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Partial solve to issue #13
This commit is contained in:
Paul W. Egeler, MS, GStat
pegeler
parent
7eb7d5b459
commit
a2dcdc73a9
@ -2,7 +2,7 @@
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*
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* FILE: REDCap_split.sas
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*
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* VERSION: 0.0.0
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* VERSION: 0.1.0
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*
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* PURPOSE: Take a REDCap dataset with multiple events and make into several
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* tables with primary and foreign keys
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@ -50,10 +50,27 @@
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%MACRO REDCAP_SPLIT(
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DATA_SET = REDCAP /* The name of the SAS dataset created by REDCap */,
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DATA_DICTIONARY = REDCAP_DATA_DICTIONARY /* The name of the SAS dataset of the data dictionary */
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DATA_DICTIONARY = REDCAP_DATA_DICTIONARY /* The name of the SAS dataset of the data dictionary */,
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NUMERIC_SUBTABLES = N /* Y/N: Should the subtables be numbered (Y) or should the be based on the name of the repeating instrument (N)? */
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);
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/* Find the key that links the base table to child tables */
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/* Also check that REDCAP_REPEAT_INSTRUMENT is present in the data */
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%LET DSID = %SYSFUNC(OPEN(&DATA_SET));
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%LET KEY = %SYSFUNC(VARNAME(&DSID, 1));
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%LET CHECK = %SYSFUNC(VARNUM(&DSID, REDCAP_REPEAT_INSTRUMENT));
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%LET RC = %SYSFUNC(CLOSE(&DSID));
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%IF &CHECK EQ 0 %THEN %DO;
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%PUT ERROR: The dataset &DATA_SET does not contain repeating instruments.;
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%PUT ERROR: Stopping MACRO.;
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%GOTO FINISH;
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%END;
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/* Remove formatting from repeat instrument field */
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%PUT NOTE: Removing formatting from REDCAP_REPEAT_INSTRUMENT in &DATA_SET..;
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DATA &DATA_SET.;
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SET &DATA_SET.;
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FORMAT REDCAP_REPEAT_INSTRUMENT;
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@ -73,120 +90,140 @@
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%LET N_SUBTABLES = &SQLOBS;
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%PUT INSTRUMENTS: %LEFT(&INSTRUMENTS);
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%PUT INSTRUMENT LIST: %LEFT(&INSTRUMENT_LIST);
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%PUT N SUBTABLES: %LEFT(&N_SUBTABLES);
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QUIT;
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%IF &N_SUBTABLES GT 0 %THEN %DO;
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/* Get information on the variables in the dataset */
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PROC CONTENTS
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DATA = &DATA_SET.
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OUT = REDCAP_VARNAMES(KEEP=NAME VARNUM)
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NOPRINT;
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RUN;
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%IF &N_SUBTABLES EQ 0 %THEN %DO;
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/* Find the key that links the base table to child tables */
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DATA _NULL_;
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SET REDCAP_VARNAMES;
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IF VARNUM EQ 1 THEN DO;
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CALL SYMPUT("KEY", NAME);
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STOP;
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END;
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RUN;
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/* Make a list of fields and their associated forms based on data dictionary */
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DATA REDCAP_FIELDS(KEEP=VAR_NAME FORM_NAME);
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SET &DATA_DICTIONARY.;
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IF FIELD_TYPE EQ "checkbox" THEN DO;
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BASENAME = VAR_NAME;
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DO I = 1 TO N;
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SET REDCAP_VARNAMES POINT=I NOBS=N;
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IF PRXMATCH("/^"!!trim(BASENAME)!!"___.+$/", NAME) THEN DO;
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VAR_NAME = NAME;
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OUTPUT;
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END;
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END;
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END;
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ELSE OUTPUT;
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RUN;
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%PUT WARNING: There were no records containing repeating instruments in the dataset %LEFT(&DATA_SET).;
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%PUT WARNING: No action was taken.;
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%GOTO FINISH;
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/* Add instrument status fields to list of fields */
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PROC SQL;
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%END;
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%PUT N SUBTABLES: %LEFT(&N_SUBTABLES);
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%PUT INSTRUMENTS: %LEFT(&INSTRUMENTS);
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%PUT INSTRUMENT LIST: %LEFT(%BQUOTE(&INSTRUMENT_LIST));
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/* Get information on the variables in the dataset */
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PROC CONTENTS
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DATA = &DATA_SET.
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OUT = REDCAP_VARNAMES(KEEP=NAME VARNUM)
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NOPRINT;
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RUN;
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/* Make a list of fields and their associated forms based on data dictionary */
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DATA REDCAP_FIELDS(KEEP=VAR_NAME FORM_NAME);
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SET &DATA_DICTIONARY.;
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IF FIELD_TYPE EQ "checkbox" THEN DO;
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BASENAME = VAR_NAME;
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DO I = 1 TO N;
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SET REDCAP_VARNAMES POINT=I NOBS=N;
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IF PRXMATCH("/^"!!trim(BASENAME)!!"___.+$/", NAME) THEN DO;
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VAR_NAME = NAME;
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OUTPUT;
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END;
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END;
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END;
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ELSE OUTPUT;
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RUN;
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/* Add instrument status fields to list of fields */
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PROC SQL;
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CREATE TABLE REDCAP_INSTRUMENT_STATUS_FIELDS AS
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SELECT DISTINCT TRIM(FORM_NAME)!!"_complete" AS VAR_NAME LENGTH=200, FORM_NAME
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FROM REDCAP_DATA_DICTIONARY;
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SELECT DISTINCT TRIM(FORM_NAME)!!"_complete" AS VAR_NAME LENGTH=200, FORM_NAME
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FROM &DATA_DICTIONARY.;
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QUIT;
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QUIT;
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PROC APPEND
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BASE=REDCAP_FIELDS
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DATA=REDCAP_INSTRUMENT_STATUS_FIELDS;
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RUN;
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/* Sort out the field names */
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PROC SQL NOPRINT;
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PROC APPEND
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BASE=REDCAP_FIELDS
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DATA=REDCAP_INSTRUMENT_STATUS_FIELDS;
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RUN;
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SELECT VAR_NAME
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INTO :VARS_BASE SEPARATED BY ' '
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FROM REDCAP_FIELDS AS A
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WHERE FORM_NAME NOT IN (&INSTRUMENT_LIST);
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DATA REDCAP_FIELDS;
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SET REDCAP_FIELDS;
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%put Base vars: &VARS_BASE;
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%DO I = 1 %TO &N_SUBTABLES;
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IF LENGTH(VAR_NAME) GT 32 THEN DO;
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PUT "WARNING: The variable " VAR_NAME "is too long (MAX 32 CHARACTERS).";
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PUT "WARNING: " VAR_NAME "will not be included in the output dataset.";
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DELETE;
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END;
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%LET INSTRUMENT_I = %SCAN(&INSTRUMENTS,&I,%STR( ));
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SELECT VAR_NAME
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INTO :VARS_&INSTRUMENT_I. SEPARATED BY ' '
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FROM REDCAP_FIELDS AS A
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WHERE FORM_NAME EQ "&INSTRUMENT_I.";
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RUN;
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%put &INSTRUMENT_I. vars: &&VARS_&INSTRUMENT_I;
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%END;
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/* Sort out the field names */
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PROC SQL NOPRINT;
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SELECT VAR_NAME
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INTO :VARS_BASE SEPARATED BY ' '
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FROM REDCAP_FIELDS AS A
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WHERE FORM_NAME NOT IN (&INSTRUMENT_LIST);
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QUIT;
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%put Base vars: &VARS_BASE;
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/* Make new data sets based on field names above */
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DATA &DATA_SET._BASE (KEEP = &VARS_BASE);
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SET &DATA_SET;
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IF MISSING(REDCAP_REPEAT_INSTRUMENT);
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RUN;
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%DO I = 1 %TO &N_SUBTABLES;
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%LET INSTRUMENT_I = %SCAN(&INSTRUMENTS,&I,%STR( ));
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DATA &DATA_SET._&INSTRUMENT_I. (KEEP = &KEY redcap_repeat_instance &&VARS_&INSTRUMENT_I);
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SET &DATA_SET;
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IF REDCAP_REPEAT_INSTRUMENT EQ "&INSTRUMENT_I.";
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RUN;
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SELECT VAR_NAME
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INTO :VARS_&I. SEPARATED BY ' '
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FROM REDCAP_FIELDS AS A
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WHERE FORM_NAME EQ "&INSTRUMENT_I.";
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%PUT &INSTRUMENT_I. vars: &&VARS_&I;
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%END;
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QUIT;
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/* Make new data sets based on field names above */
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DATA &DATA_SET._BASE (KEEP = &VARS_BASE);
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SET &DATA_SET;
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IF MISSING(REDCAP_REPEAT_INSTRUMENT);
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RUN;
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%DO I = 1 %TO &N_SUBTABLES;
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%LET INSTRUMENT_I = %SCAN(&INSTRUMENTS,&I,%STR( ));
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/* Create either numeric table name or name based on repeating instrument name (see issue #12) */
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%IF &NUMERIC_SUBTABLES EQ N %THEN %DO;
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%LET SUBTABLE_NAME = &DATA_SET._&INSTRUMENT_I.;
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%IF %LENGTH(&SUBTABLE_NAME) GT 32 %THEN %DO;
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%PUT ERROR: The table name &SUBTABLE_NAME is %LENGTH(&SUBTABLE_NAME) characters long (MAX 32 CHARACTERS).;
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%PUT ERROR: &SUBTABLE_NAME will be skipped. Consider setting NUMERIC_SUBTABLES = Y.;
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%GOTO SKIP;
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%END;
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%END;
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%ELSE %DO;
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%LET SUBTABLE_NAME = &DATA_SET._&I.;
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%END;
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DATA &SUBTABLE_NAME (KEEP = &KEY redcap_repeat_instance &&VARS_&I);
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SET &DATA_SET;
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IF REDCAP_REPEAT_INSTRUMENT EQ "&INSTRUMENT_I.";
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RUN;
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%PUT NOTE: Records from instrument &INSTRUMENT_I have been placed in &SUBTABLE_NAME;
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%SKIP:
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%END;
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/* Clean up temporary datasets */
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PROC DATASETS MEMTYPE=DATA LIBRARY=WORK NOLIST;
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DELETE REDCAP_FIELDS REDCAP_VARNAMES REDCAP_INSTRUMENT_STATUS_FIELDS;
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RUN;
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%END;
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%ELSE %DO;
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%PUT THERE WERE NO REPEAT INSTRUMENTS IN THE DATASET %LEFT(&DATA_SET);
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%PUT NO ACTION WAS TAKEN;
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%END;
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%FINISH:
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%MEND REDCAP_SPLIT;
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