Update documentation to include visit tables

OHDSI · Dec 1, 2023 · fbb7557 · fbb7557
1 parent fa75978
commit fbb7557
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Showing 7 changed files with 20 additions and 19 deletions.
diff --git a/docs/articles/Measurement.html b/docs/articles/Measurement.html
diff --git a/docs/articles/visit_detail.html b/docs/articles/visit_detail.html
diff --git a/docs/articles/visit_occurrence.html b/docs/articles/visit_occurrence.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -16,5 +16,5 @@ articles:
   provider: provider.html
   visit_detail: visit_detail.html
   visit_occurrence: visit_occurrence.html
-last_built: 2023-11-30T22:40Z
+last_built: 2023-12-01T20:06Z
 
diff --git a/vignettes/Measurement.Rmd b/vignettes/Measurement.Rmd
@@ -40,7 +40,7 @@ vignette: >
 
 | Destination Field | Source field | Logic | Comment field |
 | --- | --- | --- | --- |
-| measurement_id |  |  |  |
+| measurement_id |  |Autogenerated  |  |
 | person_id | patient | Map by mapping person.person_source_value to patient.  Find person.person_id by mapping encouters.patient to person.person_source_value. |  |
 | measurement_concept_id | code | Use code to lookup target_concept_id in CTE_TARGET_VOCAB_MAP:    select ctvm.target_concept_id    from observations o     join cte_target_vocab_map ctvm       on ctvm.source_code              = o.code     and ctvm.target_domain_id       = 'Measurement'     and ctvm.target_standard_concept = 'S'     and ctvm.target_invalid_reason is NULL |  |
 | measurement_date | date |  |  |

diff --git a/vignettes/visit_detail.Rmd b/vignettes/visit_detail.Rmd
@@ -27,13 +27,13 @@ https://github.com/OHDSI/ETL-Synthea/blob/main/inst/sql/sql_server/cdm_version/v
 | visi_detail_t_end_date | stop |  |  |
 | visit_detail__end_datetime | stop |  |  |
 | visit__detail_type_concept_id |  |  Set all records as concept_id 44818517 (Visit derived from encounter on claim).  | |
-| provider_id | encounters.provider_id |  |  |
+| provider_id | encounters.provider |  |  |
 | care_site_id |  | Set to null for all records |  |
 | admitted_from_source_concept_id |  | Set to 0 for all records |  |
 | admitted_from_source_value |  | Set to null for all record |  |
 | discharged_to_concept_id |  | Set to 0 for all records |  |
 | discharged_to_source_value |  | Set to null for all record  |  |
-| preceding_visit_detail__id |  | lag(av.visit_occurrence_id) over(partition by p.person_id order by av.visit_start_date) + 1000000  |  |
-| visit_detail_source_value | encounter_id |  |  |
+| preceding_visit_detail__id |  | lag(all_visits.visit_occurrence_id) over(partition by person.person_id order by all_visits.visit_start_date) + 1000000  |  |
+| visit_detail_source_value | all_visits.encounter_id |  |  |
 | visit_detail_source_concept_id |  | Set to 0 for all record |  |
 
diff --git a/vignettes/visit_occurrence.Rmd b/vignettes/visit_occurrence.Rmd
@@ -33,7 +33,7 @@ For claim type in ('ambulatory', 'wellness', 'outpatient') (OP)
 1. Sort data in ascending order by PATIENT, START, END.
 2. Then by PERSON_ID take START as VISIT_START_DATE, MAX(END) as VISIT_END_DATE, and ‘OP’ as PLACE_OF_SERVICE_SOURCE_VALUE.
 
-Use logic found here:
+Use logic found here (depending on cdm version - CDM v5.4 provided as example):
 https://github.com/OHDSI/ETL-Synthea/blob/main/inst/sql/sql_server/cdm_version/v540/AllVisitTable.sql
 
 | Destination Field | Source field | Logic | Comment field |
@@ -45,14 +45,14 @@ https://github.com/OHDSI/ETL-Synthea/blob/main/inst/sql/sql_server/cdm_version/v
 | visit_start_datetime | start |  |  |
 | visit_end_date | stop |  |  |
 | visit_end_datetime | stop |  |  |
-| visit_type_concept_id |  |  |Set all records as concept_id 44818517 (Visit derived from encounter on claim).  |
+| visit_type_concept_id |  |  Set all records as concept_id 44818517 (Visit derived from encounter on claim).  | |
 | provider_id |encounters.provider  |  |  |
 | care_site_id |  | Set to null for all records  |  |
-| visit_source_value | encounters.id |  |  |
+| visit_source_value | all_visits.encounters_id |  |  |
 | visit_source_concept_id |  | Set to 0 for all records  |  |
 | admitted_from_concept_id |  | Set to 0 for all records |  |
 | admitted_from_source_value |  | Set to null for all records  |  |
 | discharge_to_concept_id |  | Set to 0 for all records |  |
 | discharge_to_source_value |  | Set to null for all records |  |
-| preceding_visit_occurrence_id |  |lag(av.visit_occurrence_id) over(partition by p.person_id order by av.visit_start_date)  |  |
+| preceding_visit_occurrence_id |  |lag(all_visits.visit_occurrence_id) over(partition by person.person_id order by all_visits.visit_start_date)  |  |