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Improving SAS code.
This commit is contained in:
Egeler, Paul W
parent
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59
README.md
59
README.md
@ -22,32 +22,49 @@ possible fields; this has the effect of nesting the output table in a
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way that is not useful in most analysis software. Therefore, I have made
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a solution to handle the problem in both SAS and R.
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## Supported Platforms
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- R
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- SAS
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### Coming Soon
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- Python
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- VBA
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## Instructions
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### SAS
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1. Run the macro definition in the source editor or using `%include`.
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2. Run the SAS code provided by REDCap to import the data BUT COMMENT
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THIS LINE:
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```format redcap_repeat_instrument redcap_repeat_instrument_.;```
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3. Open the data dictionary in MS Excel. We will need to do some pre-
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processing to the data dictionary file before reading it in because
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some of the user entry points (such as **Field Label**) allows for newline
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characters, which can break our data ingestion. MS Excel will read in
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the newline characters correctly.
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- Copy the first four columns and paste into a new sheet.
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- Save the new sheet as a .csv file.
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- Close the file.
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4. Call the macro, adjusting parameters as needed.
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### R
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The function definition file contains an example to assist you.
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The function definition file contains [roxygen2](https://cran.r-project.org/package=roxygen2) comments to assist you.
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1. Run the function definition in the source editor or using `source()`.
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2. Download the record dataset and metadata and import them. This can
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1. Download the record dataset and metadata. This can
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be accomplished either by traditional methods or using the API. The
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`read.csv()` function should be able to handle newline characters within
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records, so no pre-processing of metadata csv is needed.
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3. Call the function, pointing it to your record dataset and metadata
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`data.frame`s.
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1. Call the function, pointing it to your record dataset and metadata
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`data.frame`s.
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### SAS
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1. Download the data, SAS code to load the data, and the data dictionary from REDCap
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1. Run the SAS code provided by REDCap to import the data BUT COMMENT
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THIS LINE:
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```format redcap_repeat_instrument redcap_repeat_instrument_.;```
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1. Run the RECapRITS macro definitions in the source editor or using `%include`.
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1. Run the macro call `%REDCAP_READ_DATA_DICT()` to load the data dictionry into your SAS session, pointing to the file location of your REDCap data dictionary.
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1. Run the macro call `%REDCAP_SPLIT()`. You will have an output dataset for
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your main table as well as for each repeating instrument.
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## Issues
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Suggestions and contributions are more than welcome! Please feel free to create an issue or pull request.
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## About REDCap
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This code was written for [REDCap electronic data capture tools](https://projectredcap.org/).^1^ Code for this project was tested on the REDCap instance hosted at Spectrum Health, Grand Rapids, MI. REDCap (Research Electronic Data Capture) is a secure, web-based application designed to support data capture for research studies, providing 1) an intuitive interface for validated data entry; 2) audit trails for tracking data manipulation and export procedures; 3) automated export procedures for seamless data downloads to common statistical packages; and 4) procedures for importing data from external sources.
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## References
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^1^Paul A. Harris, Robert Taylor, Robert Thielke, Jonathon Payne, Nathaniel Gonzalez, Jose G. Conde, Research electronic data capture (REDCap) – A metadata-driven methodology and workflow process for providing translational research informatics support, J Biomed Inform. 2009 Apr;42(2):377-81.
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171
REDCap_split.sas
171
REDCap_split.sas
@ -20,112 +20,117 @@
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*
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* format redcap_repeat_instrument redcap_repeat_instrument_.;
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*
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* 2. Open the data dictionary in MS Excel.
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*
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* 2a. Copy the first four columns and paste into a new sheet.
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*
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* 2b. Save the new sheet as a .csv file.
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*
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* 2c. Close the file.
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*
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* 3. Change the data dictionary name and file path in the macro call.
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*
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* 4. Run the macro definition and the macro call
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* 2. Download the data dictionary for your project.
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* 3. Run the macro definitions REDCAP_READ_DATA_DICT and REDCAP_SPLIT
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*
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* 3. Run the macro call for REDCAP_READ_DATA_DICT to load in the data dictionry.
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* This is necessary to split the tables correctly.
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*
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* 4. Run the macro call for REDCAP_SPLIT. You will have an output dataset for
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* your main table as well as for each repeating instrument.
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*
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********************************************************************************/
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%MACRO REDCAP_READ_DATA_DICT(
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DATA_DICTIONARY /* The file path for the data dictionary */
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);
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DATA REDCAP_DATA_DICTIONARY;
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LENGTH VAR_NAME $ 200 FORM_NAME $ 200 SECTION_HEADER $ 200 FIELD_TYPE $ 200 X1-X14 $ 2250;
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INFILE "&DATA_DICTIONARY" FIRSTOBS = 2 DSD DLM = "," LRECL=32767;
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INPUT VAR_NAME $ FORM_NAME $ SECTION_HEADER $ FIELD_TYPE $ X1-X14 $;
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IF FIELD_TYPE EQ "descriptive" THEN DELETE;
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DROP SECTION_HEADER X1-X14;
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RUN;
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%MEND REDCAP_READ_DATA_DICT;
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%MACRO REDCAP_SPLIT(
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DATA_DICTIONARY /* The file path for the data dictionary */,
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DATA_SET = REDCAP/* The name of the SAS dataset created by REDCap */,
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KEY = RECORD_ID /* Variable that links base table with other tables */
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DATA_DICTIONARY = REDCAP_DATA_DICTIONARY /* The name of the SAS dataset of the data dictionary */,
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DATA_SET = REDCAP/* The name of the SAS dataset created by REDCap */,
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KEY = RECORD_ID /* Variable that links base table with other tables */
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);
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PROC SQL NOPRINT;
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PROC SQL NOPRINT;
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SELECT DISTINCT
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REDCAP_REPEAT_INSTRUMENT,
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"'"!!trim(REDCAP_REPEAT_INSTRUMENT)!!"'" AS INSTRUMENT_QUOTED
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INTO
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:INSTRUMENTS SEPARATED BY ' ',
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:INSTRUMENT_LIST SEPARATED BY ','
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FROM &DATA_SET AS A
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WHERE REDCAP_REPEAT_INSTRUMENT GT '';
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%LET N_SUBTABLES = &SQLOBS;
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SELECT DISTINCT
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REDCAP_REPEAT_INSTRUMENT,
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"'"!!trim(REDCAP_REPEAT_INSTRUMENT)!!"'" AS INSTRUMENT_QUOTED
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INTO
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:INSTRUMENTS SEPARATED BY ' ',
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:INSTRUMENT_LIST SEPARATED BY ','
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FROM &DATA_SET AS A
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WHERE REDCAP_REPEAT_INSTRUMENT GT '';
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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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%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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QUIT;
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%IF &N_SUBTABLES GT 0 %THEN %DO;
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DATA DATA_DICTIONARY;
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LENGTH VAR_NAME $ 255 FORM_NAME $ 255 SECTION_HEADER $ 255 FIELD_TYPE $ 255;
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INFILE "&DATA_DICTIONARY" FIRSTOBS = 2 DSD DLM = ",";
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INPUT VAR_NAME $ FORM_NAME $ SECTION_HEADER $ FIELD_TYPE $;
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%IF &N_SUBTABLES GT 0 %THEN %DO;
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PROC SQL NOPRINT;
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IF FIELD_TYPE EQ "descriptive" THEN DELETE;
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RUN;
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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 &DATA_DICTIONARY. AS A
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WHERE FORM_NAME NOT IN (&INSTRUMENT_LIST);
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SELECT VAR_NAME
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INTO :VARS_BASE SEPARATED BY ' '
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FROM DATA_DICTIONARY AS A
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WHERE FORM_NAME NOT IN (&INSTRUMENT_LIST);
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%put Base vars: &VARS_BASE;
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%DO I = 1 %TO &N_SUBTABLES;
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%put Base vars: &VARS_BASE;
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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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SELECT VAR_NAME
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INTO :VARS_&INSTRUMENT_I. SEPARATED BY ' '
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FROM &DATA_DICTIONARY. AS A
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WHERE FORM_NAME EQ "&INSTRUMENT_I.";
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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 DATA_DICTIONARY AS A
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WHERE FORM_NAME EQ "&INSTRUMENT_I.";
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%put &INSTRUMENT_I. vars: &&VARS_&INSTRUMENT_I;
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%END;
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%put &INSTRUMENT_I. vars: &&VARS_&INSTRUMENT_I;
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%END;
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QUIT;
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QUIT;
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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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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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%END;
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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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%END;
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%END;
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%END;
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%ELSE %DO;
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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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%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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%END;
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%MEND REDCAP_SPLIT;
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