Merge branch 'master' into ibms-tests-updates

docs/CPRD/CPRD_Additional_STEM.md

@@ -36,7 +36,7 @@ These concatenated source values will then be mapped to standard concepts using
 | concept_id |  | Map the source value (add_int.enttype + '-' + add_int.category + '-' + add_int.description + '-' + add_int.data) to a concept using the [SOURCE_TO_STANDARD_QUERY](https://github.com/OHDSI/ETL-LambdaBuilder/blob/master/docs/Standard%20Queries/SOURCE_TO_STANDARD.sql) with the filters: <br><br>   WHERE source_vocabulary_id = 'JNJ_CPRD_ADD_ENTTYPE'  AND standard_concept = 'S'  AND target_invalid_reason is NULL  | |
 | source_value |  | Concatenate add_int.enttype + '-' + add_int.category + '-' + add_int.description + '-' + add_int.data. |  This will retain the information from the entity table about the record and the specific data field being mapped. Please refer to [appendix 2](https://github.com/OHDSI/ETL-LambdaBuilder/blob/master/docs/CPRD/Appendix_2_Additional_Table_Descriptions.xlsx) which is a table showing the enttypes and data_field descriptions from the additional table and counts of each. |
 | source_concept_id |  | 0 | |
-| type_concept_id |  | Use **32851** - Health professional filled survey |  
+| type_concept_id |  | Use **32817** - EHR |  
 | unit_concept_id |  | Look up add_int.unit_source_value in the CONCEPT table where vocabulary_id = 'UCUM' and standard_concept = 'S' and invalid_reason is NULL. |  |
 | unit_source_value | add_int.unit_source_value |  | |
 | start_date | add_int.eventdate |  | For the additional table, the adid is used to link back to the clinical table to get the eventdate. |

docs/CPRD/CPRD_Clinical_STEM.md

@@ -38,4 +38,4 @@ Any record with one of the SARS-COV-2 read codes listed below should be mapped t
 | concept_id | medcode | Use the medcode to link to the medical table to find the read code. Use the [SOURCE_TO_STANDARD](https://github.com/OHDSI/ETL-LambdaBuilder/blob/master/docs/Standard%20Queries/SOURCE_TO_STANDARD.sql) query to map the read code to standard concept(s) with the following filters: <br> <br>  Where source_vocabulary_id = 'Read'  and Target_standard_concept = 'S'  and target_invalid_reason is NULL<br><br>*BE CAREFUL - READ CODES ARE CASE SENSITIVE*. If there is no mapping available, set concept_id to zero. | See the query [CPRD_Clinical_Medcodes.sql](https://github.com/OHDSI/ETL-LambdaBuilder/blob/master/docs/CPRD/Queries/CPRD_Clinical_Medcodes.sql) as a high-level look at the domains covered by this table and how the link to the medical table should be made. |
 | source_value | medical.read_code | Use the medcode to link to the medical table to find the read code. Store read code as source_value. | |
 | source_concept_id | medcode | Use the medcode to link to the medical table to find the read code.     Use the [SOURCE_TO_SOURCE](https://github.com/OHDSI/ETL-LambdaBuilder/blob/master/docs/Standard%20Queries/SOURCE_TO_SOURCE.sql) query to map the read code to a source concept id with the following filters:<br><br> Where source_vocabulary_id = 'Read' <br><br>*BE CAREFUL - READ CODES ARE CASE SENSITIVE*. If there is no mapping available set source_concept_id to zero. | |
-| type_concept_id |  | Use **32827** - EHR encounter record |  |
+| type_concept_id |  | Use **32817** - EHR |  |

docs/CPRD/CPRD_Death.md

@@ -34,7 +34,7 @@ Per CPRD cause-specific mortality is not reliably recorded in the General Practi
 PERSON_ID|Patient.Patid||
 DEATH_DATE|Patient.Deathdate|
 DEATH_DATETIME|Set time to 00:00:00 UTC Tz||
-DEATH_TYPE_CONCEPT_ID|32815 (Death Certificate)
+DEATH_TYPE_CONCEPT_ID|32817 (EHR)
 CAUSE_OF_DEATH_CONCEPT_ID|0||
 CAUSE_OF_DEATH_SOURCE_VALUE|0||
-CAUSE_SOURCE_CONCEPT_ID|0||
+CAUSE_SOURCE_CONCEPT_ID|0||

docs/CPRD/CPRD_Immunisation_STEM.md

@@ -29,4 +29,4 @@ In the below table, only the relevant STEM fields are shown. Any fields that do
 | concept_id | medcode | Use the medcode to link to the medical table to find the read code. Use the [SOURCE_TO_STANDARD](https://github.com/OHDSI/ETL-LambdaBuilder/blob/master/docs/Standard%20Queries/SOURCE_TO_STANDARD.sql) query to map the read code to standard concept(s) with the following filters: <br> <br>  Where source_vocabulary_id = 'Read'  and Target_standard_concept = 'S'  and target_invalid_reason is NULL<br><br>*BE CAREFUL - READ CODES ARE CASE SENSITIVE*. If there is no mapping available, set concept_id to zero.  | See the query [CPRD_Immunisation_Medcodes.sql](https://github.com/OHDSI/ETL-LambdaBuilder/blob/master/docs/CPRD/Queries/CPRD_Immunisation_Medcodes.sql) as a high-level look at the domains covered by this table and how the link to the medical table should be made. |
 | source_value | medical.read_code | Use the medcode to link to the medical table to find the read code. Store read code as source_value. |  |
 | source_concept_id | medcode | Use the medcode to link to the medical table to find the read code.     Use the [SOURCE_TO_SOURCE](https://github.com/OHDSI/ETL-LambdaBuilder/blob/master/docs/Standard%20Queries/SOURCE_TO_SOURCE.sql) query to map the read code to a source concept id with the following filters:<br><br> Where source_vocabulary_id = 'Read' <br><br>*BE CAREFUL - READ CODES ARE CASE SENSITIVE*. If there is no mapping available set source_concept_id to zero. | |
-| type_concept_id |  | Use **32827** - EHR encounter record |  |
+| type_concept_id |  | Use **32818** - EHR administration |  |

docs/CPRD/CPRD_Referral_STEM.md

@@ -38,5 +38,5 @@ Any record with one of the SARS-COV-2 read codes listed below should be mapped t
 | concept_id | medcode | Use the medcode to link to the medical table to find the read code. Use the [SOURCE_TO_STANDARD](https://github.com/OHDSI/ETL-LambdaBuilder/blob/master/docs/Standard%20Queries/SOURCE_TO_STANDARD.sql) query to map the read code to standard concept(s) with the following filters: <br> <br>  Where source_vocabulary_id = 'Read'  and Target_standard_concept = 'S'  and target_invalid_reason is NULL<br><br>*BE CAREFUL - READ CODES ARE CASE SENSITIVE*. If there is no mapping available, set concept_id to zero. | See [CPRD_Referral_Medcodes.sql](https://github.com/OHDSI/ETL-LambdaBuilder/blob/master/docs/CPRD/Queries/CPRD_Referral_Medcodes.sql) for an idea of how the codes in the referral table map to the vocabulary and how the link between the referral table and medical table should be made.  |
 | source_value | medical.read_code | Use the medcode to link to the medical table to find the read code. Store read code as source_value. |  |  |
 | source_concept_id | medcode | Use the medcode to link to the medical table to find the read code.     Use the [SOURCE_TO_SOURCE](https://github.com/OHDSI/ETL-LambdaBuilder/blob/master/docs/Standard%20Queries/SOURCE_TO_SOURCE.sql) query to map the read code to a source concept id with the following filters:<br><br> Where source_vocabulary_id = 'Read' <br><br>*BE CAREFUL - READ CODES ARE CASE SENSITIVE*. If there is no mapping available set source_concept_id to zero. | |
-| type_concept_id |  | Use **32842** - EHR referral record |  |
+| type_concept_id |  | Use **32817** - EHR |  |
 

docs/CPRD/CPRD_Visit_Detail.md

@@ -29,7 +29,7 @@ For datetime fields, set time to midnight 00:00:00.
 | visit_detail_start_datetime | eventdate | Use the same logic used to set visit_detail_start_date. Set time to 00:00:00 |  |
 | visit_detail_end_date |  | Set as visit_detail_start_date  | |
 | visit_detail_end_datetime |  | Set as visit_detail_start_datetime |  |
-| visit_detail_type_concept_id |  | Use **32827** - EHR encounter record |  |
+| visit_detail_type_concept_id |  | Use **32817** - EHR |  |
 | provider_id | staffid |  |  |
 | care_site_id | patid | Use the last three digits of the patid (removing leading zeros) to look up the care_site_id in the care_site table. |  |
 | visit_detail_source_value | constype | Use the consid to link back to the consultation table. Use the constype from the consultation table as the visit_detail_source_value. If there are two based on how the visit detail was defined, choose one. |  |

docs/CPRD/CPRD_Visit_Occurrence.md

@@ -25,7 +25,7 @@ For datetime fields, set time to midnight 00:00:00.
 | visit_start_datetime | visit_detail_start_datetime | |  |
 | visit_end_date | visit_detail_end_date | | |
 | visit_end_datetime | visit_detail_end_datetime ||  |
-| visit_type_concept_id |  | Use **32827** - EHR encounter record |  |
+| visit_type_concept_id |  | Use **32817** - EHR |  |
 | provider_id | visit_detail.provider_id | Choose one provider_id if a patient saw more than one provider on the same day. |  |
 | care_site_id | visit_detail.care_site_id| |  |
 | visit_source_value | visit_detail_source_value | Choose one visit_detail_source_value for this field if a patient had more than one visit_detail_source_value on the same day. |  |

docs/IBM_CCAE_MDCR/Test Cases/code to run.R

@@ -54,8 +54,9 @@ executeSql(conn, paste0("TRUNCATE TABLE ",nativeDatabaseSchema,".GEOLOC; INSERT
           ".GEOLOC (EGEOLOC, EGEOLOC_Description, STATE) VALUES (11, 'New Jersey', 'NJ'); INSERT INTO ",
           nativeDatabaseSchema,
           ".GEOLOC (EGEOLOC, EGEOLOC_Description, STATE) VALUES (38, 'Virginia', 'VA')"))
+
 }
-  
+
 #IF TESTING CCAE  YOU NEED A COPY OF HRA_QUESTON_REF, HRA_VARIABLE_REF IN YOUR RAW
 if (frameworkType == "CCAE" ){
   executeSql(conn, paste0("TRUNCATE TABLE ",nativeDatabaseSchema,".HRA_VARIABLE_REF;

docs/OPTUM_PANTHER/Optum_Panther_Observation_Period.md

@@ -11,7 +11,7 @@ description: "Description for how to build the Optum Panther Observation Period
 
 ## Reading from OPTUM_EHR.Encounter
 
-The OBSERVATION_PERIOD table should be built by setting the OBSERVATION_PERIOD_START_DATE as the date of the earliest encounter available in the data and the OBSERVATION_PERIOD_END_DATE should the the date of the latest encounter in the data. 
+The OBSERVATION_PERIOD table should be built by setting the OBSERVATION_PERIOD_START_DATE as the date of the earliest encounter available in the data and the OBSERVATION_PERIOD_END_DATE should the the date of the latest encounter in the data, data from the oncology module (type_concept_id=32882) should not be used in the OBSERVATION_PERIOD table creation.
 
 
 |     Destination Field    |     Source Field    |     Logic    |     Comment    |
@@ -25,5 +25,8 @@ The OBSERVATION_PERIOD table should be built by setting the OBSERVATION_PERIOD_S
 ## Change Log
 - Removed the use of *first_month_active* and *last_month_active* and changed to using the encounter dates instead
 
+### 04-Dec-2023
+- Oncology event dates excluded from the OBSERVATION PERIOD table
+
 ### 07-Aug-2023
 - Cut of dates before 01-Jan-2007 rule added

docs/Optum Clinformatics/Optum_death.md

@@ -19,7 +19,7 @@ description: "DEATH table mapping from DOD DEATH table, MEDICAL_CLAIMS and MED_D
 ### **Deriving date of death in DOD**
 
 - If there are outpatient or pharmacy visits (VISIT_CONCEPT_ID in 9202, 581458) with visit start date after 30 days of death date, delete the visit record. 
-- If there are inpatient or ER visits (VISIT_CONCEPT_ID in 9202, 9203) with visit start date after 30 days of death date, delete the death record. 
+- If there are inpatient or ER visits (VISIT_CONCEPT_ID in 9201, 9203) with visit start date after 30 days of death date, delete the death record. 
 - If the death date occurs before the patient's date of birth, then delete the death record.
 - If person is absent in **Death** table, but the fact of death is confirmed by the SES logic (see below), populate the DEATH table as well.
 
@@ -86,6 +86,9 @@ CAUSE_SOURCE_CONCEPT_ID|0||
 
 ## Change log
 
+### 04-Dec-2024
+- fixed misprint in the delete death record rule (DOD), inpatient VISIT_CONCEPT_ID 9202 -> 9201
+
 ### 11-Aug-2023
 
 - table is revived since in CDM v5.4 the death table is present (the file was retired in intent of migration to CDM v6)

docs/Optum Clinformatics/Test Cases/.gitignore

@@ -21,4 +21,7 @@ src/*.o
 src/*.so
 src/*.dll
 /Debug
-standalone/build/*
+standalone/build/*
+
+#VSCode files
+.vscode/

docs/Optum Clinformatics/Test Cases/R/CareSiteTests.R

@@ -3,34 +3,35 @@ createCareSiteTests <- function()
   provider <- createProvider()
   declareTest("CARE_SITE - Creates a CARE_SITE entry from a record found in native provider table where prov_type is NULL.", #PASS V2.0.0.19
               id = provider$provider_id)
-  add_provider(prov_unique = provider$provid, prov_type = NULL)
+  add_provider(prov_unique = provider$provid, prov_type = NULL, grp_practice = NULL, hosp_affil = NULL)
   expect_care_site(care_site_id = provider$provider_id, care_site_source_value = provider$provider_id, place_of_service_concept_id = 0)
 
 
   provider <- createProvider()
   declareTest("CARE_SITE - Creates a CARE_SITE entry from a record found in native provider table where prov_type = 2.", #PASS V2.0.0.19
               id = provider$provider_id)
-  add_provider(prov_unique = provider$provid, prov_type = 2)
+  add_provider(prov_unique = provider$provid, prov_type = 2, grp_practice = NULL, hosp_affil = NULL)
   expect_care_site(care_site_id = provider$provider_id, care_site_source_value = provider$provider_id, place_of_service_concept_id = 8717)
 
   provider <- createProvider()
   declareTest("CARE_SITE - Creates a CARE_SITE entry from a record found in native provider table where prov_type = 3.", #PASS V2.0.0.19
               id = provider$provider_id)
-  add_provider(prov_unique = provider$provid, prov_type = 3)
+  add_provider(prov_unique = provider$provid, prov_type = 3, grp_practice = NULL, hosp_affil = NULL)
   expect_care_site(care_site_id = provider$provider_id, care_site_source_value = provider$provider_id, place_of_service_concept_id = 38004693)
 
   provider <- createProvider()
   declareTest("CARE_SITE - Creates a CARE_SITE entry from a record found in native provider table where prov_type = 4.", #PASS V2.0.0.19
               id = provider$provider_id)
-  add_provider(prov_unique = provider$provid, prov_type = 4)
+  add_provider(prov_unique = provider$provid, prov_type = 4, grp_practice = NULL, hosp_affil = NULL)
   expect_care_site(care_site_id = provider$provider_id, care_site_source_value = provider$provider_id, place_of_service_concept_id = 0)
 
 
   patient <- createPatient()
   provider <- createProvider()
   claim <- createClaim()
   declareTest("CARE_SITE - Creates a CARE_SITE entry from an Rx_claims record", id = provider$provider_id) #PASS V2.0.0.19
-  add_member_continuous_enrollment(patid = patient$patid, eligeff = '2000-05-01', eligend = '2009-12-31', gdr_cd = 'F', yrdob = 1988)
+  add_member_continuous_enrollment(patid = patient$patid, eligeff = '2000-05-01', eligend = '2009-12-31', gdr_cd = 'F', yrdob = 1988, ethnicity = NULL)
+  add_member_enrollment(patid = patient$patid, eligeff = '2000-05-01', eligend = '2009-12-31')
   add_rx_claims(patid = patient$patid, pat_planid = patient$patid, fill_dt = '2001-01-01', clmid = claim$clmid, pharm = provider$provid)
   expect_care_site(care_site_id = provider$provider_id, care_site_source_value = provider$provider_id, place_of_service_concept_id = 38004340)
 

docs/Optum Clinformatics/Test Cases/R/ConditionEraTests.R

@@ -1,3 +1,4 @@
+
 createConditionEraTests <- function()
 {
   testDiag <- '7061'
@@ -8,6 +9,7 @@ createConditionEraTests <- function()
               id = patient$person_id)
   add_member_continuous_enrollment(eligeff = '2010-05-01', eligend = '2013-10-31',
                     gdr_cd = 'F', patid = patient$patid, yrdob = 1969)
+  add_member_enrollment(patid = patient$patid, eligeff = '2010-05-01', eligend = '2013-10-31')
 
   claim <- createClaim()
   add_medical_claims(clmid = claim$clmid, clmseq = '001', lst_dt = '2013-07-01',