepvars=usubjid visitnum chg);
data ADSL;
merge EMPTY_ADSL
cln.DM (in = inDM)
responders (in = inresp where=(visitnum=2))
;
by usubjid;
* convert RFSTDTC to a numeric SAS date named TRTSDT;
%cln_160dtc2dt (RFSTDTC, prefix=TRTS );
* create BRTHDT, RANDDT, TRTEDT;
%cln_160dtc2dt (BRTHDTC, prefix=BRTH);
%cln_160dtc2dt (RANDDTC, prefix=RAND);
%cln_160dtc2dt (RFENDTC, prefix=TRTE);
* created flags for ITT and safety-evaluable;
ittfl = put(randdt, popfl.);
saffl = put(trtsdt, popfl.);
trt01p = ARM;
trt01a = trt01p;
trt01pn = input(put(trt01p, $trt01pn.), best.);
trt01an = trt01pn;
agegr1n = input(put(age, agegr1n.), best.);
agegr1 = put(agegr1n, agegr1_.);
RESPFL = put((.z <= chg <= -2), _0n1y.);
run;
**** SORT ADSL ACCORDING TO METADATA AND SAVE PERMANENT DATASET;
%cln_120mkesrtodr(metadatafile=&gbl_root/xls/cln_adamMetadata.xlsx, dataset=ADSL);
proc sort
data=adsl
(keep = &ADSLKEEPSTRING)
out=cln.adsl;
by &ADSLSORTSTRING;
run;
libname xpt xport "&gbl_root/xpt/cln_adamadsl.xpt";
data xpt.adsl;
set cln.adsl;
run;quit;
libname xpt clear;
/*
Middle Observation(30 ) of cln.adsl - Total Obs 60
-- CHARACTER --
STUDYID C15 XYZ123 Study Identifier
USUBJID C25 UNI506 Unique Subject Identifier
SUBJID C7 506 Subject Identifier for the Study
SITEID C7 500 Study Site Identifier
AGEU C5 YEARS Age Units
AGEGR1 C40 <55 YEARS Pooled Age Group 1
SEX C1 W Sex
RACE C40 White Race
RACEOTH C40 Race, Other, Specify
ARM C40 Placebo Description of Planned Arm
TRT01P C40 Placebo Planned Treatment for Period 01
TRT01A C40 Placebo Actual Treatment for Period 01
COUNTRY C3 USA Country
ITTFL C1 N Intent-To-Treat Population Flag
SAFFL C1 Y Safety Population Flag
RESPFL C1 N Efficacy Responder Flag
TOTOBS C16 60 TOTOBS
-- NUMERIC --
RANDDT N8 Date of Randomization
TRTSDT N8 18282 Date of First Exposure to Treatment
TRTEDT N8 18463 Date of Last Exposure to Treatment
BRTHDT N8 1664 Date of Birth
AGE N8 45 Age
AGEGR1N N8 1 Pooled Age Group 1 (N)
TRT01PN N8 0 Planned Treatment for Period 01 (N)
TRT01AN N8 0 Actual Treatment for Period 01 (N)
*/
%mend cln_615adamAdsl;
;;;;
run;quit;
/*
%inc "&gbl_root/oto/cln_615adamAdsl.sas";
%cln_615adamAdsl;
*/
/*
_ ____ ____ _ _ _____
/ /_|___ \| ___| __ _ __| | __ _ _ __ ___ / \ | ____|
| `_ \ __) |___ \ / _` |/ _` |/ _` | `_ ` _ \ / _ \ | _|
| (_) / __/ ___) | (_| | (_| | (_| | | | | | |/ ___ \| |___
\___/_____|____/ \__,_|\__,_|\__,_|_| |_| |_/_/ \_\_____|
*/
filename ft15f001 "&gbl_root/oto/cln_625adamAdae.sas";
parmcards4;
%macro cln_625adamAdae ;
*---------------------------------------------------------------*;
* ADAE.sas creates the ADaM ADAE-structured data set
* for AE data (ADAE), saved to the ADaM libref.
*---------------------------------------------------------------*;
**** CREATE EMPTY ADAE DATASET CALLED EMPTY_ADAE;
%cln_140mkeMtyTbl(metadatafile=&gbl_root/xls/cln_adamMetadata.xlsx,dataset=ADAE);
%put &=adaekeepstring;
proc sort
data = cln.adsl
(keep = usubjid siteid country age agegr1 agegr1n sex race trtsdt trt01a trt01an saffl)
out = adsl;
by usubjid;
run;quit;
data adae;
/*merge sdtm.ae (in = inae) adsl (in = inadsl); */
merge cln.ae (in = inae) cln.adsl (in = inadsl);
by usubjid ;
if inae and not inadsl then
put 'PROB' 'LEM: Subject missing from ADSL?-- ' usubjid= inae= inadsl= ;
rename trt01a = trta
trt01an = trtan
;
if inadsl and inae;
%cln_160dtc2dt(aestdtc, prefix=ast, refdt=trtsdt);
%cln_160dtc2dt(aeendtc, prefix=aen, refdt=trtsdt);
if index(AEDECOD, 'PAIN')>0 or AEDECOD='HEADACHE' then
CQ01NAM = 'PAIN EVENT';
else
CQ01NAM = ' ';
aereln = input(put(upcase(aerel), $aereln.), best.);
aesevn = input(put(upcase(aesev), $aesevn.), best.);
relgr1n = (aereln); ** group related events (AERELN>0);
relgr1 = put(relgr1n, relgr1n.);
if astdt>=trtsdt then
trtemfl = 'Y';
format astdt aendt yymmdd10.;
run;quit;
** ASSIGN VARIABLE ORDER AND LABELS;
data adae;
retain &adaeKEEPSTRING;
set EMPTY_adae adae;
run;
**** SORT adae ACCORDING TO METADATA AND SAVE PERMANENT DATASET;
%cln_120mkesrtodr(metadatafile=&gbl_root/xls/cln_adamMetadata.xlsx, dataset=ADAE);
proc sort
data=adae(keep = &adaeKEEPSTRING)
out=cln.adae;
by &adaeSORTSTRING;
run;
libname xpt xport "&gbl_root/xpt/cln_adamadae.xpt";
data xpt.adae;
set cln.adae;
run;quit;
libname xpt clear;
/*
Middle Observation(20 ) of cln.adae - Total Obs 40
-- CHARACTER --
STUDYID C15 XYZ123 Study Identifier
USUBJID C25 UNI305 Unique Subject Identifier
SITEID C7 300 Study Site Identifier
COUNTRY C3 USA Country
AGEGR1 C20 <55 YEARS Pooled Age Group 1
SEX C1 W Sex
TRTA C40 Active Actual Treatment
AETERM C200 POUNDING HEART Reported Term for the Adverse Event
AEDECOD C200 PALPITATIONS Dictionary-Derived Term
AEBODSYS C200 CARDIAC DISORDER Body System or Organ Class
SAFFL C1 Y Safety Population Flag
AESEV C40 severe Severity/Intensity
AESER C40 N Serious Event
AEACN C40 no dose change Action Taken with Study Treatment
AEREL C40 not Causality
CQ01NAM C200 CQ 01 Name
RELGR1 C10 NOT RELATE Pooled Causality Group 1
TRTEMFL C1 Y Treatment Emergent Flag
TOTOBS C16 40 TOTOBS
-- NUMERIC --
AESEQ N8 1 Sequence Number
AGE N8 44 Unique Subject Identifier
AGEGR1N N8 1 Pooled Age Group 1 (N)
TRTAN N8 Actual Treatment (N)
ASTDT N8 18540 Start Date/Time of Adverse Events
AENDT N8 18540 End Date/Time of Adverse Events
ASTDY N8 118 Study Day of Start of Adverse Event
AESEVN N8 3 Severity/Intensity (N)
AENDY N8 118 Study Day of End of Adverse Event
AERELN N8 0 Causality (N)
RELGR1N N8 0 Pooled Causality Group 1 (N)
*/
%mend cln_625adamAdAe;
;;;;
run;quit;
/*
%inc "&gbl_root/oto/cln_625adamAdae.sas";
%cln_625adamAdAe;
*/
/*__ ____ ___ _ _ _ __
/ /_| ___| / _ \ __ _ __| | __ _ _ __ ___ / \ __| | ___ / _|
| `_ \___ \| | | |/ _` |/ _` |/ _` | `_ ` _ \ / _ \ / _` |/ _ \ |_
| (_) |__) | |_| | (_| | (_| | (_| | | | | | |/ ___ \ (_| | __/ _|
\___/____/ \___/ \__,_|\__,_|\__,_|_| |_| |_/_/ \_\__,_|\___|_|
*/
filename ft15f001 "&gbl_root/oto//cln_650adamAdef.sas";
parmcards4;
%macro cln_650adamAdef ;
*---------------------------------------------------------------*;
* ADEF.sas creates the ADaM BDS-structured data set
* for efficacy data (ADEF), saved to the ADaM libref.
*---------------------------------------------------------------*;
**** CREATE EMPTY ADEF DATASET CALLED EMPTY_ADEF;
%cln_140mkeMtyTbl(metadatafile=&gbl_root/xls/cln_adamMetadata.xlsx,dataset=ADEF);
%cln_130cfb(indata=cln.xp, outdata=adef, dayvar=xpdy, avalvar= xpstresn);
proc sort
data = cln.adsl
(keep = usubjid siteid country age agegr1 agegr1n sex race randdt trt01p trt01pn ittfl)
out = adsl;
by usubjid;
run;quit;
data adef;
merge adef (in = inadef) adsl (in = inadsl);
by usubjid ;
if not(inadsl and inadef) then
put 'PROB' 'LEM: Missing subject?-- ' usubjid= inadef= inadsl= ;
rename trt01p = trtp
trt01pn = trtpn
xptest = param
xptestcd = paramcd
visit = avisit
xporres = avalc
;
if inadsl and inadef;
avisitn = input(put(visitnum, avisitn.), best.);
%cln_160dtc2dt(xpdtc, refdt=randdt);
retain crit1 "Pain improvement from baseline of at least 2 points";
RESPFL = put((.z <= chg <= -2), _0n1y.);
if RESPFL='Y' then
crit1fl = 'Y';
else
crit1fl = 'N';
run;
** assign variable order and labels;
data adef;
retain &ADEFKEEPSTRING;
set EMPTY_ADEF adef;
run;
**** SORT ADEF ACCORDING TO METADATA AND SAVE PERMANENT DATASET;
%cln_120mkesrtodr(metadatafile=&gbl_root/xls/cln_adamMetadata.xlsx, dataset=ADEF);
%put &=ADEFKEEPSTRING;
%put &=ADEFSORTSTRING;
/*
proc sort
data=adef(keep = &ADEFKEEPSTRING)
out=cln.adef;
by &ADEFSORTSTRING; * not in meta data?;
run;
*/
data cln.adef;
set adef(keep = &ADEFKEEPSTRING);
run;quit;
libname xpt xport "&gbl_root/xpt/cln_adamadef.xpt";
data xpt.adef;
set cln.adef;
run;quit;
libname xpt clear;
/*
Middle Observation(88 ) of cln.adef - Total Obs 177
-- CHARACTER --
STUDYID C15 XYZ123 Study Identifier
USUBJID C25 UNI507 Unique Subject Identifier
AGEGR1 C20 <55 YEARS Pooled Age Group 1
SEX C1 W Sex
SITEID C7 500 Study Site Identifier
TRTP C40 Active Planned Treatment
PARAMCD C8 XPPAIN Parameter Code
PARAM C40 Pain Score Parameter
COUNTRY C3 USA Country
AVISIT C16 baseline Analysis Visit
ABLFL C1 Y Baseline Record Flag
AVALC C12 Severe Analysis Value (C)
CRIT1FL C1 N Criterion 1 Evaluation Result Flag
CRIT1 C60 Pain improvement Analysis Criterion 1
ITTFL C1 N Intent-to-Treat Flag
TOTOBS C16 177 TOTOBS
-- NUMERIC --
AGE N8 33 Age
AGEGR1N N8 1 Pooled Age Group 1 (N)
RANDDT N8 Date of Randomization
TRTPN N8 Planned Treatment (N)
AVISITN N8 0 Analysis Visit (N)
XPSEQ N8 1 Sequence Number
VISITNUM N8 0 Visit Number
ADT N8 18358 Analysis Date
ADY N8 Analysis Relative Day
AVAL N8 3 Analysis Value
BASE N8 3 Baseline Value
CHG N8 0 Change from Baseline
*/
%mend cln_650adamAdef;
;;;;
run;quit;
/*
%inc "&gbl_root/oto//cln_650adamAdef.sas";
%cln_650adamAdef;
*/
/*__ _____ ____ _ _ _ _____ _
/ /|___ | ___| __ _ __| | __ _ _ __ ___ / \ __| |_ _| |_ ___
| `_ \ / /|___ \ / _` |/ _` |/ _` | `_ ` _ \ / _ \ / _` | | | | __/ _ \
| (_) / / ___) | (_| | (_| | (_| | | | | | |/ ___ \ (_| | | | | || __/
\___/_/ |____/ \__,_|\__,_|\__,_|_| |_| |_/_/ \_\__,_| |_| \__\___|
*/
filename ft15f001 "&gbl_root/oto/cln_675adamAdTte.sas";
parmcards4;
%macro cln_675adamAdTte ;
*---------------------------------------------------------------*;
* ADTTE.sas creates the ADaM BDS-structured data set
* for a time-to-event analysis (ADTTE), saved to the ADaM libref.
*---------------------------------------------------------------*;
**** CREATE EMPTY ADTTE DATASET CALLED EMPTY_ADTTE;
%cln_140mkeMtyTbl(metadatafile=&gbl_root/xls/cln_adamMetadata.xlsx,dataset=ADTTE);
%put &=adttekeepstring;
proc sort
data = cln.adsl
(keep = studyid usubjid siteid country age agegr1 agegr1n sex race randdt trt01p trt01pn
ittfl trtedt)
out = adtte;
by usubjid;
run;quit;
proc sort
data = cln.adef
(keep = usubjid paramcd chg adt visitnum xpseq)
out = adef;
where paramcd='XPPAIN' and visitnum>0 and (chg<0 or chg>0);
by usubjid adt;
run;quit;
data adef;
set adef;
by usubjid adt;
drop paramcd visitnum;
if first.usubjid;
run;
proc sort
data = cln.adae
(keep = usubjid cq01nam astdt trtemfl aeseq)
out = adae;
where cq01nam ne '' and trtemfl='Y';
by usubjid astdt;
run;
** keep only the first occurence of a pain event;
data adae;
set adae;
by usubjid astdt;
if first.usubjid;
run;
** get the sequence number for the last EX record;
proc sort
data = cln.ex
(keep = usubjid exseq)
out = lstex
nodupkey;
by usubjid exseq;
run;quit;
data lstex;
set lstex;
by usubjid exseq;
if last.usubjid;
run;quit;
data adtte;
merge adtte (in = inadtte rename=(randdt=startdt))
adef (in = inadef)
adae (in = inadae)
lstex (in = inlstex)
;
by usubjid ;
retain param "TIME TO FIRST PAIN RELIEF" paramcd "TTPNRELF";
rename trt01p = trtp
trt01pn = trtpn
;
length srcvar $10. srcdom $4.;
if (.<chg<0) and (adt<astdt or not inadae) then
do;
cnsr = 0;
adt = adt;
evntdesc = put(cnsr, evntdesc.) ;
srcdom = 'ADEF';
srcvar = 'XPDY';
srcseq = xpseq;
end;
else if chg>0 and (adt<astdt or not inadae) then
do;
cnsr = 1;
adt = adt;
evntdesc = put(cnsr, evntdesc.) ;
srcdom = 'XP';
srcvar = 'XPDY';
srcseq = xpseq;
end;
else if (.<astdt<adt) then
do;
cnsr = 2;
adt = astdt;
evntdesc = put(cnsr, evntdesc.) ;
srcdom = 'ADAE';
srcvar = 'ASTDY';
srcseq = aeseq;
end;
else
do;
cnsr = 3;
adt = trtedt;
evntdesc = put(cnsr, evntdesc.) ;
srcdom = 'ADSL';
srcvar = 'TRTEDT';
srcseq = .;
end;
aval = adt - startdt + 1;
format startdt adt yymmdd10.;
run;
** assign variable order and labels;
data adtte;
retain &adtteKEEPSTRING;
set EMPTY_adtte adtte;
run;
**** SORT adtte ACCORDING TO METADATA AND SAVE PERMANENT DATASET;
%cln_120mkesrtodr(metadatafile=&gbl_root/xls/cln_adamMetadata.xlsx, dataset=ADTTE);
%put &=adttekeepstring;
proc sort
data=adtte(keep = &adtteKEEPSTRING )
out=cln.adtte;
by &adtteSORTSTRING;
run;
libname xpt xport "&gbl_root/xpt/cln_adamadtte.xpt";
data xpt.adtte;
set cln.adtte;
run;quit;
libname xpt clear;
/*
Middle Observation(30 ) of cln.adtte - Total Obs 60
-- CHARACTER --
STUDYID C15 XYZ123 Study Identifier
USUBJID C25 UNI506 Domain Abbreviation
AGEGR1 C20 <55 YEARS Pooled Age Group 1
SEX C1 W Sex
SITEID C7 500 Study Site Identifier
TRTP C40 Placebo Planned Treatment
PARAMCD C8 TTPNRELF Parameter Code
PARAM C40 TIME TO FIRST PA Parameter
COUNTRY C3 USA Country
EVNTDESC C40 COMPLETED STUDY Event or Censoring Description
SRCDOM C6 ADSL Source Domain
SRCVAR C8 TRTEDT Source Variable
ITTFL C1 N Intent-to-Treat Flag
TOTOBS C16 60 TOTOBS
-- NUMERIC --
AGE N8 45 Unique Subject Identifier
AGEGR1N N8 1 Pooled Age Group 1 (N)
TRTPN N8 0 Planned Treatment (N)
ADT N8 18463 Analysis Date
AVAL N8 Analysis Value
STARTDT N8 Time to Event Origin Date for Subject
CNSR N8 3 Censor
SRCSEQ N8 Source Sequence Number
*/
%mend cln_675adamAdTte;
;;;;
run;quit;
/*
%inc "&gbl_root/oto/cln_675adamAdTte.sas";
%cln_675adamAdTte;
*/
/*
FINAL STATE OF DIRECTORIES
- added files
Directory of &gbl_root/cln
cln_fmt.sas7bcat * formats
cln_rawadverse.sas7bdat * raw data
cln_rawdemographic.sas7bdat
cln_rawdosing.sas7bdat
cln_rawlabs.sas7bdat
cln_rawpain.sas7bdat
adae.sas7bdat * adams;
adef.sas7bdat
adsl.sas7bdat
adtte.sas7bdat
ae.sas7bdat *sdtms;
dm.sas7bdat
ex.sas7bdat
lb.sas7bdat
suppdm.sas7bdat
xp.sas7bdat
<DIR> b64
cln_adamMetadata.b64 *base 64 of excel mata data for adam datasets;
cln_sdtmMetadata.b64 *base 64 of excel mata data for sdtm datasets;
cln_rawadverse.b64 * base 64 encoded raw sas datasets;
cln_rawdemographic.b64
cln_rawdosing.b64
cln_rawlabs.b64
cln_rawpain.b64
<DIR> log
<DIR> oto
cln_010.sas * many macro tools;
cln_010.sas * SAS Tools
cln_100makedefine.sas * CDISC utilities ( extract meta data from excel tabs;
cln_110mkesdtmdy.sas
cln_120mkesrtodr.sas
cln_130cfb.sas
cln_140mkeMtyTbl.sas
cln_150domainx.sas
cln_160dtc2dt.sas
cln_170mrgsup.sas
cln_500sdtmDm.sas * create sdtm datasets DM;
cln_525sdtmAe.sas * AE
cln_550sdtmEx.sas * EX
cln_575sdtmLb.sas * LB
cln_600sdtmXp.sas * XP
- cln_615adamAdsl.sas * create adam datasets ADSL
- cln_625adamAdae.sas * ADSL
- cln_650adamAdef.sas * ADAE
- cln_675adamAdTte.sas * ADEF
<DIR> pdf
<DIR> pin
<DIR> png
<DIR> rtf
<DIR> sas
<DIR> xls
cln_adamMetadata.xlsx * excel mata data for adam datasets;
cln_sdtmMetadata.xlsx * excel mata data for sdtm datasets;
<DIR> xml
cln_adamDefine.xml * concatenation of all odm sections below
cln_adamdefine_header.xml * excel odm section created from excel tab header
cln_adamanalysisresults.xml ..
cln_adamcompmethod.xml
cln_adamitemdef.xml
cln_adamitemdef_value.xml
cln_adamitemgroupdef.xml
cln_adamleaves.xml
cln_adamvaluelist.xml
cln_sdtmcompmethod.xml
cln_sdtmDefine.xml * concatenation of all stdm sections below
cln_sdtmdefine_header.xml * excel odm section created from excel tab header
cln_sdtmitemdef.xml ..
cln_sdtmitemdef_value.xml
cln_sdtmitemgroupdef.xml
cln_sdtmvaluelist.xml
<DIR> xpt
- cln_adamadtte.xpt
- cln_adamadae.xpt
- cln_adamadef.xpt
- cln_adamadsl.xpt
cln_sdtmAe.xpt
cln_sdtmdm.xpt
cln_sdtmsEx.xpt
cln_sdtmsuppdm.xpt
cln_sdtmsXp.xpt
*/
/* _ _
__| |_ __(_)_ _____ _ __
/ _` | `__| \ \ / / _ \ `__|
| (_| | | | |\ V / __/ |
\__,_|_| |_| \_/ \___|_|
*/
%utlopts;
* just in case you change a macro and forget to overwrite the one in sasmacr;
%inc "&gbl_root/oto/cln_010.sas" / nosource;;
%inc "&gbl_root/oto/cln_100makedefine.sas" / nosource;
%inc "&gbl_root/oto/cln_110mkesdtmdy.sas" / nosource;
%inc "&gbl_root/oto/cln_120mkesrtodr.sas" / nosource;
%inc "&gbl_root/oto/cln_130cfb.sas" / nosource;
%inc "&gbl_root/oto/cln_140mkeMtyTbl.sas" / nosource;
%inc "&gbl_root/oto/cln_150domainx.sas" / nosource;
%inc "&gbl_root/oto/cln_160dtc2dt.sas" / nosource;
%inc "&gbl_root/oto/cln_170mrgsup.sas" / nosource;
%inc "&gbl_root/oto/cln_500sdtmDm.sas" / nosource;
%inc "&gbl_root/oto/cln_525sdtmAe.sas" / nosource;
%inc "&gbl_root/oto/cln_550sdtmEx.sas" / nosource;
%inc "&gbl_root/oto/cln_575sdtmLb.sas" / nosource;
%inc "&gbl_root/oto/cln_600sdtmXp.sas" / nosource;
%inc "&gbl_root/oto/cln_615adamAdsl.sas" / nosource;
%inc "&gbl_root/oto/cln_625adamAdae.sas" / nosource;
%inc "&gbl_root/oto/cln_650adamAdef.sas" / nosource;
%inc "&gbl_root/oto/cln_675adamAdTte.sas"/ nosource;
%cln_500sdtmDm ;
%cln_525sdtmAe;
%cln_550sdtmEx ;
%cln_575sdtmLb ;
%cln_600sdtmXp ;
%cln_615adamAdsl ;
%cln_625adamAdae ;
%cln_650adamAdef ;
%cln_675adamAdTte ;
/*____ _ _ ____
| ____| \ | | _ \
| _| | \| | | | |
| |___| |\ | |_| |
|_____|_| \_|____/
*/