From 04d02a650f5a74320ccaa4712a66b489bf0c9571 Mon Sep 17 00:00:00 2001 From: Evanette Burrows Date: Fri, 29 Dec 2023 12:26:47 -0500 Subject: [PATCH 01/10] Add support for loading synthea v3.1 and v3.2 --- R/CreateSyntheaTables.r | 8 +- R/LoadSyntheaTables.r | 10 +- .../v310/create_synthea_tables.sql | 326 ++++++++++++++++++ .../v320/create_synthea_tables.sql | 326 ++++++++++++++++++ 4 files changed, 666 insertions(+), 4 deletions(-) create mode 100644 inst/sql/sql_server/synthea_version/v310/create_synthea_tables.sql create mode 100644 inst/sql/sql_server/synthea_version/v320/create_synthea_tables.sql diff --git a/R/CreateSyntheaTables.r b/R/CreateSyntheaTables.r index 173c740..df7e522 100644 --- a/R/CreateSyntheaTables.r +++ b/R/CreateSyntheaTables.r @@ -10,7 +10,7 @@ #' Server, this should specify both the database and the schema, #' so for example 'cdm_instance.dbo'. #' @param syntheaVersion The version of Synthea used to generate the csv files. -#' Currently "2.7.0" and "3.0.0" are is supported. +#' Currently "2.7.0", "3.0.0", "3.1.0", and "3.2.0" are is supported. #' #'@export @@ -25,8 +25,12 @@ CreateSyntheaTables <- sqlFilePath <- "synthea_version/v270" else if (syntheaVersion == "3.0.0") sqlFilePath <- "synthea_version/v300" + else if (syntheaVersion == "3.1.0") + sqlFilePath <- "synthea_version/v310" + else if (syntheaVersion == "3.2.0") + sqlFilePath <- "synthea_version/v320" else - stop("Invalid synthea version specified. Currently \"2.7.0\" and \"3.0.0\" are supported.") + stop("Invalid synthea version specified. Currently \"2.7.0\", \"3.0.0\", \"3.1.0\" and \"3.2.0\" are supported.") sqlFilename <- paste0(sqlFilePath, "/", "create_synthea_tables.sql") diff --git a/R/LoadSyntheaTables.r b/R/LoadSyntheaTables.r index ca356bb..699df3c 100644 --- a/R/LoadSyntheaTables.r +++ b/R/LoadSyntheaTables.r @@ -11,7 +11,7 @@ #' \cr\code{./run_synthea -p 1000} #' #' You can enable csv records in src/main/resources/synthea.properties by setting exporter.csv.export = true. -#' As of the time of this writing the csv files can be found at synthe/output/csv. +#' As of the time of this writing the csv files can be found at synthea/output/csv. #' For more details: \href{https://github.com/synthetichealth/synthea/wiki/Basic-Setup-and-Running}{Synthea Basic Setup} #' #' @param connectionDetails An R object of type\cr\code{connectionDetails} created using the @@ -35,7 +35,7 @@ LoadSyntheaTables <- { csvList <- list.files(syntheaFileLoc, pattern = "*.csv") - + conn <- DatabaseConnector::connect(connectionDetails) for (csv in csvList) { @@ -60,6 +60,12 @@ LoadSyntheaTables <- if ("DATE" %in% colnames(syntheaTable)) syntheaTable$DATE <- as.Date(syntheaTable$DATE, format = "%Y-%m-%d") + if ("START_DATE" %in% colnames(syntheaTable)) + syntheaTable$START_DATE <- + as.Date(syntheaTable$START_DATE, format = "%Y-%m-%d") + if ("END_DATE" %in% colnames(syntheaTable)) + syntheaTable$END_DATE <- + as.Date(syntheaTable$END_DATE, format = "%Y-%m-%d") if ("BIRTHDATE" %in% colnames(syntheaTable)) syntheaTable$BIRTHDATE <- as.Date(syntheaTable$BIRTHDATE, format = "%Y-%m-%d") diff --git a/inst/sql/sql_server/synthea_version/v310/create_synthea_tables.sql b/inst/sql/sql_server/synthea_version/v310/create_synthea_tables.sql new file mode 100644 index 0000000..984c16b --- /dev/null +++ b/inst/sql/sql_server/synthea_version/v310/create_synthea_tables.sql @@ -0,0 +1,326 @@ + +--HINT DISTRIBUTE_ON_RANDOM +create table @synthea_schema.allergies ( +start date, +stop date, +patient varchar(1000), +encounter varchar(1000), +code varchar(100), +system varchar(255), +description varchar(255), +"type" varchar(255), +category varchar(255), +reaction1 varchar(255), +description1 varchar(255), +severity1 varchar(255), +reaction2 varchar(255), +description2 varchar(255), +severity2 varchar(255) +); + +--HINT DISTRIBUTE_ON_RANDOM +create table @synthea_schema.careplans ( +id varchar(1000), +start date, +stop date, +patient varchar(1000), +encounter varchar(1000), +code varchar(100), +description varchar(255), +reasoncode varchar(255), +reasondescription varchar(255) +); + +--HINT DISTRIBUTE_ON_RANDOM +create table @synthea_schema.conditions ( +start date, +stop date, +patient varchar(1000), +encounter varchar(1000), +code varchar(100), +description varchar(255) +); + +--HINT DISTRIBUTE_ON_RANDOM +create table @synthea_schema.encounters ( +id varchar(1000), +start date, +stop date, +patient varchar(1000), +organization varchar(1000), +provider varchar(1000), +payer varchar(1000), +encounterclass varchar(1000), +code varchar(100), +description varchar(255), +base_encounter_cost numeric, +total_claim_cost numeric, +payer_coverage numeric, +reasoncode varchar(100), +reasondescription varchar(255) +); + +--HINT DISTRIBUTE_ON_RANDOM +create table @synthea_schema.immunizations ( +"date" date, +patient varchar(1000), +encounter varchar(1000), +code varchar(100), +description varchar(255), +base_cost numeric +); + +--HINT DISTRIBUTE_ON_RANDOM +create table @synthea_schema.imaging_studies ( +id varchar(1000), +"date" date, +patient varchar(1000), +encounter varchar(1000), +series_uid varchar(1000), +bodysite_code varchar(100), +bodysite_description varchar(255), +modality_code varchar(100), +modality_description varchar(255), +instance_uid varchar(1000), +SOP_code varchar(100), +SOP_description varchar(255), +procedure_code varchar(255) +); + +--HINT DISTRIBUTE_ON_RANDOM +create table @synthea_schema.medications ( +start date, +stop date, +patient varchar(1000), +payer varchar(1000), +encounter varchar(1000), +code varchar(100), +description varchar(1000), +base_cost numeric, +payer_coverage numeric, +dispenses int, +totalcost numeric, +reasoncode varchar(100), +reasondescription varchar(255) +); + +--HINT DISTRIBUTE_ON_RANDOM +create table @synthea_schema.observations ( +"date" date, +patient varchar(1000), +encounter varchar(1000), +category varchar(1000), +code varchar(100), +description varchar(255), +value varchar(1000), +units varchar(100), +"type" varchar(100) +); + +--HINT DISTRIBUTE_ON_RANDOM +create table @synthea_schema.organizations ( +id varchar(1000), +"name" varchar(1000), +address varchar(1000), +city varchar(100), +state varchar(100), +zip varchar(100), +lat numeric, +lon numeric, +phone varchar(100), +revenue numeric, +utilization varchar(100) +); + +--HINT DISTRIBUTE_ON_RANDOM +create table @synthea_schema.patients ( +id varchar(1000), +birthdate date, +deathdate date, +ssn varchar(100), +drivers varchar(100), +passport varchar(100), +prefix varchar(100), +first varchar(100), +last varchar(100), +suffix varchar(100), +maiden varchar(100), +marital varchar(100), +race varchar(100), +ethnicity varchar(100), +gender varchar(100), +birthplace varchar(100), +address varchar(100), +city varchar(100), +state varchar(100), +county varchar(100), +fips varchar(100), +zip varchar(100), +lat numeric, +lon numeric, +healthcare_expenses numeric, +healthcare_coverage numeric, +income int +); + +--HINT DISTRIBUTE_ON_RANDOM +create table @synthea_schema.procedures ( +start date, +stop date, +patient varchar(1000), +encounter varchar(1000), +code varchar(100), +description varchar(255), +base_cost numeric, +reasoncode varchar(1000), +reasondescription varchar(1000) +); + +--HINT DISTRIBUTE_ON_RANDOM +create table @synthea_schema.providers ( +id varchar(1000), +organization varchar(1000), +"name" varchar(100), +gender varchar(100), +speciality varchar(100), +address varchar(255), +city varchar(100), +state varchar(100), +zip varchar(100), +lat numeric, +lon numeric, +encounters int, +"procedures" int +); + +--HINT DISTRIBUTE_ON_RANDOM +create table @synthea_schema.devices ( +start date, +stop date, +patient varchar(1000), +encounter varchar(1000), +code varchar(100), +description varchar(255), +udi varchar(255) +); + +--HINT DISTRIBUTE_ON_RANDOM +create table @synthea_schema.claims ( + id varchar(1000), + patientid varchar(1000), + providerid varchar(1000), + primarypatientinsuranceid varchar(1000), + secondarypatientinsuranceid varchar(1000), + departmentid varchar(1000), + patientdepartmentid varchar(1000), + diagnosis1 varchar(1000), + diagnosis2 varchar(1000), + diagnosis3 varchar(1000), + diagnosis4 varchar(1000), + diagnosis5 varchar(1000), + diagnosis6 varchar(1000), + diagnosis7 varchar(1000), + diagnosis8 varchar(1000), + referringproviderid varchar(1000), + appointmentid varchar(1000), + currentillnessdate date, + servicedate date, + supervisingproviderid varchar(1000), + status1 varchar(1000), + status2 varchar(1000), + statusp varchar(1000), + outstanding1 numeric, + outstanding2 numeric, + outstandingp numeric, + lastbilleddate1 date, + lastbilleddate2 date, + lastbilleddatep date, + healthcareclaimtypeid1 numeric, + healthcareclaimtypeid2 numeric +); + +--HINT DISTRIBUTE_ON_RANDOM +create table @synthea_schema.claims_transactions ( + id varchar(1000), + claimid varchar(1000), + chargeid numeric, + patientid varchar(1000), + "type" varchar(1000), + amount numeric, + method varchar(1000), + fromdate date, + todate date, + placeofservice varchar(1000), + procedurecode varchar(1000), + modifier1 varchar(1000), + modifier2 varchar(1000), + diagnosisref1 numeric, + diagnosisref2 numeric, + diagnosisref3 numeric, + diagnosisref4 numeric, + units numeric, + departmentid numeric, + notes varchar(1000), + unitamount numeric, + transferoutid numeric, + transfertype varchar(1000), + payments numeric, + adjustments numeric, + transfers numeric, + outstanding numeric, + appointmentid varchar(1000), + linenote varchar(1000), + patientinsuranceid varchar(1000), + feescheduleid numeric, + providerid varchar(1000), + supervisingproviderid varchar(1000) +); + +--HINT DISTRIBUTE_ON_RANDOM +create table @synthea_schema.payer_transitions ( + patient varchar(1000), + memberid varchar(1000), + start_date date, + end_date date, + payer varchar(1000), + secondary_payer varchar(1000), + plan_ownership varchar(1000), + owner_name varchar(1000) +); + +--HINT DISTRIBUTE_ON_RANDOM +create table @synthea_schema.payers ( + id varchar(1000), + "name" varchar(1000), + ownership varchar NULL, + address varchar(1000), + city varchar(1000), + state_headquartered varchar(1000), + zip varchar(1000), + phone varchar(1000), + amount_covered numeric, + amount_uncovered numeric, + revenue numeric, + covered_encounters numeric, + uncovered_encounters numeric, + covered_medications numeric, + uncovered_medications numeric, + covered_procedures numeric, + uncovered_procedures numeric, + covered_immunizations numeric, + uncovered_immunizations numeric, + unique_customers numeric, + qols_avg numeric, + member_months numeric +); + +--HINT DISTRIBUTE_ON_RANDOM +create table @synthea_schema.supplies ( + "date" date, + patient varchar(1000), + encounter varchar(1000), + code varchar(1000), + description varchar(1000), + quantity numeric +); + diff --git a/inst/sql/sql_server/synthea_version/v320/create_synthea_tables.sql b/inst/sql/sql_server/synthea_version/v320/create_synthea_tables.sql new file mode 100644 index 0000000..984c16b --- /dev/null +++ b/inst/sql/sql_server/synthea_version/v320/create_synthea_tables.sql @@ -0,0 +1,326 @@ + +--HINT DISTRIBUTE_ON_RANDOM +create table @synthea_schema.allergies ( +start date, +stop date, +patient varchar(1000), +encounter varchar(1000), +code varchar(100), +system varchar(255), +description varchar(255), +"type" varchar(255), +category varchar(255), +reaction1 varchar(255), +description1 varchar(255), +severity1 varchar(255), +reaction2 varchar(255), +description2 varchar(255), +severity2 varchar(255) +); + +--HINT DISTRIBUTE_ON_RANDOM +create table @synthea_schema.careplans ( +id varchar(1000), +start date, +stop date, +patient varchar(1000), +encounter varchar(1000), +code varchar(100), +description varchar(255), +reasoncode varchar(255), +reasondescription varchar(255) +); + +--HINT DISTRIBUTE_ON_RANDOM +create table @synthea_schema.conditions ( +start date, +stop date, +patient varchar(1000), +encounter varchar(1000), +code varchar(100), +description varchar(255) +); + +--HINT DISTRIBUTE_ON_RANDOM +create table @synthea_schema.encounters ( +id varchar(1000), +start date, +stop date, +patient varchar(1000), +organization varchar(1000), +provider varchar(1000), +payer varchar(1000), +encounterclass varchar(1000), +code varchar(100), +description varchar(255), +base_encounter_cost numeric, +total_claim_cost numeric, +payer_coverage numeric, +reasoncode varchar(100), +reasondescription varchar(255) +); + +--HINT DISTRIBUTE_ON_RANDOM +create table @synthea_schema.immunizations ( +"date" date, +patient varchar(1000), +encounter varchar(1000), +code varchar(100), +description varchar(255), +base_cost numeric +); + +--HINT DISTRIBUTE_ON_RANDOM +create table @synthea_schema.imaging_studies ( +id varchar(1000), +"date" date, +patient varchar(1000), +encounter varchar(1000), +series_uid varchar(1000), +bodysite_code varchar(100), +bodysite_description varchar(255), +modality_code varchar(100), +modality_description varchar(255), +instance_uid varchar(1000), +SOP_code varchar(100), +SOP_description varchar(255), +procedure_code varchar(255) +); + +--HINT DISTRIBUTE_ON_RANDOM +create table @synthea_schema.medications ( +start date, +stop date, +patient varchar(1000), +payer varchar(1000), +encounter varchar(1000), +code varchar(100), +description varchar(1000), +base_cost numeric, +payer_coverage numeric, +dispenses int, +totalcost numeric, +reasoncode varchar(100), +reasondescription varchar(255) +); + +--HINT DISTRIBUTE_ON_RANDOM +create table @synthea_schema.observations ( +"date" date, +patient varchar(1000), +encounter varchar(1000), +category varchar(1000), +code varchar(100), +description varchar(255), +value varchar(1000), +units varchar(100), +"type" varchar(100) +); + +--HINT DISTRIBUTE_ON_RANDOM +create table @synthea_schema.organizations ( +id varchar(1000), +"name" varchar(1000), +address varchar(1000), +city varchar(100), +state varchar(100), +zip varchar(100), +lat numeric, +lon numeric, +phone varchar(100), +revenue numeric, +utilization varchar(100) +); + +--HINT DISTRIBUTE_ON_RANDOM +create table @synthea_schema.patients ( +id varchar(1000), +birthdate date, +deathdate date, +ssn varchar(100), +drivers varchar(100), +passport varchar(100), +prefix varchar(100), +first varchar(100), +last varchar(100), +suffix varchar(100), +maiden varchar(100), +marital varchar(100), +race varchar(100), +ethnicity varchar(100), +gender varchar(100), +birthplace varchar(100), +address varchar(100), +city varchar(100), +state varchar(100), +county varchar(100), +fips varchar(100), +zip varchar(100), +lat numeric, +lon numeric, +healthcare_expenses numeric, +healthcare_coverage numeric, +income int +); + +--HINT DISTRIBUTE_ON_RANDOM +create table @synthea_schema.procedures ( +start date, +stop date, +patient varchar(1000), +encounter varchar(1000), +code varchar(100), +description varchar(255), +base_cost numeric, +reasoncode varchar(1000), +reasondescription varchar(1000) +); + +--HINT DISTRIBUTE_ON_RANDOM +create table @synthea_schema.providers ( +id varchar(1000), +organization varchar(1000), +"name" varchar(100), +gender varchar(100), +speciality varchar(100), +address varchar(255), +city varchar(100), +state varchar(100), +zip varchar(100), +lat numeric, +lon numeric, +encounters int, +"procedures" int +); + +--HINT DISTRIBUTE_ON_RANDOM +create table @synthea_schema.devices ( +start date, +stop date, +patient varchar(1000), +encounter varchar(1000), +code varchar(100), +description varchar(255), +udi varchar(255) +); + +--HINT DISTRIBUTE_ON_RANDOM +create table @synthea_schema.claims ( + id varchar(1000), + patientid varchar(1000), + providerid varchar(1000), + primarypatientinsuranceid varchar(1000), + secondarypatientinsuranceid varchar(1000), + departmentid varchar(1000), + patientdepartmentid varchar(1000), + diagnosis1 varchar(1000), + diagnosis2 varchar(1000), + diagnosis3 varchar(1000), + diagnosis4 varchar(1000), + diagnosis5 varchar(1000), + diagnosis6 varchar(1000), + diagnosis7 varchar(1000), + diagnosis8 varchar(1000), + referringproviderid varchar(1000), + appointmentid varchar(1000), + currentillnessdate date, + servicedate date, + supervisingproviderid varchar(1000), + status1 varchar(1000), + status2 varchar(1000), + statusp varchar(1000), + outstanding1 numeric, + outstanding2 numeric, + outstandingp numeric, + lastbilleddate1 date, + lastbilleddate2 date, + lastbilleddatep date, + healthcareclaimtypeid1 numeric, + healthcareclaimtypeid2 numeric +); + +--HINT DISTRIBUTE_ON_RANDOM +create table @synthea_schema.claims_transactions ( + id varchar(1000), + claimid varchar(1000), + chargeid numeric, + patientid varchar(1000), + "type" varchar(1000), + amount numeric, + method varchar(1000), + fromdate date, + todate date, + placeofservice varchar(1000), + procedurecode varchar(1000), + modifier1 varchar(1000), + modifier2 varchar(1000), + diagnosisref1 numeric, + diagnosisref2 numeric, + diagnosisref3 numeric, + diagnosisref4 numeric, + units numeric, + departmentid numeric, + notes varchar(1000), + unitamount numeric, + transferoutid numeric, + transfertype varchar(1000), + payments numeric, + adjustments numeric, + transfers numeric, + outstanding numeric, + appointmentid varchar(1000), + linenote varchar(1000), + patientinsuranceid varchar(1000), + feescheduleid numeric, + providerid varchar(1000), + supervisingproviderid varchar(1000) +); + +--HINT DISTRIBUTE_ON_RANDOM +create table @synthea_schema.payer_transitions ( + patient varchar(1000), + memberid varchar(1000), + start_date date, + end_date date, + payer varchar(1000), + secondary_payer varchar(1000), + plan_ownership varchar(1000), + owner_name varchar(1000) +); + +--HINT DISTRIBUTE_ON_RANDOM +create table @synthea_schema.payers ( + id varchar(1000), + "name" varchar(1000), + ownership varchar NULL, + address varchar(1000), + city varchar(1000), + state_headquartered varchar(1000), + zip varchar(1000), + phone varchar(1000), + amount_covered numeric, + amount_uncovered numeric, + revenue numeric, + covered_encounters numeric, + uncovered_encounters numeric, + covered_medications numeric, + uncovered_medications numeric, + covered_procedures numeric, + uncovered_procedures numeric, + covered_immunizations numeric, + uncovered_immunizations numeric, + unique_customers numeric, + qols_avg numeric, + member_months numeric +); + +--HINT DISTRIBUTE_ON_RANDOM +create table @synthea_schema.supplies ( + "date" date, + patient varchar(1000), + encounter varchar(1000), + code varchar(1000), + description varchar(1000), + quantity numeric +); + From d064f84d15e3adbb29447cdeac30abe29996932f Mon Sep 17 00:00:00 2001 From: Evanette Burrows Date: Fri, 29 Dec 2023 12:32:52 -0500 Subject: [PATCH 02/10] Update package and documentation --- R/CreateMapAndRollupTables.r | 7 +++---- docs/pkgdown.yml | 2 +- docs/reference/CreateMapAndRollupTables.html | 6 +----- docs/reference/CreateSyntheaTables.html | 2 +- docs/reference/LoadSyntheaTables.html | 2 +- man/CreateMapAndRollupTables.Rd | 4 +--- man/CreateSyntheaTables.Rd | 2 +- man/LoadSyntheaTables.Rd | 2 +- man/createExtraIndices.Rd | 2 +- 9 files changed, 11 insertions(+), 18 deletions(-) diff --git a/R/CreateMapAndRollupTables.r b/R/CreateMapAndRollupTables.r index 77378c7..71ac7d6 100644 --- a/R/CreateMapAndRollupTables.r +++ b/R/CreateMapAndRollupTables.r @@ -19,12 +19,11 @@ #' so for example 'cdm_instance.dbo'. #' @param cdmVersion The version of your CDM. Currently "5.3" and "5.4". #' @param syntheaVersion The version of Synthea used to generate the csv files. -#' Currently "2.7.0" and "3.0.0" are supported. +#' Currently "2.7.0", "3.0.0", "3.1.0" and "3.2.0" are supported. #' @param cdmSourceName The source name to insert into the CDM_SOURCE table. Default is Synthea synthetic health database. #' @param cdmSourceAbbreviation The source abbreviation to insert into the CDM_SOURCE table. Default is Synthea. #' @param cdmHolder The holder to insert into the CDM_SOURCE table. Default is OHDSI #' @param cdmSourceDescription The description of the source data. Default is generic Synthea description. -#' @param createIndices A boolean that determines whether or not to create indices on CDM tables before the ETL. #' @param sqlOnly A boolean that determines whether or not to perform the load or generate SQL scripts. Default is FALSE. #' #'@export @@ -51,10 +50,10 @@ CreateMapAndRollupTables <- function(connectionDetails, stop("Unsupported CDM specified. Supported CDM versions are \"5.3\" and \"5.4\".") } - supportedSyntheaVersions <- c("2.7.0", "3.0.0") + supportedSyntheaVersions <- c("2.7.0", "3.0.0","3.1.0","3.2.0") if (!(syntheaVersion %in% supportedSyntheaVersions)) - stop("Invalid Synthea version specified. Currently \"2.7.0\" and \"3.0.0\" are supported.") + stop("Invalid Synthea version specified. Currently \"2.7.0\", \"3.0.0\",\"3.1.0\", and \"3.2.0\" are supported.") # Create Vocabulary mapping tables CreateVocabMapTables(connectionDetails, cdmSchema, cdmVersion, sqlOnly) diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 6c848e0..77fc03b 100644 --- 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: 2023-12-28T20:36Z +last_built: 2023-12-29T17:31Z diff --git a/docs/reference/CreateMapAndRollupTables.html b/docs/reference/CreateMapAndRollupTables.html index 9e9612b..c6e21be 100644 --- a/docs/reference/CreateMapAndRollupTables.html +++ b/docs/reference/CreateMapAndRollupTables.html @@ -138,7 +138,7 @@

Arguments

syntheaVersion

The version of Synthea used to generate the csv files. -Currently "2.7.0" and "3.0.0" are supported.

+Currently "2.7.0", "3.0.0", "3.1.0" and "3.2.0" are supported.

cdmSourceName
@@ -160,10 +160,6 @@

Arguments

sqlOnly

A boolean that determines whether or not to perform the load or generate SQL scripts. Default is FALSE.

- -
createIndices
-

A boolean that determines whether or not to create indices on CDM tables before the ETL.

-

Details

diff --git a/docs/reference/CreateSyntheaTables.html b/docs/reference/CreateSyntheaTables.html index 3af41c0..dc14d45 100644 --- a/docs/reference/CreateSyntheaTables.html +++ b/docs/reference/CreateSyntheaTables.html @@ -113,7 +113,7 @@

Arguments

syntheaVersion

The version of Synthea used to generate the csv files. -Currently "2.7.0" and "3.0.0" are is supported.

+Currently "2.7.0", "3.0.0", "3.1.0", and "3.2.0" are is supported.

diff --git a/docs/reference/LoadSyntheaTables.html b/docs/reference/LoadSyntheaTables.html index fd6c9c7..a366282 100644 --- a/docs/reference/LoadSyntheaTables.html +++ b/docs/reference/LoadSyntheaTables.html @@ -134,7 +134,7 @@

Details


./gradlew build check test
./run_synthea -p 1000

You can enable csv records in src/main/resources/synthea.properties by setting exporter.csv.export = true. - As of the time of this writing the csv files can be found at synthe/output/csv. + As of the time of this writing the csv files can be found at synthea/output/csv. For more details: Synthea Basic Setup

diff --git a/man/CreateMapAndRollupTables.Rd b/man/CreateMapAndRollupTables.Rd index aa0f651..b4732da 100644 --- a/man/CreateMapAndRollupTables.Rd +++ b/man/CreateMapAndRollupTables.Rd @@ -36,7 +36,7 @@ so for example 'cdm_instance.dbo'.} \item{cdmVersion}{The version of your CDM. Currently "5.3" and "5.4".} \item{syntheaVersion}{The version of Synthea used to generate the csv files. -Currently "2.7.0" and "3.0.0" are supported.} +Currently "2.7.0", "3.0.0", "3.1.0" and "3.2.0" are supported.} \item{cdmSourceName}{The source name to insert into the CDM_SOURCE table. Default is Synthea synthetic health database.} @@ -47,8 +47,6 @@ Currently "2.7.0" and "3.0.0" are supported.} \item{cdmSourceDescription}{The description of the source data. Default is generic Synthea description.} \item{sqlOnly}{A boolean that determines whether or not to perform the load or generate SQL scripts. Default is FALSE.} - -\item{createIndices}{A boolean that determines whether or not to create indices on CDM tables before the ETL.} } \description{ This function creates the vocabulary mapping and visit roll-up intermediate tables from created diff --git a/man/CreateSyntheaTables.Rd b/man/CreateSyntheaTables.Rd index 62382d7..03a4d72 100644 --- a/man/CreateSyntheaTables.Rd +++ b/man/CreateSyntheaTables.Rd @@ -17,7 +17,7 @@ Server, this should specify both the database and the schema, so for example 'cdm_instance.dbo'.} \item{syntheaVersion}{The version of Synthea used to generate the csv files. -Currently "2.7.0" and "3.0.0" are is supported.} +Currently "2.7.0", "3.0.0", "3.1.0", and "3.2.0" are is supported.} } \description{ This function creates all Synthea tables. diff --git a/man/LoadSyntheaTables.Rd b/man/LoadSyntheaTables.Rd index 7c22fe6..e5c9107 100644 --- a/man/LoadSyntheaTables.Rd +++ b/man/LoadSyntheaTables.Rd @@ -38,6 +38,6 @@ This function assumes \cr\code{createSyntheaTables()} has already been run. Add \cr\code{./run_synthea -p 1000} You can enable csv records in src/main/resources/synthea.properties by setting exporter.csv.export = true. - As of the time of this writing the csv files can be found at synthe/output/csv. + As of the time of this writing the csv files can be found at synthea/output/csv. For more details: \href{https://github.com/synthetichealth/synthea/wiki/Basic-Setup-and-Running}{Synthea Basic Setup} } diff --git a/man/createExtraIndices.Rd b/man/createExtraIndices.Rd index 158d861..f003b4e 100644 --- a/man/createExtraIndices.Rd +++ b/man/createExtraIndices.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/CreateExtraIndices.R +% Please edit documentation in R/createExtraIndices.R \name{CreateExtraIndices} \alias{CreateExtraIndices} \title{Create Optional Extra Indices for ETL Performance} From 0e377d2bf3ee438b3fa672b5b595fe3072e060c1 Mon Sep 17 00:00:00 2001 From: Evanette Burrows Date: Fri, 29 Dec 2023 14:03:40 -0500 Subject: [PATCH 03/10] Add synthea version to source description Resolves https://github.com/OHDSI/ETL-Synthea/issues/168 --- R/LoadEventTables.r | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/LoadEventTables.r b/R/LoadEventTables.r index a381fa9..491caba 100644 --- a/R/LoadEventTables.r +++ b/R/LoadEventTables.r @@ -233,7 +233,7 @@ LoadEventTables <- function(connectionDetails, cdm_source_name = cdmSourceName, cdm_source_abbreviation = cdmSourceAbbreviation, cdm_holder = cdmHolder, - source_description = cdmSourceDescription + source_description = paste("Synthea version: ",syntheaVersion," ",cdmSourceDescription) ) runStep(sql, fileQuery) From 4d46e237fa3cc8c073d9328e86bb5079675e0144 Mon Sep 17 00:00:00 2001 From: Evanette Burrows Date: Fri, 29 Dec 2023 14:25:25 -0500 Subject: [PATCH 04/10] Update load scripts and documentation --- R/LoadEventTables.r | 8 ++++---- .../cdm_version/v531/insert_payer_plan_period.sql | 7 ++++++- .../cdm_version/v540/insert_payer_plan_period.sql | 5 +++++ vignettes/Payer_plan_period.Rmd | 4 ++-- 4 files changed, 17 insertions(+), 7 deletions(-) diff --git a/R/LoadEventTables.r b/R/LoadEventTables.r index 491caba..568e07a 100644 --- a/R/LoadEventTables.r +++ b/R/LoadEventTables.r @@ -18,7 +18,7 @@ #' so for example 'cdm_instance.dbo'. #' @param cdmVersion The version of your CDM. Currently "5.3" and "5.4". #' @param syntheaVersion The version of Synthea used to generate the csv files. -#' Currently "2.7.0" and "3.0.0" are supported. +#' Currently "2.7.0","3.0.0","3.1.0" and "3.2.0" are supported. #' @param cdmSourceName The source name to insert into the CDM_SOURCE table. Default is Synthea synthetic health database. #' @param cdmSourceAbbreviation The source abbreviation to insert into the CDM_SOURCE table. Default is Synthea. #' @param cdmHolder The holder to insert into the CDM_SOURCE table. Default is OHDSI @@ -51,10 +51,10 @@ LoadEventTables <- function(connectionDetails, stop("Unsupported CDM specified. Supported CDM versions are \"5.3\" and \"5.4\".") } - supportedSyntheaVersions <- c("2.7.0", "3.0.0") + supportedSyntheaVersions <- c("2.7.0", "3.0.0","3.1.0","3.2.0") if (!(syntheaVersion %in% supportedSyntheaVersions)) - stop("Invalid Synthea version specified. Currently \"2.7.0\" and \"3.0.0\" are supported.") + stop("Invalid Synthea version specified. Currently \"2.7.0\", \"3.0.0\",\"3.1.0\", and \"3.2.0\" are supported.") if (createIndices) { print("Creating Indices on CDM Tables....") @@ -274,7 +274,7 @@ LoadEventTables <- function(connectionDetails, # cost if (syntheaVersion == "2.7.0") fileQuery <- "insert_cost_v270.sql" - else if (syntheaVersion == "3.0.0") + else if (syntheaVersion %in% c("3.0.0","3.1.0","3.2.0")) fileQuery <- "insert_cost_v300.sql" sql <- SqlRender::loadRenderTranslateSql( diff --git a/inst/sql/sql_server/cdm_version/v531/insert_payer_plan_period.sql b/inst/sql/sql_server/cdm_version/v531/insert_payer_plan_period.sql index b9b356b..bf95ea9 100644 --- a/inst/sql/sql_server/cdm_version/v531/insert_payer_plan_period.sql +++ b/inst/sql/sql_server/cdm_version/v531/insert_payer_plan_period.sql @@ -31,7 +31,12 @@ select ROW_NUMBER()OVER(ORDER BY pat.id, pt.start_year) payer_plan_period_id, CAST(pt.start_year AS DATE) payer_plan_period_start_date, CAST(pt.end_year AS DATE) payer_plan_period_end_date, } - + + {@synthea_version == "3.1.0" | @synthea_version == "3.2.0" } ? { + CAST(pt.start_date AS DATE) payer_plan_period_start_date, + CAST(pt.end_date AS DATE) payer_plan_period_end_date, + } + 0 payer_concept_id, pt.payer payer_source_value, 0 payer_source_concept_id, diff --git a/inst/sql/sql_server/cdm_version/v540/insert_payer_plan_period.sql b/inst/sql/sql_server/cdm_version/v540/insert_payer_plan_period.sql index b9b356b..06812e0 100644 --- a/inst/sql/sql_server/cdm_version/v540/insert_payer_plan_period.sql +++ b/inst/sql/sql_server/cdm_version/v540/insert_payer_plan_period.sql @@ -31,6 +31,11 @@ select ROW_NUMBER()OVER(ORDER BY pat.id, pt.start_year) payer_plan_period_id, CAST(pt.start_year AS DATE) payer_plan_period_start_date, CAST(pt.end_year AS DATE) payer_plan_period_end_date, } + + {@synthea_version == "3.1.0" | @synthea_version == "3.2.0" } ? { + CAST(pt.start_date AS DATE) payer_plan_period_start_date, + CAST(pt.end_date AS DATE) payer_plan_period_end_date, + } 0 payer_concept_id, pt.payer payer_source_value, diff --git a/vignettes/Payer_plan_period.Rmd b/vignettes/Payer_plan_period.Rmd index 5e9e5f3..6853bc6 100644 --- a/vignettes/Payer_plan_period.Rmd +++ b/vignettes/Payer_plan_period.Rmd @@ -17,8 +17,8 @@ vignette: > | --- | --- | --- | --- | | payer_plan_period | |Autogenerated based on the patient.id and payer transition start year | | | person_id | patient | Map by mapping person.person_source_value to payer_transitions.patient. Find person.person_id by mapping payer_transitions.patient to person.person_source_value. | | -| payer_plan_period_start_date | start_year | For synthea v2.7.0 CAST(CONCAT('01-JAN-',CAST(pt.start_year AS VARCHAR)) AS DATE) For synthea v3.0.0 CAST(pt.start_year AS DATE) | | -| payer_plan_period_start_date | end_year | For synthea v2.7.0 CAST(CONCAT('01-JAN-',CAST(pt.end_year AS VARCHAR)) AS DATE) For synthea v3.0.0 CAST(pt.end_year AS DATE) | | +| payer_plan_period_start_date | start_year | For synthea v2.7.0 CAST(CONCAT('01-JAN-',CAST(pt.start_year AS VARCHAR)) AS DATE) For synthea v3.0.0 CAST(pt.start_year AS DATE) For synthea v3.1.0 and v3.2.0 CAST(pt.start_date AS DATE) | | +| payer_plan_period_start_date | end_year | For synthea v2.7.0 CAST(CONCAT('01-JAN-',CAST(pt.end_year AS VARCHAR)) AS DATE) For synthea v3.0.0 CAST(pt.end_year AS DATE) For synthea v3.1.0 and v3.2.0 CAST(pt.end_date AS DATE) | | | payer_concept_id | | Set to 0 for all records | | | payer_source_value | payer | | | | payer_source_concept_id | | Set to 0 for all records | | From 3428ffc38616fe21bc265fc6326f870845f78a2a Mon Sep 17 00:00:00 2001 From: Evanette Burrows Date: Fri, 29 Dec 2023 14:42:15 -0500 Subject: [PATCH 05/10] Update additional files --- R/DropSyntheaTables.r | 4 ++-- R/createExtraIndices.R | 4 ++-- inst/sql/sql_server/extra_indices.sql | 2 +- 3 files changed, 5 insertions(+), 5 deletions(-) diff --git a/R/DropSyntheaTables.r b/R/DropSyntheaTables.r index 4c81280..4814e65 100644 --- a/R/DropSyntheaTables.r +++ b/R/DropSyntheaTables.r @@ -40,7 +40,7 @@ DropSyntheaTables <- function(connectionDetails, syntheaSchema) conn <- DatabaseConnector::connect(connectionDetails) allTables <- DatabaseConnector::getTableNames(conn, syntheaSchema) tablesToDrop <- allTables[which(allTables %in% syntheaTables)] - + if (length(tablesToDrop) > 0) { writeLines("Dropping Synthea tables...") sql <- @@ -57,6 +57,6 @@ DropSyntheaTables <- function(connectionDetails, syntheaSchema) } else { print(sprintf("No synthea tables to drop in schema %s",syntheaSchema)) } - + on.exit(DatabaseConnector::disconnect(conn)) } diff --git a/R/createExtraIndices.R b/R/createExtraIndices.R index b4899a9..9d435d8 100644 --- a/R/createExtraIndices.R +++ b/R/createExtraIndices.R @@ -8,13 +8,13 @@ #' Server, this should specify both the database and the schema, so for example 'cdm_instance.dbo'. #' @param syntheaSchema The name of the Synthea database schema. Requires read and write permissions to this schema. On SQL #' Server, this should specify both the database and the schema, so for example 'synthea.dbo'. -#' @param syntheaVersion Your Synthea version. Currently "2.7.0" and "3.0.0" are supported. +#' @param syntheaVersion Your Synthea version. Currently "2.7.0", "3.0.0", "3.1.0" and "3.2.0" are supported. #' @param outputFolder Location of the SQL scripts if sqlOnly = TRUE. Default is NULL. #' @param sqlOnly A boolean that determines whether to create the indices or generate a SQL scripts. Default is FALSE. #' #' @details This function creates indices which have been found to speed up certain long-running INSERT queries in LoadEventTables, #' for some users. Indices are created on the intermediate vocabulary mapping tables; the person & provider CDM tables; -#' and the claims_transactions Synthea table (in Synthea 3.0.0). +#' and the claims_transactions Synthea table (in Synthea 3.0.0, 3.1.0 and 3.2.0) . #' #' @importFrom utils head #' diff --git a/inst/sql/sql_server/extra_indices.sql b/inst/sql/sql_server/extra_indices.sql index 7a703ec..3bbdb97 100644 --- a/inst/sql/sql_server/extra_indices.sql +++ b/inst/sql/sql_server/extra_indices.sql @@ -31,7 +31,7 @@ CREATE INDEX person_psv ON @cdmDatabaseSchema.person ( person_source_value ); -{@syntheaVersion == '3.0.0'}?{ +{@syntheaVersion == '3.0.0' | @syntheaVersion == '3.1.0' | @syntheaVersion == '3.2.0' }?{ CREATE INDEX claims_transactions_cpap ON @syntheaSchema.claims_transactions ( claimid, patientid, From 2747d1658599fe87ef6bd72296a042b75807594b Mon Sep 17 00:00:00 2001 From: Evanette Burrows Date: Fri, 29 Dec 2023 14:46:05 -0500 Subject: [PATCH 06/10] Update overall package documentation --- docs/articles/Payer_plan_period.html | 6 ++++-- docs/pkgdown.yml | 2 +- docs/reference/LoadEventTables.html | 2 +- docs/reference/createExtraIndices.html | 4 ++-- extras/codeToRun.R | 4 ++++ man/LoadEventTables.Rd | 2 +- man/createExtraIndices.Rd | 4 ++-- 7 files changed, 15 insertions(+), 9 deletions(-) diff --git a/docs/articles/Payer_plan_period.html b/docs/articles/Payer_plan_period.html index 3b49cd2..6206775 100644 --- a/docs/articles/Payer_plan_period.html +++ b/docs/articles/Payer_plan_period.html @@ -157,14 +157,16 @@

Readin payer_plan_period_start_date start_year For synthea v2.7.0 CAST(CONCAT(‘01-JAN-’,CAST(pt.start_year AS -VARCHAR)) AS DATE) For synthea v3.0.0 CAST(pt.start_year AS DATE) +VARCHAR)) AS DATE) For synthea v3.0.0 CAST(pt.start_year AS DATE) For +synthea v3.1.0 and v3.2.0 CAST(pt.start_date AS DATE) payer_plan_period_start_date end_year For synthea v2.7.0 CAST(CONCAT(‘01-JAN-’,CAST(pt.end_year AS -VARCHAR)) AS DATE) For synthea v3.0.0 CAST(pt.end_year AS DATE) +VARCHAR)) AS DATE) For synthea v3.0.0 CAST(pt.end_year AS DATE) For +synthea v3.1.0 and v3.2.0 CAST(pt.end_date AS DATE) diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 77fc03b..c699a67 100644 --- 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: 2023-12-29T17:31Z +last_built: 2023-12-29T19:45Z diff --git a/docs/reference/LoadEventTables.html b/docs/reference/LoadEventTables.html index 947dde0..96c8e33 100644 --- a/docs/reference/LoadEventTables.html +++ b/docs/reference/LoadEventTables.html @@ -137,7 +137,7 @@

Arguments

syntheaVersion

The version of Synthea used to generate the csv files. -Currently "2.7.0" and "3.0.0" are supported.

+Currently "2.7.0","3.0.0","3.1.0" and "3.2.0" are supported.

cdmSourceName
diff --git a/docs/reference/createExtraIndices.html b/docs/reference/createExtraIndices.html index 1f682cd..a06fb53 100644 --- a/docs/reference/createExtraIndices.html +++ b/docs/reference/createExtraIndices.html @@ -121,7 +121,7 @@

Arguments

syntheaVersion
-

Your Synthea version. Currently "2.7.0" and "3.0.0" are supported.

+

Your Synthea version. Currently "2.7.0", "3.0.0", "3.1.0" and "3.2.0" are supported.

outputFolder
@@ -136,7 +136,7 @@

Arguments

Details

This function creates indices which have been found to speed up certain long-running INSERT queries in LoadEventTables, for some users. Indices are created on the intermediate vocabulary mapping tables; the person & provider CDM tables; - and the claims_transactions Synthea table (in Synthea 3.0.0).

+ and the claims_transactions Synthea table (in Synthea 3.0.0, 3.1.0 and 3.2.0) .

diff --git a/extras/codeToRun.R b/extras/codeToRun.R index 13957d8..bf7cf33 100644 --- a/extras/codeToRun.R +++ b/extras/codeToRun.R @@ -33,5 +33,9 @@ ETLSyntheaBuilder::CreateSyntheaTables(connectionDetails,syntheaSchema, syntheaV ETLSyntheaBuilder::LoadSyntheaTables(connectionDetails,syntheaSchema,syntheaFileLoc) # Populate vocabulary tables ETLSyntheaBuilder::LoadVocabFromCsv(connectionDetails,cdmDatabaseSchema,vocabFileLoc) +# Create intermediate vocabulary mapping and visit rollup tables +ETLSyntheaBuilder::CreateMapAndRollupTables(connectionDetails = cd, cdmSchema = cdmSchema, syntheaSchema = syntheaSchema, cdmVersion = cdmVersion, syntheaVersion = syntheaVersion) +## Optional Step to create extra indices +ETLSyntheaBuilder::CreateExtraIndices(connectionDetails = cd, cdmSchema = cdmSchema, syntheaSchema = syntheaSchema, cdmVersion = cdmVersion, syntheaVersion = syntheaVersion) # Populate event tables ETLSyntheaBuilder::LoadEventTables(connectionDetails,cdmDatabaseSchema,syntheaSchema,cdmVersion,syntheaVersion) diff --git a/man/LoadEventTables.Rd b/man/LoadEventTables.Rd index cb1800f..64dcbf9 100644 --- a/man/LoadEventTables.Rd +++ b/man/LoadEventTables.Rd @@ -37,7 +37,7 @@ so for example 'cdm_instance.dbo'.} \item{cdmVersion}{The version of your CDM. Currently "5.3" and "5.4".} \item{syntheaVersion}{The version of Synthea used to generate the csv files. -Currently "2.7.0" and "3.0.0" are supported.} +Currently "2.7.0","3.0.0","3.1.0" and "3.2.0" are supported.} \item{cdmSourceName}{The source name to insert into the CDM_SOURCE table. Default is Synthea synthetic health database.} diff --git a/man/createExtraIndices.Rd b/man/createExtraIndices.Rd index f003b4e..03cfdc8 100644 --- a/man/createExtraIndices.Rd +++ b/man/createExtraIndices.Rd @@ -23,7 +23,7 @@ Server, this should specify both the database and the schema, so for example 'cd \item{syntheaSchema}{The name of the Synthea database schema. Requires read and write permissions to this schema. On SQL Server, this should specify both the database and the schema, so for example 'synthea.dbo'.} -\item{syntheaVersion}{Your Synthea version. Currently "2.7.0" and "3.0.0" are supported.} +\item{syntheaVersion}{Your Synthea version. Currently "2.7.0", "3.0.0", "3.1.0" and "3.2.0" are supported.} \item{outputFolder}{Location of the SQL scripts if sqlOnly = TRUE. Default is NULL.} @@ -35,5 +35,5 @@ This function creates indices for certain tables which may help to speed up Load \details{ This function creates indices which have been found to speed up certain long-running INSERT queries in LoadEventTables, for some users. Indices are created on the intermediate vocabulary mapping tables; the person & provider CDM tables; - and the claims_transactions Synthea table (in Synthea 3.0.0). + and the claims_transactions Synthea table (in Synthea 3.0.0, 3.1.0 and 3.2.0) . } From b6c2f0631ea6b16a46af58bfac95c8b20d90183a Mon Sep 17 00:00:00 2001 From: Evanette Burrows Date: Fri, 29 Dec 2023 14:52:37 -0500 Subject: [PATCH 07/10] Updating main page --- README.md | 2 +- docs/index.html | 2 +- docs/pkgdown.yml | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index df16582..58b603b 100644 --- a/README.md +++ b/README.md @@ -15,7 +15,7 @@ Follow the steps on the [synthea wiki](https://github.com/synthetichealth/synthe # 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. + # The Synthea version we use in this example is 2.7.0. However, at this time we also support 3.0.0, 3.1.0 and 3.2.0. # 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". diff --git a/docs/index.html b/docs/index.html index 124030e..29b8128 100644 --- a/docs/index.html +++ b/docs/index.html @@ -131,7 +131,7 @@

Step by Step Example# 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. + # The Synthea version we use in this example is 2.7.0. However, at this time we also support 3.0.0, 3.1.0 and 3.2.0. # 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". diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index c699a67..ed4a25a 100644 --- 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: 2023-12-29T19:45Z +last_built: 2023-12-29T19:51Z From d2cf2d0fd4dfe4e23fd8dd4c6e086b41cd68662d Mon Sep 17 00:00:00 2001 From: Evanette Burrows Date: Tue, 2 Jan 2024 08:38:17 -0500 Subject: [PATCH 08/10] Update documentation --- DESCRIPTION | 7 ++++--- docs/404.html | 4 ++-- docs/articles/Condition_occurrence.html | 4 ++-- docs/articles/Cost.html | 4 ++-- docs/articles/Device_exposure.html | 4 ++-- docs/articles/Drug_exposure.html | 4 ++-- docs/articles/Measurement.html | 4 ++-- docs/articles/Payer_plan_period.html | 4 ++-- docs/articles/death.html | 4 ++-- docs/articles/index.html | 4 ++-- docs/articles/observation.html | 4 ++-- docs/articles/observation_period.html | 4 ++-- docs/articles/person.html | 4 ++-- docs/articles/procedure_occurrence.html | 4 ++-- docs/articles/provider.html | 4 ++-- docs/articles/visit_detail.html | 4 ++-- docs/articles/visit_occurrence.html | 4 ++-- docs/authors.html | 16 ++++++++-------- docs/index.html | 6 +++--- docs/pkgdown.yml | 2 +- .../CreateCDMIndexAndConstraintScripts.html | 4 ++-- docs/reference/CreateCDMIndices.html | 4 ++-- docs/reference/CreateCDMTables.html | 4 ++-- docs/reference/CreateMapAndRollupTables.html | 4 ++-- docs/reference/CreateSyntheaTables.html | 4 ++-- docs/reference/CreateVisitRollupTables.html | 4 ++-- docs/reference/CreateVocabMapTables.html | 4 ++-- docs/reference/DropEventTables.html | 4 ++-- docs/reference/DropMapAndRollupTables.html | 4 ++-- docs/reference/DropSyntheaTables.html | 4 ++-- docs/reference/DropVocabTables.html | 4 ++-- docs/reference/ETLSyntheaBuilder-package.html | 4 ++-- docs/reference/LoadEventTables.html | 4 ++-- docs/reference/LoadSyntheaTables.html | 4 ++-- docs/reference/LoadVocabFromCsv.html | 4 ++-- docs/reference/LoadVocabFromSchema.html | 4 ++-- docs/reference/TruncateEventTables.html | 4 ++-- docs/reference/TruncateVocabTables.html | 4 ++-- docs/reference/backupCDM.html | 4 ++-- docs/reference/createExtraIndices.html | 4 ++-- docs/reference/createPrunedTables.html | 4 ++-- docs/reference/exportToSQLite.html | 4 ++-- docs/reference/getEventConceptId.html | 4 ++-- docs/reference/index.html | 4 ++-- docs/reference/pruneCDM.html | 4 ++-- docs/reference/restoreCDMTables.html | 4 ++-- 46 files changed, 100 insertions(+), 99 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 376ed67..620d0bb 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,12 +1,13 @@ Package: ETLSyntheaBuilder Type: Package Title: A Builder for Converting the Synthea Data to the OMOP CDM -Version: 1.0 +Version: 2.0 mDate: 2021-12-04 Author: Anthony Molinaro [aut, cre], Clair Blacketer [aut], - Frank DeFalco [aut] -Maintainer: Anthony Molinaro + Frank DeFalco [aut], + Evanette Burrows [aut] +Maintainer: Evanette Burrows Description: 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 diff --git a/docs/404.html b/docs/404.html index 22887cb..2536686 100644 --- a/docs/404.html +++ b/docs/404.html @@ -32,7 +32,7 @@ ETLSyntheaBuilder - 1.0 + 2.0 @@ -124,7 +124,7 @@

Page not found (404)