This macro computes the numerators for each cohort and calls many other macros. More...

Detailed Description

This macro computes the numerators for each cohort and calls many other macros.

01: Set up variables needed for the run.
02: Import input files in SAS format.
03: Jump to checkpoint if restarting QRP.
04: Initialize macro variables and process input file parameters.
05: Process ranges "-" and wilcards "*" in lookup codes.
06: Extract raw data and run envelope or create combo records (if applicable).
07: Reconcile all enrollment spans.
08: Create worktemp.meds partition.
09: Process pregnancy outcomes.
10: Loop through Group(s).
- 10.a: Loop pre-processing.
- 10.b: Extract loop-specific records.
- 10.c: Shave enrollment spans.
- 10.d: Create claims dataset based on age or calendar date.
- 10.e: Apply StockPiling.
- 10.f: Create raw POVs datasets.
- 10.g: POV1: Find all potential index dates.
- 10.h: POV2: identify all type 4 MOI index dates that are free of POV2 records in washper. For all other types, this is assesed with POV3.
- 10.i: POV3: identify all index dates meeting inclusion Exclusion.
- 10.j: POV4: Create at-risk episodes.
- 10.k: Create final record wrt index date.
- 10.l: Finalize episode list.
- 10.m: Calculate additional metrics.
  - Denominators, never exposed cohort, MOI stats, PSA/covariate stratification, multiple events, concomitant use, overlap, tree extraction.

Program inputs

infolder.&COHORTCODES. (Dataset with codes used to define exposures and outcomes of interest.)
infolder.&COHORTFILE. (Dataset used to define enrollment and demographic requirements, type of cohort identification strategy.)
infolder.&COMBOFILE. (Datasets that specifies how combination items should be created.)
infolder.&CONCFILE. (Dataset to specify GROUP values from a Type 2 analysis and perform additional analyses.)
infolder.&COVARIATECODES. (Dataset for request of covariates presence and analytic adjustment.)
infolder.&COVSTRATFILE. (Dataset describing parameters for a covariate stratification analyses.)
infolder.&DRUGCLASSFILE. (Dataset required for the use of drug utilization metrics.)
infolder.&ICD10ICD9MAP. (ICD-10-CM-ICD-9-CM Mapping lookup file for TreeScan analyses.)
infolder.&INCLUSIONCODES. (Dataset with codes used to define additional cohort inclusion/exclusion criteria.)
infolder.&IPTWFILE. (Dataset specifying the parameters for an IPTW analysis.)
infolder.&ITSFILE. (Dataset with ITS analysis specifications.)
infolder.&METADATAFILE. (Dataset that defines the metadata generated for each time period request for sequential analysis.)
infolder.&MFUFILE. (Dataset for most frequent utilization MFU assessment.)
infolder.&MICOHORTFILE. (Dataset for Type 4 analysis with pregnancy cohorts among pregnancies matched to an infant specification.)
infolder.&MONITORINGFILE. (Dataset with monitoring periods for descriptive, inferential and sequential analyses.)
infolder.&MULTEVENTFILE. (Dataset to specify COHORTGRP values from a Type 2 analysis and perform additional analyses.)
infolder.&MULTEVENTFILE_ADHERE. (Dataset to specify multiple criteria to determine overall adherence for a Type 2 multiple events analysis.)
infolder.&OVERLAPFILE. (Dataset characterizing an overlap of primary and secondary treatment episodes during the observation window.)
infolder.&OVERLAPFILE_ADHERE. (Dataset to specify multiple criteria to determine overall adherence for a concomitant use analysis.)
infolder.&PREGNANCYCODES. (Dataset for Type 4 cohort identification strategy.)
infolder.&PREGNANCYDURATION. (Dataset for Type 4 cohort identification strategy.)
infolder.&PREGNANCYMETA. (Dataset for Type 4 cohort identification strategy.)
infolder.&PSCSSUBGROUPFILE. (Dataset with all subgroups and subgroup levels for each analysis group.)
infolder.&PSESTIMATIONFILE. (Dataset with the parameters for estimating a PS model and is required for PS-based analyses.)
infolder.&PSMATCHFILE. (Dataset with parameters for a PS matching analysis.)
infolder.&RISKSCORECODES. (Dataset for risk score calculation if requested.)
infolder.&RISKSCOREFILE. (Dataset required for calculating one or more risk scores.)
infolder.&STOCKPILINGFILE. (Dataset with valid dispensings selection used by the stockpiling algorithm to create exposure episodes.)
infolder.&STRATIFICATIONFILE. (Dataset with parameters for a PS stratification analysis and required for PS-based analyses.)
infolder.&TREATMENTPATHWAYS. (Dataset with identification and computation of switch pattern episodes.)
infolder.&TREEFILE. (Dataset with parameters required to execute multiple SI analyses from a basic QRP execution.)
infolder.&TREELOOKUP. (Dataset with hierarchical tree of codes that are eligible to be HOI.)
infolder.&TYPE1FILE. (Dataset required for a background rate calculation cohort identification strategy.)
infolder.&TYPE2FILE. (Dataset required for an exposures and follow-up time cohort identification strategy.)
infolder.&TYPE3FILE. (Dataset required for a self-controlled risk interval design cohort identification strategy.)
infolder.&TYPE4FILE. (Dataset required for a pregnancy episodes identification strategy.)
infolder.&TYPE5FILE. (Dataset required for medical product utilization cohort identification strategy.)
infolder.&TYPE6FILE. (Dataset required for evaluating manufacture level product utilization and switching patterns.)
infolder.&USERSTRATA. (Dataset with ouput tables and stratifications specification.)
infolder.&UTILFILE. (Dataset with medical or drug utilization metrics specification.)
infolder.&ZIPFILE. (Lookup table required if a request requires stratification of results by geographic location.)

Program outputs

dplocal.&RUNID._adjusted (Dataset for covariate stratification and propensity score estimations, ps stratum weighting analysis, inverse probability of treatment weights (IPTW) analysis, and matching strategies and time period.)
dplocal.&RUNID._ads_mstr (Dataset containing one record per GROUP, PATID, and INDEXDT.)
dplocal.&RUNID._ads_mstr_concomitance (Dataset for Type 2 analyses with the add on tools for concomitant use event/outcome containing one record per ANALYSISGRP, PATID, and INDEXDT.)
dplocal.&RUNID._ads_mstr_mi (Dataset for Type 4 analyses creating cohorts for further processing with the PSA module and containing one record per PATID per GROUP.)
dplocal.&RUNID._ads_mstr_multevent (Dataset for Type 2 analyses with the add on tools for multiple events containing one record per ANALYSISGRP, PATID, and INDEXDT.)
dplocal.&RUNID._ads_mstr_nopreg (Dataset for Type 4 analyses containing one record per GROUP, PATID, and INDEXDT for the non-pregnant cohort.)
dplocal.&RUNID._ads_mstr_overlap (Dataset for Type 2 analyses with the add on tools for overlap containing one record per ANALYSISGRP, PATID, and INDEXDT.)
dplocal.&RUNID._ads_mstr_preg (Dataset for Type 4 analyses containing one record per GROUP, PATID, and INDEXDT for the pregnant cohort.)
dplocal.&RUNID._ads_t6_switchepisodes (Dataset for Type 6 analyses representing the patient-level baseline characteristics for the switching cohort at index date prior to any switching.)
dplocal.&RUNID._alldeliveries (Dataset with all deliveries contained in &RUNID._mstr, plus those that do not meet the enrollment eligibility criterion.)
dplocal.&RUNID._combo_diag (Dataset containing combination items that behave like DX.)
dplocal.&RUNID._combo_drug (Dataset containing combination items that behave like RX.)
dplocal.&RUNID._combo_proc (Dataset containing combination items that behave like PX.)
dplocal.&RUNID._concepi_mstr_nopreg_tri (Dataset produced when using a type 4 analysis for the non-pregnant cohort. It contains trimester statistics for each pregnancy outcome and medical product of interest. It contains one row per individual [patid] per MOI episode.)
dplocal.&RUNID._concepi_mstr_preg_tri (Dataset for Type 4 analysis for the pregnant cohort containing trimester statistics for each pregnancy outcome and medical product of interest.)
dplocal.&RUNID._cumulative_mstr_for_ps (Dataset produced for analysis types 2 and 4 when ANALYSIS=TREE. It contains the unmatched population across all looks. Only data from the current look is included in the other output files. It is used to re-compute the propensity score using patients from all looks.)
dplocal.&RUNID._dispensings (Dataset for Type 5 and Type 6 analyses containing one row per cohort, patient, and dispensing date and only contains valid claims that occur during valid enrollment spans and episodes.)
dplocal.&RUNID._mstr (Dataset for Type 1 and Type 2 analyses with one record per individual per index date for every GROUP.)
dplocal.&RUNID._mstr_concomitance (Dataset for Type 2 analyses when using the concomitant use tool containing one row per patient PATID per concomitant episode.)
dplocal.&RUNID._mstr_mi (Dataset for Type 4 analyses produced for exposed and comparator/unexposed pregnant cohorts.)
dplocal.&RUNID._mstr_multevent (Dataset for Type 2 analyses when using the multiple events functionality containing one row per patient PATID per primary episode.)
dplocal.&RUNID._mstr_nopreg (Dataset containing one record per individual per index date for the non-pregnant cohort (i.e., one row per pregnancy episode).)
dplocal.&RUNID._mstr_overlap (Dataset for Type 2 analyses when using the Overlap Tool containaining one row per patient PATID per primary episode.)
dplocal.&RUNID._mstr_preg (Dataset containing one record per individual per index date for the pregnant cohort (i.e., one row per pregnancy episode).)
dplocal.&RUNID._mstr_tree (Dataset produced for Type 2, 3, and 4 analyses when ANALYSIS=TREE. It contains 1 row per ascertained outcome.)
dplocal.&RUNID._scores (Dataset for every propensity score and covariate stratification and matching strategies and time period.)
dplocal.&RUNID._sec (Dataset generated for Type 4 requests. It contains each medical product of interest episode for both the pregnancy and comparator cohorts.)
dplocal.&RUNID._t6_switchepisodes (Dataset containing patient-switch pattern episode level information.)
freedir.&RUNID._deathtable (Dataset with subset of patient level death data.)
freedir.&RUNID._demtable (Dataset with subset of patient level demographic data.)
freedir.&RUNID._diatable (Dataset with subset of patient level diagnosis data.)
freedir.&RUNID._distable (Dataset with subset of patient level dispensing data.)
freedir.&RUNID._enctable (Dataset with subset of patient level encounter data.)
freedir.&RUNID._enrtable (Dataset with subset of patient level enrollment data.)
freedir.&RUNID._factable (Dataset with facility data.)
freedir.&RUNID._labtable (Dataset with subset of patient level lab result data.)
freedir.&RUNID._miltable (Dataset with subset of patient level mother-infant linkage data.)
freedir.&RUNID._pretable (Dataset with subset of patient level prescribing data.)
freedir.&RUNID._proctable (Dataset with subset of patient level procedure data.)
freedir.&RUNID._pvdtable (Dataset with provider data.)
freedir.&RUNID._signature_freezedata (Dataset produced when FREEZEDATA is specified containing metadata associated with the request.)
freedir.&RUNID._vittable (Dataset with subset of patient level vital signs data.)
msoc.&RUNID._runtimes (Dataset containing metrics on total run time, cohort creation run time, and run time for several program processes.)
msoc.&RUNID._signature (Dataset containing metadata associated with the request, including request identifiers, program identifiers, database version, run time metrics, and SAS environment information.)
msoc.&RUNID._t6_productsdates (Dataset for Type 6 analysis providing overview of the calendar dates that were computed and may have been used to compute various episode durations and switching metrics.)
work._ptslist (Dataset containing eligible patients.)
work._ptslist2 (Dataset containing eligible patients for type 4.)
work.gi&ITGROUP. (Dataset with valid index date.)
work.medspartition (Dataset containing patid and partition.)
work.signature (Dataset containing metadata associated with the request, including request identifiers, program identifiers, database version, run time metrics, and SAS environment information.)
worktemp.codextract (Dataset with cause of death data.)

Usage

%ms_cidanum(RUNID=&RUNID.,
            PROJID=&PROJID.,  
            WPTYPE=&WPTYPE.,
            WPID=&WPID.,
            DPID=&DPID.,
            VERID=&VERID.,
            PERIODIDSTART=&PERIODIDSTART.,
            PERIODIDEND=&PERIODIDEND.,
            ANALYSIS=&ANALYSIS.,
            MONITORINGFILE=&MONITORINGFILE.,
            USERSTRATA=&USERSTRATA.,
            COMBOFILE=&COMBOFILE.,
            COHORTFILE=&COHORTFILE.,
            COHORTCODES=&COHORTCODES.,
            INCLUSIONCODES=&INCLUSIONCODES.,
            STOCKPILINGFILE=&STOCKPILINGFILE.,
            RUN_ENVELOPE=&RUN_ENVELOPE.,
            FREEZEDATA=&FREEZEDATA.,
            ZIPFILE=&ZIPFILE.,
            LABCODESMAP=&LABCODESMAP.,
            DISTINDEX=&DISTINDEX.,
            TYPE1FILE=&TYPE1FILE.,
            TYPE2FILE=&TYPE2FILE.,
            TYPE3FILE=&TYPE3FILE.,
            TYPE4FILE=&TYPE4FILE.,
            PREGNANCYMETA=&PREGNANCYMETA.,
            PREGNANCYCODES=&PREGNANCYCODES.,
            PREGNANCYDURATION=&PREGNANCYDURATION.,
            TYPE5FILE=&TYPE5FILE.,
            TYPE6FILE=&TYPE6FILE.,
            METADATAFILE=&METADATAFILE.,
            SURVEILLANCEMODE=&SURVEILLANCEMODE.,
            COVARIATECODES=&COVARIATECODES.,
            UTILFILE=&UTILFILE.,                                          
            RISKSCOREFILE=&RISKSCOREFILE.,
            RISKSCORECODES=&RISKSCORECODES.,
            DRUGCLASSFILE=&DRUGCLASSFILE.,
            PROFILE=&PROFILE.,
            MFUFILE=&MFUFILE.,
            MULTEVENTFILE=&MULTEVENTFILE.,
            MULTEVENTFILE_ADHERE=&MULTEVENTFILE_ADHERE.,
            CONCFILE=&CONCFILE.,
            OVERLAPFILE=&OVERLAPFILE.,
            OVERLAPFILE_ADHERE=&OVERLAPFILE_ADHERE.,
            ITSFILE=&ITSFILE.,
            TREATMENTPATHWAYS=&TREATMENTPATHWAYS.,
            MICOHORTFILE=&MICOHORTFILE.,
            TREEFILE=&TREEFILE.,
            TREELOOKUP=&TREELOOKUP.,
            ICD10ICD9MAP=&ICD10ICD9MAP.,
            HDVARSEL_INPUT=&RUNID._claims_ICDDX09 &RUNID._claims_ICDDX10 &RUNID._claims_DRUGCLASS &RUNID._claims_CPT &RUNID._claims_ICDPX09 &RUNID._claims_ICDPX10 &RUNID._claims_HCPCS,                    
            PSESTIMATIONFILE=&PSESTIMATIONFILE.,
            PSMATCHFILE=&PSMATCHFILE.,
            STRATIFICATIONFILE=&STRATIFICATIONFILE.,
            COVSTRATFILE=&COVSTRATFILE.,
            IPTWFILE=&IPTWFILE.,
            PSCSSUBGROUPFILE=&PSCSSUBGROUPFILE.,
            INDLEVEL=&INDLEVEL.,
            DIAGNOSTICS=&DIAGNOSTICS.
            );

Parameters

[in]	RUNID	Run identifier to denote each execution of the program.
[in]	PROJID	SOC-defined value.
[in]	WPTYPE	SOC-defined value.
[in]	WPID	SOC-defined value.
[in]	DPID	SOC-defined value.
[in]	VERID	SOC-defined value.
[in]	PERIODIDSTART	Starting PERIODID from the MONITORINGFILE.
[in]	PERIODIDEND	Ending PERIODID from the MONITORINGFILE.
[in]	ANALYSIS	Indicates whether to perform tree extraction.
[in]	MONITORNGFILE	Name of the SAS dataset that defines the relevant query periods for execution.
[in]	USERSTRATA	Name of the SAS dataset that defines the stratifications to return in the MSOC folder.
[in]	COMBOFILE	Name of the SAS dataset that will be used to create combination items. When this parameter is specified, "CODES" input files is required, and "STOCK" is optional.
[in]	COHORTFILE	Name of the SAS dataset that defines how the cohort should be created (gaps, coverage,...).
[in]	COHORTCODES	Name of the SAS dataset that includes the codes defining the cohort.
[in]	INCLUSIONCODES	Name of the SAS dataset that includes the codes defining inclusions/exclusions.
[in]	STOCKPILINGFILE	Name of the SAS dataset that defines how the stockpiling algorithm should be performed.
[in]	RUN_ENVELOPE	Indicates if the envelope macro should include Adate or be turned off entirely.
[in]	FREEZEDATA	Indicates if SDD patient data should be copied to DPLocal.
[in]	ZIPFILE	Name of the SAS dataset that contains list of valid zip to geographical area mappings.
[in]	LABCODESMAP	Name of the SAS dataset that contains laboratory matching information.
[in]	DISTINDEX	Indicates if distribution of index defining codes should be output to MSOC folder.
[in]	TYPE1FILE	Name of the SAS dataset that defines type 1 cohort parameters (washouts, cohortdef, ...).
[in]	TYPE2FILE	Name of the SAS dataset that defines type 2 cohort parameters (washouts, cohortdef, ...).
[in]	TYPE3FILE	Name of the SAS dataset that defines type 3 cohort parameters (washouts, cohortdef, ...).
[in]	TYPE4FILE	Name of the SAS dataset that defines type 4 cohort parameters (washouts, cohortdef, ...).
[in]	PREGNANCYMETA	Name of the SAS dataset that contains metadata on each pregnancy outcome for type 4 analyis.
[in]	PREGNANCYCODES	Name of the SAS dataset that includes the codes for pregnancy outcomes.
[in]	PREGNANCYDURATION	Name of the SAS dataset that includes the codes for length of pregnancy duration to outcome.
[in]	TYPE5FILE	Name of the SAS dataset that defines type 5 cohort parameters (washouts, cohortdef, ...).
[in]	TYPE6FILE	Name of the SAS dataset that defines type 6 cohort parameters (washouts, cohortdef, ...).
[in]	METADATAFILE	Name of the SAS dataset that defines the metadata generated for each time period request for sequential analysis.
[in]	SURVEILLANCEMODE	Indicates if the module should be executed in suveilance mode and which type.
[in]	COVARIATECODES	Name of the SAS dataset that includes the codes associated with covariate exctraction.
[in]	UTILFILE	Name of the SAS dataset that defines how medical and drug utilization metrics should be calculated.
[in]	RISKSCOREFILE	Name of the SAS dataset that defines how the requested risk scores should be calculated.
[in]	RISKSCORECODES	Name of the SAS dataset that includes the codes required to compute the requested risk scores.
[in]	DRUGCLASSFILE	Name of the SAS dataset that lists NDCs by generic and class names and allows the program to count the number of distinct generic names and class names.
[in]	PROFILE	Indicates if a covariate profile file should be produced.
[in]	MFUFILE	Name of the SAS dataset that defines how MFU analysis should be performed.
[in]	MULTEVENTFILE	Name of the SAS dataset that defines how a multiple events analysis should be performed.
[in]	MULTEVENTFILE_ADHERE	Name of the SAS dataset that defines how adherence is calculated for a multiple events analysis.
[in]	CONCFILE	Name of the SAS dataset that defines how concomitant episodes should be created and evaluated.
[in]	OVERLAPFILE	Name of the SAS dataset that defines how secondary episode overlap of primary episodes should be evaluated.
[in]	OVERLAPFILE_ADHERE	Name of the SAS dataset that defines how adherence is calculated for a overlapping episodes analysis.
[in]	ITSFILE	Name of the SAS dataset that defines parameters for an Interupted Time Series (ITS) analysis.
[in]	TREATMENTPATHWAYS	Name of the SAS dataset that defines how the switching module should be performed.
[in]	MICOHORTFILE	Name of the SAS dataset that defines how Type 4 PSA/Mother-Infant cohorts will be created.
[in]	TREEFILE	Name of the SAS dataset that defines parameters for tree extraction.
[in]	TREELOOKUP	Name of the SAS dataset that defines the parent-child nodes for tree extraction.
[in]	ICD10ICD9MAP	Name of the SAS dataset that maps ICD 9 to ICD 10 codes.
[in]	HDVARSEL_INPUT	For requests calculating a HDPS, lists each data dimension dataset.
[in]	PSESTIMATIONFILE	Name of the SAS dataset describing parameters for estimating a PS model.
[in]	PSMATCHFILE	Name of the SAS dataset describing parameters for a PS Matching analysis.
[in]	STRATIFICATIONFILE	Name of the SAS dataset describing parameters for a PS stratification analyses.
[in]	COVSTRATFILE	Name of the SAS dataset describing parameters for a covariate stratification analyses.
[in]	IPTWFILE	Name of the SAS dataset describing parameters for Inverse Probability Treatment Weight(IPTW) analyses.
[in]	PSCSSUBGROUPFILE	Name of the SAS dataset describing parameters for subgroups within the PS/CS submodule.
[in]	INDLEVEL	Indicates whether to return an individual level file after PS or Covariate Stratification analysis in the MSOC folder.
[in]	DIAGNOSTICS	Indicates if proc logistic diagnostic output files should be generated.

SAS Macros Dependencies

Author: Sentinel Coordinating Center (info@.nosp@m.sent.nosp@m.inels.nosp@m.yste.nosp@m.m.org)

	QRP