From ec478220b037c85c9d9fb304d81d899a121cf4c5 Mon Sep 17 00:00:00 2001 From: Evanette Burrows Date: Wed, 29 Nov 2023 15:22:16 -0500 Subject: [PATCH] Update documentation --- docs/404.html | 4 +- docs/articles/Condition_occurrence.html | 31 ++-- docs/articles/Drug_exposure.html | 53 ++++--- docs/articles/Measurement.html | 54 ++++--- docs/articles/index.html | 4 +- docs/articles/observation.html | 54 ++++--- docs/articles/observation_period.html | 16 +- docs/articles/person.html | 24 +-- docs/articles/procedure_occurrence.html | 30 ++-- docs/articles/visit_occurrence.html | 51 +++++-- docs/authors.html | 8 +- docs/index.html | 89 +++++------ docs/pkgdown.yml | 6 +- .../CreateCDMIndexAndConstraintScripts.html | 24 ++- docs/reference/CreateCDMIndices.html | 143 ++++++++++++++++++ docs/reference/CreateCDMTables.html | 31 +++- docs/reference/CreateSyntheaTables.html | 17 ++- docs/reference/CreateVisitRollupTables.html | 27 +++- docs/reference/CreateVocabMapTables.html | 17 ++- docs/reference/DropEventTables.html | 17 ++- docs/reference/DropMapAndRollupTables.html | 11 +- docs/reference/DropSyntheaTables.html | 11 +- docs/reference/DropVocabTables.html | 11 +- docs/reference/ETLSyntheaBuilder-package.html | 102 +++++++++++++ docs/reference/LoadEventTables.html | 46 +++++- docs/reference/LoadSyntheaTables.html | 26 +++- docs/reference/LoadVocabFromCsv.html | 15 +- docs/reference/LoadVocabFromSchema.html | 13 +- docs/reference/TruncateEventTables.html | 15 +- docs/reference/TruncateVocabTables.html | 11 +- docs/reference/backupCDM.html | 13 +- docs/reference/createPrunedTables.html | 15 +- docs/reference/exportToSQLite.html | 13 +- docs/reference/getEventConceptId.html | 13 +- docs/reference/index.html | 60 ++++---- docs/reference/pruneCDM.html | 13 +- docs/reference/restoreCDMTables.html | 13 +- docs/sitemap.xml | 74 ++++----- 38 files changed, 879 insertions(+), 296 deletions(-) create mode 100644 docs/reference/CreateCDMIndices.html create mode 100644 docs/reference/ETLSyntheaBuilder-package.html diff --git a/docs/404.html b/docs/404.html index f445c63..fca9e9d 100644 --- a/docs/404.html +++ b/docs/404.html @@ -42,7 +42,7 @@ Reference
  • -

    pkgdown 2.0.0.

    +

    Site built with pkgdown 2.0.7.

    diff --git a/docs/articles/Condition_occurrence.html b/docs/articles/Condition_occurrence.html index 8e7cbea..2d2624b 100644 --- a/docs/articles/Condition_occurrence.html +++ b/docs/articles/Condition_occurrence.html @@ -43,7 +43,7 @@ Reference
  • -

    -

    -

    Reading from Synthea table conditions.csv +

    Condition_occurrence

    +
    +

    Reading from Synthea table conditions.csv +

    @@ -128,13 +128,20 @@

    Reading from Synthea table co

    - + - + @@ -182,7 +189,8 @@

    Reading from Synthea table co

    - + @@ -200,7 +208,10 @@

    Reading from Synthea table co

    - + @@ -238,7 +249,7 @@

    Reading from Synthea table co

    -

    Site built with pkgdown 2.0.0.

    +

    Site built with pkgdown 2.0.7.

    diff --git a/docs/articles/Drug_exposure.html b/docs/articles/Drug_exposure.html index 709ecad..c169f03 100644 --- a/docs/articles/Drug_exposure.html +++ b/docs/articles/Drug_exposure.html @@ -43,7 +43,7 @@ Reference
  • -

    -

    -

    Reading from Synthea medications.csv +

    Drug_exposure

    +
    +

    Reading from Synthea medications.csv +

    • person_id patientMap by mapping person.person_source_value to patient. Find person.person_id by mapping encouters.patient to person.person_source_value.Map by mapping person.person_source_value to patient. Find +person.person_id by mapping encouters.patient to +person.person_source_value.
    condition_concept_id codeUse the following SQL code to lookup target_concept_id in CTE_TARGET_VOCAB_MAP: select ctvm.target_concept_id from conditions c join cte_target_vocab_map ctvm on ctvm.source_code = c.code and ctvm.target_domain_id = ‘Condition’ and ctvm.target_vocabulary_id = ‘SNOMED’ and ctvm.target_invalid_reason is NULL and ctvm.target_standard_concept = ‘S’Use the following SQL code to lookup target_concept_id in +CTE_TARGET_VOCAB_MAP: select ctvm.target_concept_id from conditions c +join cte_target_vocab_map ctvm on ctvm.source_code = c.code and +ctvm.target_domain_id = ‘Condition’ and ctvm.target_vocabulary_id = +‘SNOMED’ and ctvm.target_invalid_reason is NULL and +ctvm.target_standard_concept = ‘S’
    visit_occurrence_id encounterLookup visit_occurrence_id using encounter, joining to temp table defined in AllVisitTable.sql.Lookup visit_occurrence_id using encounter, joining to temp table +defined in AllVisitTable.sql.
    condition_source_concept_id codeUse the following SQL code to lookup the source_concept_id in CTE_SOURCE_VOCAB_MAP: select csvm.source_concept_id from cte_source_vocab_map csvm join conditions c on csvm.source_code = c.code and csvm.source_vocabulary_id = ‘SNOMED’Use the following SQL code to lookup the source_concept_id in +CTE_SOURCE_VOCAB_MAP: select csvm.source_concept_id from +cte_source_vocab_map csvm join conditions c on csvm.source_code = c.code +and csvm.source_vocabulary_id = ‘SNOMED’
    @@ -128,13 +128,19 @@

    Reading from Synthea medications.c

    - + - + @@ -224,7 +230,8 @@

    Reading from Synthea medications.c

    - + @@ -242,7 +249,9 @@

    Reading from Synthea medications.c

    - + @@ -260,9 +269,9 @@

    Reading from Synthea medications.c

    person_id patientMap by mapping person.person_source_value to patient. Find person.person_id by mapping medications.patient to person.person_source_value.Map by mapping person.person_source_value to patient. Find +person.person_id by mapping medications.patient to +person.person_source_value.
    drug_concept_id codeUse code to lookup target_concept_id in CTE_TARGET_VOCAB_MAP: select ctvm.target_concept_id from medications m join cte_target_vocab_map ctvm on ctvm.source_code = m.code and ctvm.target_domain_id = ‘Drug’ and ctvm.target_vocabulary_id = ‘RxNorm’ and ctvm.target_standard_concept = ‘S’ and ctvm.target_invalid_reason is NULLUse code to lookup target_concept_id in CTE_TARGET_VOCAB_MAP: select +ctvm.target_concept_id from medications m join cte_target_vocab_map ctvm +on ctvm.source_code = m.code and ctvm.target_domain_id = ‘Drug’ and +ctvm.target_vocabulary_id = ‘RxNorm’ and ctvm.target_standard_concept = +‘S’ and ctvm.target_invalid_reason is NULL
    visit_occurrence_id encounterLookup visit_occurrence_id using encounter, joining to temp table defined in AllVisitTable.sql.Lookup visit_occurrence_id using encounter, joining to temp table +defined in AllVisitTable.sql.
    drug_source_concept_id codeUse code to lookup target_concept_id in CTE_SOURCE_VOCAB_MAP: select csvm.source_concept_id from medications m join cte_source_vocab_map csvm on cvm.source_code = m.code and cvm.source_vocabulary_id = ‘RxNorm’Use code to lookup target_concept_id in CTE_SOURCE_VOCAB_MAP: select +csvm.source_concept_id from medications m join cte_source_vocab_map csvm +on cvm.source_code = m.code and cvm.source_vocabulary_id = ‘RxNorm’
    -
    -

    Reading from Synthea.immunizations.csv -

    +
    +

    Reading from Synthea.immunizations.csv +

    @@ -286,13 +295,19 @@

    Reading from Synthea.immunizatio

    - + - + @@ -382,7 +397,8 @@

    Reading from Synthea.immunizatio

    - + @@ -400,7 +416,10 @@

    Reading from Synthea.immunizatio

    - + @@ -438,7 +457,7 @@

    Reading from Synthea.immunizatio

    -

    Site built with pkgdown 2.0.0.

    +

    Site built with pkgdown 2.0.7.

    diff --git a/docs/articles/Measurement.html b/docs/articles/Measurement.html index 9d47f91..b6f750c 100644 --- a/docs/articles/Measurement.html +++ b/docs/articles/Measurement.html @@ -43,7 +43,7 @@ Reference
  • -

    -

    -

    Reading from procedures.csv +

    Measurement

    +
    +

    Reading from procedures.csv +

    • person_id patientMap by mapping person.person_source_value to patient. Find person.person_id by mapping immunizations.patient to person.person_source_value.Map by mapping person.person_source_value to patient. Find +person.person_id by mapping immunizations.patient to +person.person_source_value.
    drug_concept_id codeUse code to lookup target_concept_id in CTE_TARGET_VOCAB_MAP: select ctvm.target_concept_id from immunizations i join cte_target_vocab_map ctvm on ctvm.source_code = i.code and ctvm.target_domain_id = ‘Drug’ and ctvm.target_vocabulary_id = ‘CVX’ and ctvm.target_standard_concept = ‘S’ and ctvm.target_invalid_reason is NULLUse code to lookup target_concept_id in CTE_TARGET_VOCAB_MAP: select +ctvm.target_concept_id from immunizations i join cte_target_vocab_map +ctvm on ctvm.source_code = i.code and ctvm.target_domain_id = ‘Drug’ and +ctvm.target_vocabulary_id = ‘CVX’ and ctvm.target_standard_concept = ‘S’ +and ctvm.target_invalid_reason is NULL
    visit_occurrence_id encounterLookup visit_occurrence_id using encounter, joining to temp table defined in AllVisitTable.sql.Lookup visit_occurrence_id using encounter, joining to temp table +defined in AllVisitTable.sql.
    drug_source_concept_id codeUse code to lookup target_concept_id in CTE_SOURCE_VOCAB_MAP: select csvm.source_concept_id from immunizations i join cte_source_vocab_map csvm on csvm.source_code = i.code and csvm.source_vocabulary_id = ‘CVX’Use code to lookup target_concept_id in CTE_SOURCE_VOCAB_MAP: select +csvm.source_concept_id from immunizations i join cte_source_vocab_map +csvm on csvm.source_code = i.code and csvm.source_vocabulary_id = +‘CVX’
    @@ -128,13 +128,19 @@

    Reading from procedures.csv

    - + - + @@ -206,7 +212,8 @@

    Reading from procedures.csv

    - + @@ -224,7 +231,10 @@

    Reading from procedures.csv

    - + @@ -242,9 +252,9 @@

    Reading from procedures.csv -

    Reading from observations.csv -

    +
    +

    Reading from observations.csv +

    person_id patientLookup in the person table: map by mapping person.person_source_value to patient.Lookup in the person table: map by mapping +person.person_source_value to patient.
    measurement_concept_id codeUse code to lookup target_concept_id in CTE_TARGET_VOCAB_MAP: select ctvm.target_concept_id from procedures pr join cte_target_vocab_map ctvm on ctvm.source_code = pr.code and ctvm.target_domain_id = ‘Measurement’ and ctvm.target_vocabulary_id = ‘SNOMED’ and ctvm.target_standard_concept = ‘S’ and ctvm.target_invalid_reason is NULLUse code to lookup target_concept_id in CTE_TARGET_VOCAB_MAP: select +ctvm.target_concept_id from procedures pr join cte_target_vocab_map ctvm +on ctvm.source_code = pr.code and ctvm.target_domain_id = ‘Measurement’ +and ctvm.target_vocabulary_id = ‘SNOMED’ and +ctvm.target_standard_concept = ‘S’ and ctvm.target_invalid_reason is +NULL
    visit_occurrence_id encounterLookup visit_occurrence_id using encounter, joining to temp table defined in AllVisitTable.sql.Lookup visit_occurrence_id using encounter, joining to temp table +defined in AllVisitTable.sql.
    measurement_source_concept_id codeUse code to lookup source_concept_id in CTE_SOURCE_VOCAB_MAP: select csvm.source_concept_id from cte_source_vocab_map csvm join procedures pr on csvm.source_code = pr.code and csvm.source_vocabulary_id = ‘SNOMED’Use code to lookup source_concept_id in CTE_SOURCE_VOCAB_MAP: select +csvm.source_concept_id from cte_source_vocab_map csvm join procedures pr +on csvm.source_code = pr.code and csvm.source_vocabulary_id = +‘SNOMED’
    @@ -268,13 +278,19 @@

    Reading from observations.csv

    - + - + @@ -346,7 +362,8 @@

    Reading from observations.csv

    - + @@ -364,7 +381,10 @@

    Reading from observations.csv

    - + @@ -402,7 +422,7 @@

    Reading from observations.csv

    -

    Site built with pkgdown 2.0.0.

    +

    Site built with pkgdown 2.0.7.

    diff --git a/docs/articles/index.html b/docs/articles/index.html index 3f62ca6..aca3eae 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -26,7 +26,7 @@ Reference
  • -

    pkgdown 2.0.0.

    +

    Site built with pkgdown 2.0.7.

    diff --git a/docs/articles/observation.html b/docs/articles/observation.html index 453df30..b70df29 100644 --- a/docs/articles/observation.html +++ b/docs/articles/observation.html @@ -43,7 +43,7 @@ Reference
  • -

    -

    -

    Reading from Synthea tables allergies.csv +

    Observation

    +
    +

    Reading from Synthea tables allergies.csv +

    • person_id patientMap by mapping person.person_source_value to patient. Find person.person_id by mapping encouters.patient to person.person_source_value.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 codeUse 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 NULLUse 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
    visit_occurrence_id codeLookup visit_occurrence_id using encounter, joining to temp table defined in AllVisitTable.sql.Lookup visit_occurrence_id using encounter, joining to temp table +defined in AllVisitTable.sql.
    measurement_source_concept_id codeUse code to lookup source_concept_id in CTE_SOURCE_VOCAB_MAP: select csvm.source_concept_id from cte_source_vocab_map csvm join observations o on csvm.source_code = o.code and csvm.source_vocabulary_id = ‘SNOMED’Use code to lookup source_concept_id in CTE_SOURCE_VOCAB_MAP: select +csvm.source_concept_id from cte_source_vocab_map csvm join observations +o on csvm.source_code = o.code and csvm.source_vocabulary_id = +‘SNOMED’
    @@ -128,13 +128,20 @@

    Reading from Synthea tables a

    - + - + @@ -194,7 +201,8 @@

    Reading from Synthea tables a

    - + @@ -212,7 +220,10 @@

    Reading from Synthea tables a

    - + @@ -248,9 +259,9 @@

    Reading from Synthea tables a

    person_id patientMap by mapping person.person_source_value to patient. Find person.person_id by mapping allergies.patient to person.person_source_value.Map by mapping person.person_source_value to patient. Find +person.person_id by mapping allergies.patient to +person.person_source_value.
    observation_concept_id codeUse code to lookup target_concept_id in CTE_TARGET_VOCAB_MAP: select ctvm.target_concept_id from allergies a join cte_target_vocab_map ctvm on ctvm.source_code = a.code and ctvm.target_domain_id = ‘Observation’ and ctvm.target_vocabulary_id = ‘SNOMED’ and ctvm.target_standard_concept = ‘S’ and ctvm.target_invalid_reason is NULLUse code to lookup target_concept_id in CTE_TARGET_VOCAB_MAP: select +ctvm.target_concept_id from allergies a join cte_target_vocab_map ctvm +on ctvm.source_code = a.code and ctvm.target_domain_id = ‘Observation’ +and ctvm.target_vocabulary_id = ‘SNOMED’ and +ctvm.target_standard_concept = ‘S’ and ctvm.target_invalid_reason is +NULL
    visit_occurrence_id encounterLookup visit_occurrence_id using encounter, joining to temp table defined in AllVisitTable.sql.Lookup visit_occurrence_id using encounter, joining to temp table +defined in AllVisitTable.sql.
    observation_source_concept_id codeUse code to lookup source_concept_id in CTE_SOURCE_VOCAB_MAP: select csvm.source_concept_id from cte_source_vocab_map csvm join allergies a on csvm.source_code = a.code and csvm.source_vocabulary_id = ‘SNOMED’Use code to lookup source_concept_id in CTE_SOURCE_VOCAB_MAP: select +csvm.source_concept_id from cte_source_vocab_map csvm join allergies a +on csvm.source_code = a.code and csvm.source_vocabulary_id = +‘SNOMED’
    -
    -

    Reading from Synthea table conditions.csv -

    +
    +

    Reading from Synthea table conditions.csv +

    @@ -274,13 +285,18 @@

    Reading from Synthea table co

    - + - + @@ -340,7 +356,8 @@

    Reading from Synthea table co

    - + @@ -358,7 +375,10 @@

    Reading from Synthea table co

    - + @@ -414,7 +434,7 @@

    Reading from Synthea table co

    -

    Site built with pkgdown 2.0.0.

    +

    Site built with pkgdown 2.0.7.

    diff --git a/docs/articles/observation_period.html b/docs/articles/observation_period.html index 251711e..a24257e 100644 --- a/docs/articles/observation_period.html +++ b/docs/articles/observation_period.html @@ -43,7 +43,7 @@ Reference
  • -

    -

    -

    Reading from Synthea table encounters.csv +

    Observation_period

    +
    +

    Reading from Synthea table encounters.csv +

    • person_id patientMap by mapping person.person_source_value to patient. Find person.person_id by mapping encouters.patient to person.person_source_value.Map by mapping person.person_source_value to patient. Find +person.person_id by mapping encouters.patient to +person.person_source_value.
    observation_concept_id codeUse code to lookup target_concept_id in CTE_TARGET_VOCAB_MAP: select ctvm.target_concept_id from conditions c join cte_target_vocab_map ctvm on ctvm.source_code = c.code and ctvm.target_domain_id = ‘Observation’ and ctvm.target_vocabulary_id = ‘SNOMED’Use code to lookup target_concept_id in CTE_TARGET_VOCAB_MAP: select +ctvm.target_concept_id from conditions c join cte_target_vocab_map ctvm +on ctvm.source_code = c.code and ctvm.target_domain_id = ‘Observation’ +and ctvm.target_vocabulary_id = ‘SNOMED’
    visit_occurrence_id encounterLookup visit_occurrence_id using encounter, joining to temp table defined in AllVisitTable.sql.Lookup visit_occurrence_id using encounter, joining to temp table +defined in AllVisitTable.sql.
    observation_source_concept_id codeUse code to lookup source_concept_id in CTE_SOURCE_VOCAB_MAP: select csvm.source_concept_id from cte_source_vocab_map csvm join conditions c on csvm.source_code = c.code and csvm.source_vocabulary_id = ‘SNOMED’Use code to lookup source_concept_id in CTE_SOURCE_VOCAB_MAP: select +csvm.source_concept_id from cte_source_vocab_map csvm join conditions c +on csvm.source_code = c.code and csvm.source_vocabulary_id = +‘SNOMED’
    @@ -128,7 +128,9 @@

    Reading from Synthea table en

    - + @@ -172,7 +174,7 @@

    Reading from Synthea table en

    -

    Site built with pkgdown 2.0.0.

    +

    Site built with pkgdown 2.0.7.

    diff --git a/docs/articles/person.html b/docs/articles/person.html index 38ca1d1..8432295 100644 --- a/docs/articles/person.html +++ b/docs/articles/person.html @@ -43,7 +43,7 @@ Reference
  • -

    -

    -

    Reading from Synthea table patients.csv +

    Person

    +
    +

    Reading from Synthea table patients.csv +

    • person_id patientMap by mapping person.person_source_value to patient. Find person.person_id by mapping encouters.patient to person.person_source_value.Map by mapping person.person_source_value to patient. Find +person.person_id by mapping encouters.patient to +person.person_source_value.
    @@ -128,7 +128,8 @@

    Reading from Synthea table pati

    - + @@ -164,13 +165,18 @@

    Reading from Synthea table pati

    - + - + @@ -256,7 +262,7 @@

    Reading from Synthea table pati

    -

    Site built with pkgdown 2.0.0.

    +

    Site built with pkgdown 2.0.7.

    diff --git a/docs/articles/procedure_occurrence.html b/docs/articles/procedure_occurrence.html index 2b39f84..217ef3c 100644 --- a/docs/articles/procedure_occurrence.html +++ b/docs/articles/procedure_occurrence.html @@ -43,7 +43,7 @@ Reference
  • -

    -

    -

    Reading from Synthea table procedures.csv +

    Procedure_occurrence

    +
    +

    Reading from Synthea table procedures.csv +

    • gender_concept_id genderWhen gender = ‘M’ then set gender_concept_id to 8507, when gender = ‘F’ then set to 8532When gender = ‘M’ then set gender_concept_id to 8507, when gender = +‘F’ then set to 8532 Drop any rows with missing/unknown gender.
    race_concept_id raceWhen race = ‘WHITE’ then set as 8527, when race = ‘BLACK’ then set as 8516, when race = ‘ASIAN’ then set as 8515, otherwise set as 0When race = ‘WHITE’ then set as 8527, when race = ‘BLACK’ then set +as 8516, when race = ‘ASIAN’ then set as 8515, otherwise set as 0
    ethnicity_concept_id race ethnicityWhen race = ‘HISPANIC’, or when ethnicity in (‘CENTRAL_AMERICAN’, ‘DOMINICAN’, ‘MEXICAN’, ‘PUERTO_RICAN’, ‘SOUTH_AMERICAN’ ) then set as 38003563, otherwise set as 0 When race = ‘HISPANIC’, or when ethnicity in (‘CENTRAL_AMERICAN’, ‘DOMINICAN’, ‘MEXICAN’, ‘PUERTO_RICAN’, ‘SOUTH_AMERICAN’ ) then set as 38003563, otherwise set as 0When race = ‘HISPANIC’, or when ethnicity in (‘CENTRAL_AMERICAN’, +‘DOMINICAN’, ‘MEXICAN’, ‘PUERTO_RICAN’, ‘SOUTH_AMERICAN’ ) then set as +38003563, otherwise set as 0 When race = ‘HISPANIC’, or when ethnicity +in (‘CENTRAL_AMERICAN’, ‘DOMINICAN’, ‘MEXICAN’, ‘PUERTO_RICAN’, +‘SOUTH_AMERICAN’ ) then set as 38003563, otherwise set as 0
    @@ -128,13 +128,19 @@

    Reading from Synthea table pr

    - + - + @@ -176,7 +182,8 @@

    Reading from Synthea table pr

    - + @@ -194,7 +201,10 @@

    Reading from Synthea table pr

    - + @@ -226,7 +236,7 @@

    Reading from Synthea table pr

    -

    Site built with pkgdown 2.0.0.

    +

    Site built with pkgdown 2.0.7.

    diff --git a/docs/articles/visit_occurrence.html b/docs/articles/visit_occurrence.html index 5c517b5..17a211f 100644 --- a/docs/articles/visit_occurrence.html +++ b/docs/articles/visit_occurrence.html @@ -43,7 +43,7 @@ Reference
  • -

    -

    -

    Reading from Synthea table encounters.csv +

    Visit_occurrence

    -

    STEP 1 +

    Reading from Synthea table encounters.csv

    -

    For encounterclass = ‘Inpatient’ (IP): 1. Sort data in ascending order by PATIENT, START, END. 2. Then by PERSON_ID, collapse lines of claim as long as the time between the END of one line and the START of the next is <=1 day. 3. Each consolidated inpatient claim is then considered as one inpatient visit, set 1. MIN(START) as VISIT_START_DATE 2. MAX(END) as VISIT_END_DATE 3. ‘IP’ as PLACE_OF_SERVICE_SOURCE_VALUE 4. See if any records with encounterclass ‘outpatient’ (OP), ‘ambulatory’ (OP), ‘wellness’ (OP), ‘emergency’ (ER) or ‘urgentcare’ (ER) occur during an identified ‘inpatient’ visit. These should be consolidated into the ‘inpatient’ visit, unless it is an ‘emergency’ or ‘urgentcare’ visit that starts and ends on the first day of the ‘inpatient’ visit. Types of outpatient (OP) visits not collapsed: 1. If an OP starts before an IP but ends during an IP 2. If an OP starts before and ends after an IP visit. If an OP is collapsed into an IP and its VISIT_END_DATE is greater than the IP’s VISIT_END_DATE it does not change the IP VISIT_END_DATE.

    -

    For claim type in (‘emergency’,‘urgentcare’) (ER) 1. Sort data in ascending order by PATIENT, START, END. 2. Then by PERSON_ID, collapse all (ER) claims that start on the same day as one ER visit, then take START as VISIT_START_DATE, MAX (END) as VISIT_END_DATE, and ‘ER’ as PLACE_OF_SERVICE_SOURCE_VALUE.

    -

    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.

    +
    +

    STEP 1 +

    +

    For encounterclass = ‘Inpatient’ (IP): 1. Sort data in ascending +order by PATIENT, START, END. 2. Then by PERSON_ID, collapse lines of +claim as long as the time between the END of one line and the START of +the next is <=1 day. 3. Each consolidated inpatient claim is then +considered as one inpatient visit, set 1. MIN(START) as VISIT_START_DATE +2. MAX(END) as VISIT_END_DATE 3. ‘IP’ as PLACE_OF_SERVICE_SOURCE_VALUE +4. See if any records with encounterclass ‘outpatient’ (OP), +‘ambulatory’ (OP), ‘wellness’ (OP), ‘emergency’ (ER) or ‘urgentcare’ +(ER) occur during an identified ‘inpatient’ visit. These should be +consolidated into the ‘inpatient’ visit, unless it is an ‘emergency’ or +‘urgentcare’ visit that starts and ends on the first day of the +‘inpatient’ visit. Types of outpatient (OP) visits not collapsed: 1. If +an OP starts before an IP but ends during an IP 2. If an OP starts +before and ends after an IP visit. If an OP is collapsed into an IP and +its VISIT_END_DATE is greater than the IP’s VISIT_END_DATE it does not +change the IP VISIT_END_DATE.

    +

    For claim type in (‘emergency’,‘urgentcare’) (ER) 1. Sort data in +ascending order by PATIENT, START, END. 2. Then by PERSON_ID, collapse +all (ER) claims that start on the same day as one ER visit, then take +START as VISIT_START_DATE, MAX (END) as VISIT_END_DATE, and ‘ER’ as +PLACE_OF_SERVICE_SOURCE_VALUE.

    +

    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: https://github.com/OHDSI/ETL-Synthea/blob/master/ETL/SQL/AllVisitTable.sql

    • person_id patientMap by mapping person.person_source_value to patient. Find person.person_id by mapping encouters.patient to person.person_source_value.Map by mapping person.person_source_value to patient. Find +person.person_id by mapping encouters.patient to +person.person_source_value.
    procedure_concept_id codeUse code to lookup target_concept_id in CTE_TARGET_VOCAB_MAP: select ctvm.target_concept_id from procedures pr join cte_target_vocab_map ctvm on ctvm.source_code = pr.code and ctvm.target_domain_id = ‘Procedure’ and ctvm.target_vocabulary_id = ‘SNOMED’ and ctvm.target_invalid_reason is NULL and ctvm.target_standard_concept = ‘S’Use code to lookup target_concept_id in CTE_TARGET_VOCAB_MAP: select +ctvm.target_concept_id from procedures pr join cte_target_vocab_map ctvm +on ctvm.source_code = pr.code and ctvm.target_domain_id = ‘Procedure’ +and ctvm.target_vocabulary_id = ‘SNOMED’ and ctvm.target_invalid_reason +is NULL and ctvm.target_standard_concept = ‘S’
    visit_occurrence_id encounterLookup visit_occurrence_id using encounter, joining to temp table defined in AllVisitTable.sql.Lookup visit_occurrence_id using encounter, joining to temp table +defined in AllVisitTable.sql.
    procedure_source_concept_id codeUse code to lookup source_concept_id in CTE_SOURCE_VOCAB_MAP: select csvm.source_concept_id from cte_source_vocab_map csvm join procedures pr on csvm.source_code = pr.code and csvm.source_vocabulary_id = ‘SNOMED’Use code to lookup source_concept_id in CTE_SOURCE_VOCAB_MAP: select +csvm.source_concept_id from cte_source_vocab_map csvm join procedures pr +on csvm.source_code = pr.code and csvm.source_vocabulary_id = +‘SNOMED’
    @@ -135,13 +157,18 @@

    STEP 1

    - + - + @@ -252,7 +279,7 @@

    STEP 1

    -

    Site built with pkgdown 2.0.0.

    +

    Site built with pkgdown 2.0.7.

    diff --git a/docs/authors.html b/docs/authors.html index 64bb4ea..17f399f 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -26,7 +26,7 @@ Reference
  • -

    pkgdown 2.0.0.

    +

    Site built with pkgdown 2.0.7.

    diff --git a/docs/index.html b/docs/index.html index 64d4e9b..2c719e5 100644 --- a/docs/index.html +++ b/docs/index.html @@ -49,7 +49,7 @@ Reference
  • - 

    - devtools::install_github("OHDSI/ETL-Synthea")
-
- library(ETLSyntheaBuilder)
-
- # We are loading a version 5.4 CDM into a local PostgreSQL database called "synthea10".
- # The ETLSyntheaBuilder package leverages the OHDSI/CommonDataModel package for CDM creation.
- # Valid CDM versions are determined by executing CommonDataModel::listSupportedVersions().
- # The strings representing supported CDM versions are currently "5.3" and "5.4". 
- # The Synthea version we use in this example is 2.7.0.  Since Synthea's MASTER branch is always active, we currently
- # only support version 2.7.0.
- # The schema to load the Synthea tables is called "native".
- # The schema to load the Vocabulary and CDM tables is "cdm_synthea10".  
- # The username and pw are "postgres" and "lollipop".
- # The Synthea and Vocabulary CSV files are located in /tmp/synthea/output/csv and /tmp/Vocabulary_20181119, respectively.
- 
- # For those interested in seeing the CDM changes from 5.3 to 5.4, please see: http://ohdsi.github.io/CommonDataModel/cdm54Changes.html
- 
-cd <- DatabaseConnector::createConnectionDetails(
-  dbms     = "postgresql", 
-  server   = "localhost/synthea10", 
-  user     = "postgres", 
-  password = "lollipop", 
-  port     = 5432, 
-  pathToDriver = "d:/drivers"  
-)
-
-cdmSchema      <- "cdm_synthea10"
-cdmVersion     <- "5.4"
-syntheaVersion <- "2.7.0"
-syntheaSchema  <- "native"
-syntheaFileLoc <- "/tmp/synthea/output/csv"
-vocabFileLoc   <- "/tmp/Vocabulary_20181119"
-
-ETLSyntheaBuilder::CreateCDMTables(connectionDetails = cd, cdmSchema = cdmSchema, cdmVersion = cdmVersion)
-                                     
-ETLSyntheaBuilder::CreateSyntheaTables(connectionDetails = cd, syntheaSchema = syntheaSchema, syntheaVersion = syntheaVersion)
-                                       
-ETLSyntheaBuilder::LoadSyntheaTables(connectionDetails = cd, syntheaSchema = syntheaSchema, syntheaFileLoc = syntheaFileLoc)
-                                     
-ETLSyntheaBuilder::LoadVocabFromCsv(connectionDetails = cd, cdmSchema = cdmSchema, vocabFileLoc = vocabFileLoc)
-                                    
-ETLSyntheaBuilder::LoadEventTables(connectionDetails = cd, cdmSchema = cdmSchema, syntheaSchema = syntheaSchema, cdmVersion = cdmVersion, syntheaVersion = syntheaVersion)
    + devtools::install_github("OHDSI/ETL-Synthea") + + library(ETLSyntheaBuilder) + + # We are loading a version 5.4 CDM into a local PostgreSQL database called "synthea10". + # The ETLSyntheaBuilder package leverages the OHDSI/CommonDataModel package for CDM creation. + # Valid CDM versions are determined by executing CommonDataModel::listSupportedVersions(). + # The strings representing supported CDM versions are currently "5.3" and "5.4". + # The Synthea version we use in this example is 2.7.0. However, at this time we also support 3.0.0. + # Please note that Synthea's MASTER branch is always active and this package will be updated to support + # future versions as possible. + # The schema to load the Synthea tables is called "native". + # The schema to load the Vocabulary and CDM tables is "cdm_synthea10". + # The username and pw are "postgres" and "lollipop". + # The Synthea and Vocabulary CSV files are located in /tmp/synthea/output/csv and /tmp/Vocabulary_20181119, respectively. + + # For those interested in seeing the CDM changes from 5.3 to 5.4, please see: http://ohdsi.github.io/CommonDataModel/cdm54Changes.html + +cd <- DatabaseConnector::createConnectionDetails( + dbms = "postgresql", + server = "localhost/synthea10", + user = "postgres", + password = "lollipop", + port = 5432, + pathToDriver = "d:/drivers" +) + +cdmSchema <- "cdm_synthea10" +cdmVersion <- "5.4" +syntheaVersion <- "2.7.0" +syntheaSchema <- "native" +syntheaFileLoc <- "/tmp/synthea/output/csv" +vocabFileLoc <- "/tmp/Vocabulary_20181119" + +ETLSyntheaBuilder::CreateCDMTables(connectionDetails = cd, cdmSchema = cdmSchema, cdmVersion = cdmVersion) + +ETLSyntheaBuilder::CreateSyntheaTables(connectionDetails = cd, syntheaSchema = syntheaSchema, syntheaVersion = syntheaVersion) + +ETLSyntheaBuilder::LoadSyntheaTables(connectionDetails = cd, syntheaSchema = syntheaSchema, syntheaFileLoc = syntheaFileLoc) + +ETLSyntheaBuilder::LoadVocabFromCsv(connectionDetails = cd, cdmSchema = cdmSchema, vocabFileLoc = vocabFileLoc) + +ETLSyntheaBuilder::LoadEventTables(connectionDetails = cd, cdmSchema = cdmSchema, syntheaSchema = syntheaSchema, cdmVersion = cdmVersion, syntheaVersion = syntheaVersion)

    Simulating Data with Synthea @@ -195,7 +196,7 @@

    Developers

    -

    Site built with pkgdown 2.0.0.

    +

    Site built with pkgdown 2.0.7.

    diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 743cb19..ce6f65d 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -1,5 +1,5 @@ -pandoc: 2.14.0.3 -pkgdown: 2.0.0 +pandoc: 3.1.1 +pkgdown: 2.0.7 pkgdown_sha: ~ articles: Condition_occurrence: Condition_occurrence.html @@ -10,5 +10,5 @@ articles: person: person.html procedure_occurrence: procedure_occurrence.html visit_occurrence: visit_occurrence.html -last_built: 2021-12-22T20:18Z +last_built: 2023-11-29T18:28Z diff --git a/docs/reference/CreateCDMIndexAndConstraintScripts.html b/docs/reference/CreateCDMIndexAndConstraintScripts.html index 4333da2..94e99a8 100644 --- a/docs/reference/CreateCDMIndexAndConstraintScripts.html +++ b/docs/reference/CreateCDMIndexAndConstraintScripts.html @@ -26,7 +26,7 @@ Reference
  • -

    pkgdown 2.0.0.

    +

    Site built with pkgdown 2.0.7.

    diff --git a/docs/reference/CreateCDMIndices.html b/docs/reference/CreateCDMIndices.html new file mode 100644 index 0000000..2055f9a --- /dev/null +++ b/docs/reference/CreateCDMIndices.html @@ -0,0 +1,143 @@ + +Create Indices on Common Data Model Tables. — CreateCDMIndices • ETLSyntheaBuilder + + +
    +
    + + + +
    +
    +
    +

    Create Indices on Common Data Model Tables.

    + + +
    + +
    +

    This function creates indices for the tables in the CDM.

    +
    + +
    + 
    CreateCDMIndices(
+  connectionDetails,
+  cdmSchema,
+  cdmVersion,
+  outputFolder = NULL,
+  sqlOnly = FALSE
+)
    +
    + +
    +

    Arguments

    +
    connectionDetails
    +

    An R object of type
    connectionDetails created using the +function createConnectionDetails in the +DatabaseConnector package.

    + + +
    cdmSchema
    +

    The name of the CDM database schema. Requires read and write permissions to this database. On SQL +Server, this should specifiy both the database and the schema, +so for example 'cdm_instance.dbo'.

    + + +
    cdmVersion
    +

    Your CDM version. Currently "5.3" and "5.4" are supported.

    + + +
    outputFolder
    +

    Location of the SQL scripts if sqlOnly = TRUE. Default is NULL.

    + + +
    sqlOnly
    +

    A boolean that determines whether to create the indices or generate a SQL scripts Default is FALSE.

    + +
    +
    +

    Details

    +

    This function creates the indices specified by the function CommonDataModel::writeIndex(). + Supported CDM versions and db dialects are determined by CommonDataModel::listSupportedVersions() + and CommonDataModel::listSupportedDialects(), respectively.

    +
    + +
    + +
    + + +
    +

    Developed by Anthony Molinaro.

    +
    + +
    +

    Site built with pkgdown 2.0.7.

    +
    + +
    + + + + + + + + diff --git a/docs/reference/CreateCDMTables.html b/docs/reference/CreateCDMTables.html index a7dfbbe..2c3b884 100644 --- a/docs/reference/CreateCDMTables.html +++ b/docs/reference/CreateCDMTables.html @@ -26,7 +26,7 @@ Reference

  • - @@ -112,7 +135,7 @@

    Details

    -

    Site built with pkgdown 2.0.0.

    +

    Site built with pkgdown 2.0.7.

    diff --git a/docs/reference/CreateSyntheaTables.html b/docs/reference/CreateSyntheaTables.html index 78f9f2e..e9dcb28 100644 --- a/docs/reference/CreateSyntheaTables.html +++ b/docs/reference/CreateSyntheaTables.html @@ -26,7 +26,7 @@ Reference
  • -

    pkgdown 2.0.0.

    +

    Site built with pkgdown 2.0.7.

    diff --git a/docs/reference/CreateVisitRollupTables.html b/docs/reference/CreateVisitRollupTables.html index 3cd4fc2..1e2b76b 100644 --- a/docs/reference/CreateVisitRollupTables.html +++ b/docs/reference/CreateVisitRollupTables.html @@ -26,7 +26,7 @@ Reference
  • -

    LoadSyntheaTables(), +

    This function assumes
    createCDMTables(),
    createSyntheaTables(),
    LoadSyntheaTables(), have all been run and the Vocabulary has been loaded.

    @@ -115,7 +132,7 @@

    Details

    -

    Site built with pkgdown 2.0.0.

    +

    Site built with pkgdown 2.0.7.

    diff --git a/docs/reference/CreateVocabMapTables.html b/docs/reference/CreateVocabMapTables.html index e4f1682..58cb830 100644 --- a/docs/reference/CreateVocabMapTables.html +++ b/docs/reference/CreateVocabMapTables.html @@ -26,7 +26,7 @@ Reference
  • -

    pkgdown 2.0.0.

    +

    Site built with pkgdown 2.0.7.

    diff --git a/docs/reference/DropEventTables.html b/docs/reference/DropEventTables.html index 798a40e..a57e455 100644 --- a/docs/reference/DropEventTables.html +++ b/docs/reference/DropEventTables.html @@ -1,5 +1,5 @@ -Drop OMOP CDM Tables. — DropEventTables • ETLSyntheaBuilderDrop OMOP Event Tables. — DropEventTables • ETLSyntheaBuilder @@ -26,7 +26,7 @@ Reference
  • -

    pkgdown 2.0.0.

    +

    Site built with pkgdown 2.0.7.

    diff --git a/docs/reference/DropMapAndRollupTables.html b/docs/reference/DropMapAndRollupTables.html index a4b7c99..1726570 100644 --- a/docs/reference/DropMapAndRollupTables.html +++ b/docs/reference/DropMapAndRollupTables.html @@ -26,7 +26,7 @@ Reference
  • -

    CreateVocabMapTables() and
    CreateVisitRollupTables()

    -
    Usage,
    DropMapAndRollupTables (connectionDetails, cdmSchema)
    +
    + 
    DropMapAndRollupTables(connectionDetails, cdmSchema)
    +

    Arguments

    @@ -82,11 +84,14 @@

    Arguments

    An R object of type
    connectionDetails created using the function createConnectionDetails in the DatabaseConnector package.

    + +
    cdmSchema

    The name of the database schema that will contain the Vocab mapping tables. Requires read and write permissions to this database. On SQL Server, this should specifiy both the database and the schema, so for example 'cdm_instance.dbo'.

    +

    Details

    @@ -105,7 +110,7 @@

    Details

    -

    Site built with pkgdown 2.0.0.

    +

    Site built with pkgdown 2.0.7.

    diff --git a/docs/reference/DropSyntheaTables.html b/docs/reference/DropSyntheaTables.html index 0cf0be5..c0da680 100644 --- a/docs/reference/DropSyntheaTables.html +++ b/docs/reference/DropSyntheaTables.html @@ -26,7 +26,7 @@ Reference
  • -

    pkgdown 2.0.0.

    +

    Site built with pkgdown 2.0.7.

    diff --git a/docs/reference/DropVocabTables.html b/docs/reference/DropVocabTables.html index 68d569c..e9552d1 100644 --- a/docs/reference/DropVocabTables.html +++ b/docs/reference/DropVocabTables.html @@ -26,7 +26,7 @@ Reference
  • -

    pkgdown 2.0.0.

    +

    Site built with pkgdown 2.0.7.

    diff --git a/docs/reference/ETLSyntheaBuilder-package.html b/docs/reference/ETLSyntheaBuilder-package.html new file mode 100644 index 0000000..b674e09 --- /dev/null +++ b/docs/reference/ETLSyntheaBuilder-package.html @@ -0,0 +1,102 @@ + +ETLSyntheaBuilder: A Builder for Converting the Synthea Data to the OMOP CDM — ETLSyntheaBuilder-package • ETLSyntheaBuilder + + +
    +
    + + + +
    +
    +
    +

    ETLSyntheaBuilder: A Builder for Converting the Synthea Data to the OMOP CDM

    + + +
    + +
    +

    ETL and Builder to convert Synthea Data to the OMOP CDM. Staring with csv files for an OMOP Vocabulary and csv files for Synthea, this package creates database tables from these csv files and maps them correctly to create a full functional OMOP CDM from Synthea. As the CDM Vocabulary can be quite large, there is the option to copy the vocabulary from another schema that already has it loaded. This package assumes an RDBMS exists to which you have read/write access.

    +
    + + + +
    + +
    + + +
    +

    Developed by Anthony Molinaro.

    +
    + +
    +

    Site built with pkgdown 2.0.7.

    +
    + +
    + + + + + + + + diff --git a/docs/reference/LoadEventTables.html b/docs/reference/LoadEventTables.html index 458fe9a..3dd276c 100644 --- a/docs/reference/LoadEventTables.html +++ b/docs/reference/LoadEventTables.html @@ -26,7 +26,7 @@ Reference
  • -

    pkgdown 2.0.0.

    +

    Site built with pkgdown 2.0.7.

    diff --git a/docs/reference/LoadSyntheaTables.html b/docs/reference/LoadSyntheaTables.html index 16a7a70..e8ecace 100644 --- a/docs/reference/LoadSyntheaTables.html +++ b/docs/reference/LoadSyntheaTables.html @@ -26,7 +26,7 @@ Reference
  • -

    pkgdown 2.0.0.

    +

    Site built with pkgdown 2.0.7.

    diff --git a/docs/reference/LoadVocabFromCsv.html b/docs/reference/LoadVocabFromCsv.html index 9475b8b..a31c5b6 100644 --- a/docs/reference/LoadVocabFromCsv.html +++ b/docs/reference/LoadVocabFromCsv.html @@ -26,7 +26,7 @@ Reference
  • -

    pkgdown 2.0.0.

    +

    Site built with pkgdown 2.0.7.

    diff --git a/docs/reference/LoadVocabFromSchema.html b/docs/reference/LoadVocabFromSchema.html index 97e5fd6..e124e50 100644 --- a/docs/reference/LoadVocabFromSchema.html +++ b/docs/reference/LoadVocabFromSchema.html @@ -26,7 +26,7 @@ Reference
  • -

    pkgdown 2.0.0.

    +

    Site built with pkgdown 2.0.7.

    diff --git a/docs/reference/TruncateEventTables.html b/docs/reference/TruncateEventTables.html index 7e8cc3d..4a4e970 100644 --- a/docs/reference/TruncateEventTables.html +++ b/docs/reference/TruncateEventTables.html @@ -1,5 +1,5 @@ -Truncate Non-Vocabulary CDM Tables. — TruncateEventTables • ETLSyntheaBuilderTruncate Event Tables. — TruncateEventTables • ETLSyntheaBuilder @@ -26,7 +26,7 @@ Reference
  • -

    pkgdown 2.0.0.

    +

    Site built with pkgdown 2.0.7.

    diff --git a/docs/reference/TruncateVocabTables.html b/docs/reference/TruncateVocabTables.html index 17c72a2..ebf417b 100644 --- a/docs/reference/TruncateVocabTables.html +++ b/docs/reference/TruncateVocabTables.html @@ -26,7 +26,7 @@ Reference
  • -

    pkgdown 2.0.0.

    +

    Site built with pkgdown 2.0.7.

    diff --git a/docs/reference/backupCDM.html b/docs/reference/backupCDM.html index 491274e..0286d38 100644 --- a/docs/reference/backupCDM.html +++ b/docs/reference/backupCDM.html @@ -26,7 +26,7 @@ Reference
  • -

    pkgdown 2.0.0.

    +

    Site built with pkgdown 2.0.7.

    diff --git a/docs/reference/createPrunedTables.html b/docs/reference/createPrunedTables.html index fc1da30..3e2b42f 100644 --- a/docs/reference/createPrunedTables.html +++ b/docs/reference/createPrunedTables.html @@ -27,7 +27,7 @@ Reference
  • -

    pkgdown 2.0.0.

    +

    Site built with pkgdown 2.0.7.

    diff --git a/docs/reference/exportToSQLite.html b/docs/reference/exportToSQLite.html index 605e66f..85a0876 100644 --- a/docs/reference/exportToSQLite.html +++ b/docs/reference/exportToSQLite.html @@ -26,7 +26,7 @@ Reference
  • -

    pkgdown 2.0.0.

    +

    Site built with pkgdown 2.0.7.

    diff --git a/docs/reference/getEventConceptId.html b/docs/reference/getEventConceptId.html index 9d209e6..b5d8eaf 100644 --- a/docs/reference/getEventConceptId.html +++ b/docs/reference/getEventConceptId.html @@ -26,7 +26,7 @@ Reference
  • -

    pkgdown 2.0.0.

    +

    Site built with pkgdown 2.0.7.

    diff --git a/docs/reference/index.html b/docs/reference/index.html index b9c0141..7c3a51d 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -26,7 +26,7 @@ Reference
  • -

    • - - - + - + @@ -101,9 +97,9 @@

    All functions

    - + @@ -116,14 +112,6 @@

    All functions DropVocabTables()

    - - - - @@ -141,21 +129,37 @@

    All functions

    - + - + - + - + + + + + + + + +
    person_id patientMap by mapping person.person_source_value to patient. Find person.person_id by mapping encouters.patient to person.person_source_value.Map by mapping person.person_source_value to patient. Find +person.person_id by mapping encouters.patient to +person.person_source_value.
    visit_concept_id encounterclassWhen encounterclass is ‘emergency’ or ‘urgentcare’ then set to 9203. When encounterclass is ‘ambulatory’, ‘wellness’, or ‘outpatient’ then set to 9202. When encounterclass is ‘inpatient’ then set to 9201. Otherwise set to 0.When encounterclass is ‘emergency’ or ‘urgentcare’ then set to 9203. +When encounterclass is ‘ambulatory’, ‘wellness’, or ‘outpatient’ then +set to 9202. When encounterclass is ‘inpatient’ then set to 9201. +Otherwise set to 0.
    -

    backupCDM()

    -

    Backup Vocabulary and Event tables before pruning.

    CreateCDMIndexAndConstraintScripts()

    Create Index and Constraint DDL SQL scripts for CDM tables on rdbms that support these features.
    -

    CreateCDMTables()

    +

    CreateCDMIndices()

    Create Common Data Model Tables.

    Create Indices on Common Data Model Tables.
    -

    createPrunedTables()

    +

    CreateCDMTables()

    Create pruned CDM and Vocab tables.

    Create Common Data Model Tables.

    CreateSyntheaTables()

    Create Vocabulary Mapping Tables.
    -

    DropCDMTables()

    +

    DropEventTables()

    Drop OMOP CDM Tables.

    Drop OMOP Event Tables.

    DropMapAndRollupTables()

    Drop Vocabulary Tables.

    -

    exportToSQLite()

    -

    Export a CDM (Vocabulary and Event tables) into a SQLite Database.

    -

    getEventConceptId()

    -

    Get All Concept_ids In All Event Tables.

    LoadEventTables()

    Load Vocabulary Tables From a Preexisting Schema.
    -

    pruneCDM()

    +

    TruncateEventTables()

    Prune a CDM.

    Truncate Event Tables.
    -

    restoreCDMTables()

    +

    TruncateVocabTables()

    Restore the CDM (undo the pruning).

    Truncate Vocabulary Tables.
    -

    TruncateCDMTables()

    +

    backupCDM()

    Truncate Non-Vocabulary CDM Tables.

    Backup Vocabulary and Event tables before pruning.
    -

    TruncateVocabTables()

    +

    createPrunedTables()

    Truncate Vocabulary Tables.

    Create pruned CDM and Vocab tables.

    +

    exportToSQLite()

    +

    Export a CDM (Vocabulary and Event tables) into a SQLite Database.

    +

    getEventConceptId()

    +

    Get All Concept_ids In All Event Tables.

    +

    pruneCDM()

    +

    Prune a CDM.

    +

    restoreCDMTables()

    +

    Restore the CDM (undo the pruning).
    diff --git a/docs/reference/pruneCDM.html b/docs/reference/pruneCDM.html index 57c53f4..635d419 100644 --- a/docs/reference/pruneCDM.html +++ b/docs/reference/pruneCDM.html @@ -26,7 +26,7 @@ Reference
  • -

    pkgdown 2.0.0.

    +

    Site built with pkgdown 2.0.7.

    diff --git a/docs/reference/restoreCDMTables.html b/docs/reference/restoreCDMTables.html index 2f7bada..3ff6507 100644 --- a/docs/reference/restoreCDMTables.html +++ b/docs/reference/restoreCDMTables.html @@ -26,7 +26,7 @@ Reference
  • -

    pkgdown 2.0.0.

    +

    Site built with pkgdown 2.0.7.

    diff --git a/docs/sitemap.xml b/docs/sitemap.xml index ff310ab..fe38e43 100644 --- a/docs/sitemap.xml +++ b/docs/sitemap.xml @@ -4,73 +4,73 @@ /404.html - /articles/Condition_occurrence.html + /Condition_occurrence.html - /articles/Drug_exposure.html + /Drug_exposure.html - /articles/index.html + /Measurement.html - /articles/Measurement.html + /Observation.html - /articles/observation.html + /Observation_period.html - /articles/observation_period.html + /Person.html - /articles/person.html + /Procedure_occurrence.html - /articles/procedure_occurrence.html + /Visit_occurrence.html - /articles/visit_occurrence.html + /articles/Condition_occurrence.html - /authors.html + /articles/Drug_exposure.html - /Condition_occurrence.html + /articles/Measurement.html - /Drug_exposure.html + /articles/index.html - /index.html + /articles/observation.html - /Measurement.html + /articles/observation_period.html - /Observation.html + /articles/person.html - /Observation_period.html + /articles/procedure_occurrence.html - /Person.html + /articles/visit_occurrence.html - /Procedure_occurrence.html + /authors.html - /readme.html + /index.html - /reference/backupCDM.html + /readme.html /reference/CreateCDMIndexAndConstraintScripts.html - /reference/CreateCDMTables.html + /reference/CreateCDMIndices.html - /reference/createPrunedTables.html + /reference/CreateCDMTables.html /reference/CreateSyntheaTables.html @@ -94,13 +94,7 @@ /reference/DropVocabTables.html - /reference/exportToSQLite.html - - - /reference/getEventConceptId.html - - - /reference/index.html + /reference/ETLSyntheaBuilder-package.html /reference/LoadEventTables.html @@ -115,18 +109,30 @@ /reference/LoadVocabFromSchema.html - /reference/pruneCDM.html + /reference/TruncateEventTables.html - /reference/restoreCDMTables.html + /reference/TruncateVocabTables.html - /reference/TruncateEventTables.html + /reference/backupCDM.html - /reference/TruncateVocabTables.html + /reference/createPrunedTables.html - /Visit_occurrence.html + /reference/exportToSQLite.html + + + /reference/getEventConceptId.html + + + /reference/index.html + + + /reference/pruneCDM.html + + + /reference/restoreCDMTables.html