Clinical Trials – Make SDTM DM and EX datasets

SAS programs for making SDTM DM and EX datasets

Yupeng Wang, Ph.D., Data Scientist

Raw data

1. Metadata

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Clinical Trials – Make SDTM DM and EX datasets

2. DM raw data

3. Dosing raw data

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Clinical Trials – Make SDTM DM and EX datasets

Programs

Program 1: make_empty_dataset.sas

/*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 make_empty_dataset(metadatafile=,dataset=);

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;

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Clinical Trials – Make SDTM DM and EX datasets

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 make_empty_dataset;

Program 2: dm.sas

/*Process the raw demographic data from a CSV file*/

%include '/folders/myfolders/test1/common.sas';
%common;

filename infl '/folders/myfolders/test1/dm.csv';

proc format;
value trt
1 = "Active"
0 = "Placebo";
value gender
1 = "M"
2 = "F"
3 = "U";
value race
1 = "White"
2 = "Black"
3 = "Other";
run;

data source.demographic;
infile infl dlm='2C0D'x dsd missover;
length dob1 $10
randdt1 $10;
input subject trt gender race orace $ dob1 $ randdt1 $;
dob=input(dob1,mmddyy10.);
randdt=input(randdt1,mmddyy10.);
format dob randdt mmddyy10.;
uniqueid = 'UNI' || put(subject,3.);
gender1=put(gender,gender.);

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Clinical Trials – Make SDTM DM and EX datasets

race1=put(race,race.);
trt1=put(trt,trt.);
label subject = "Subject Number"
trt = "Treatment"
gender = "Gender"
race = "Race"
orace = "Oher Race Specify"
dob = "Date of Birth"
uniqueid = "Company Wide Subject ID"
randdt = "Randomization Date";
drop dob1 randdt1 gender race;
rename gender1=gender race1=race;
run;

Program 3: ds.sas

/*Process the raw dose data from an Excel file.

Key points: 1) make up missing dates; 2) convert Excel dates to SAS dates*/

%include '/folders/myfolders/test1/common.sas';
%common;

libname ds xlsx "/folders/myfolders/test1/ds.xlsx";

data source.dosing;
set ds.Sheet1;
if find(startdt,'/') then
do;
array var1(3) $4.;
do i=1 to 3;
var1(i)=scan(startdt,i,"/");
if var1(i)=' ' then
var1(i)='1';
end;
startdt1=mdy(input(var1(1),$4.), input(var1(2),$4.) , input(var1(3),$4.));
end;
else
startdt1=input(startdt,$10.)-21916;
if find(enddt,'/') then
do;
array var2(3) $4.;
do i=1 to 3;
var2(i)=scan(enddt,i,"/");
if var2(i)=' ' then
var2(i)='1';
end;
enddt1=mdy(input(var2(1),$4.), input(var2(2),$4.) , input(var2(3),$4.));
end;
else
enddt1=input(enddt,$10.)-21916;
uniqueid = 'UNI' || put(subject,3.);
format startdt1 enddt1 mmddyy10.;
drop i startdt enddt var11-var13 var21-var23;
rename startdt1=startdt enddt1=enddt;
run;

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Program 4: make_sort_order.sas

/* 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 make_sort_order(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 make_sort_order;

Program 5: STDM_DM.sas

/* STDM_DM.sas creates the SDTM DM and SUPPDM datasets and saves them as permanent SAS datasets to the target
libref */

%include '/folders/myfolders/test1/common.sas';
%common;

**** CREATE EMPTY DM DATASET CALLED EMPTY_DM;

%include '/folders/myfolders/test1/make_empty_dataset.sas';
%make_empty_dataset(metadatafile=/folders/myfolders/test1/SDTM_METADATA.xlsx,dataset=DM);

**** GET FIRST AND LAST DOSE DATE FOR RFSTDTC AND RFENDTC;
proc sort
data=source.dosing(keep=subject startdt enddt)
out=dosing;
by subject startdt;
run;

**** FIRSTDOSE=FIRST DOSING AND LASTDOSE=LAST DOSING;

data dosing;
set dosing;
by subject;

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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;

**** GET DEMOGRAPHICS DATA;

proc sort
data=source.demographic
out=demographic;
by subject;
run;

data demog_dose;
merge demographic
dosing;
by subject;
run;

**** 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;

%include '/folders/myfolders/test1/make_sort_order.sas';
%make_sort_order(metadatafile=/folders/myfolders/test1/SDTM_METADATA.xlsx,dataset=DM);

proc sort
data=dm(keep = &DMKEEPSTRING)

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out=target.dm;
by &DMSORTSTRING;
run;

**** CREATE EMPTY SUPPDM DATASET CALLED EMPTY_DM;

%make_empty_dataset(metadatafile=/folders/myfolders/test1/SDTM_METADATA.xlsx,dataset=SUPPDM);

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;

%make_sort_order(metadatafile=/folders/myfolders/test1/SDTM_METADATA.xlsx,dataset=SUPPDM);

proc sort
data=suppdm
out=target.suppdm;
by &SUPPDMSORTSTRING;
run;

Program 6: STDM_EX.sas
/* STDM_EX.sas creates the SDTM EX dataset and saves it as a permanent SAS dataset to the target libref */

%include '/folders/myfolders/test1/common.sas';
%common;

**** CREATE EMPTY DM DATASET CALLED EMPTY_DM;

%include '/folders/myfolders/test1/make_empty_dataset.sas';

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%make_empty_dataset(metadatafile=/folders/myfolders/test1/SDTM_METADATA.xlsx,datase
t=EX);
%include '/folders/myfolders/test1/make_sdtm_dy2.sas';
%include '/folders/myfolders/test1/make_sort_order.sas';

**** DERIVE THE MAJORITY OF SDTM EX VARIABLES;

data ex;
set EMPTY_EX
source.dosing;

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) target.dm(keep=usubjid rfstdtc arm);
by usubjid;

if inex;

%make_sdtm_dy(refdate=rfstdtc,date=exstdtc);
%make_sdtm_dy(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=;

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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;

%make_sort_order(metadatafile=/folders/myfolders/test1/SDTM_METADATA.xlsx,dataset=E
X);

proc sort
data=ex(keep = &EXKEEPSTRING)
out=target.ex;
by &EXSORTSTRING;
run;

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