diff --git a/DESCRIPTION b/DESCRIPTION index d68b0e93..14765261 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -16,3 +16,4 @@ Suggests: testthat License: Apache License Roxygen: list(wrap = TRUE) +RoxygenNote: 5.0.1 diff --git a/NAMESPACE b/NAMESPACE index e6aaf6fc..acc071b7 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -1,4 +1,4 @@ -# Generated by roxygen2 (4.1.1): do not edit by hand +# Generated by roxygen2: do not edit by hand export(achilles) export(achillesHeel) diff --git a/inst/sql/sql_server/export_v5/condition/sqlConditionsByType.sql b/inst/sql/sql_server/export_v5/condition/sqlConditionsByType.sql index c1d54e49..16749411 100644 --- a/inst/sql/sql_server/export_v5/condition/sqlConditionsByType.sql +++ b/inst/sql/sql_server/export_v5/condition/sqlConditionsByType.sql @@ -27,7 +27,7 @@ from @results_database_schema.ACHILLES_results ar1 when (concept_name like 'Inpatient%' or concept_name like 'Outpatient%' ) and (concept_name not like '%primary%' and concept_name not like '%1st position%') then 'Secondary diagnosis' else '' end as concept_group_name from @vocab_database_schema.concept - where lower(domain_id) = 'condition type' + where lower(concept_class_id) = 'condition type' ) c2 on ar1.stratum_2 = cast(c2.concept_id as VARCHAR) diff --git a/man/achilles.Rd b/man/achilles.Rd index 18b3314d..04591648 100644 --- a/man/achilles.Rd +++ b/man/achilles.Rd @@ -1,4 +1,4 @@ -% Generated by roxygen2 (4.1.1): do not edit by hand +% Generated by roxygen2: do not edit by hand % Please edit documentation in R/Achilles.R \name{achilles} \alias{achilles} @@ -8,18 +8,19 @@ achilles(connectionDetails, cdmDatabaseSchema, oracleTempSchema = cdmDatabaseSchema, resultsDatabaseSchema = cdmDatabaseSchema, sourceName = "", analysisIds, createTable = TRUE, smallcellcount = 5, cdmVersion = "4", - runHeel = TRUE, validateSchema = FALSE) + runHeel = TRUE, validateSchema = FALSE, + vocabDatabaseSchema = cdmDatabaseSchema) } \arguments{ \item{connectionDetails}{An R object of type ConnectionDetail (details for the function that contains server info, database type, optionally username/password, port)} \item{cdmDatabaseSchema}{string name of database - schema that contains OMOP CDM and vocabulary. On SQL Server, - this should specifiy both the database and the schema, so - for example 'cdm_instance.dbo'.} \item{oracleTempSchema}{For - Oracle only: the name of the database schema where you want - all temporary tables to be managed. Requires create/insert + schema that contains OMOP CDM. On SQL Server, this should + specifiy both the database and the schema, so for example + 'cdm_instance.dbo'.} \item{oracleTempSchema}{For Oracle + only: the name of the database schema where you want all + temporary tables to be managed. Requires create/insert permissions to this database.} \item{resultsDatabaseSchema} {string name of database schema that we can write results to. Default is cdmDatabaseSchema. On SQL Server, this @@ -38,11 +39,14 @@ achilles(connectionDetails, cdmDatabaseSchema, counts (<= smallcellcount) are deleted.} \item{cdmVersion} {Define the OMOP CDM version used: currently support "4" and "5". Default = "4"} \item{runHeel}{Boolean to - determine if Achilles Heel data quality reporting will be - produced based on the summary statistics. Default = TRUE} - \item{validateSchema}{Boolean to determine if CDM Schema - Validation should be run. This could be very slow. Default = - FALSE} + determine if Achilles Heel data quality reporting will + be produced based on the summary statistics. Default = + TRUE} \item{validateSchema}{Boolean to determine if CDM + Schema Validation should be run. This could be very slow. + Default = FALSE} \item{vocabDatabaseSchema}{string name of + database schema that contains OMOP Vocabulary. Default is + cdmDatabaseSchema. On SQL Server, this should specifiy both + the database and the schema, so for example 'results.dbo'.} } \value{ An object of type \code{achillesResults} containing details @@ -59,7 +63,7 @@ an entire OMOP CDM instance. \examples{ \dontrun{ connectionDetails <- createConnectionDetails(dbms="sql server", server="RNDUSRDHIT07.jnj.com") - achillesResults <- achilles(connectionDetails, cdmDatabaseSchema="cdm4_sim", resultsDatabaseSchema="scratch", sourceName="TestDB", validateSchema="TRUE") + achillesResults <- achilles(connectionDetails, cdmDatabaseSchema="cdm4_sim", resultsDatabaseSchema="scratch", sourceName="TestDB", validateSchema="TRUE", vocabDatabaseSchema="vocabulary") fetchAchillesAnalysisResults(connectionDetails, "scratch", 106) } } diff --git a/man/analysesDetails.Rd b/man/analysesDetails.Rd index 5481dc09..c9f5c4dc 100644 --- a/man/analysesDetails.Rd +++ b/man/analysesDetails.Rd @@ -1,4 +1,4 @@ -% Generated by roxygen2 (4.1.1): do not edit by hand +% Generated by roxygen2: do not edit by hand % Please edit documentation in R/Achilles-package.R \docType{data} \name{analysesDetails} diff --git a/man/exportConditionEraToJson.Rd b/man/exportConditionEraToJson.Rd index 726b174f..8663809b 100644 --- a/man/exportConditionEraToJson.Rd +++ b/man/exportConditionEraToJson.Rd @@ -1,11 +1,12 @@ -% Generated by roxygen2 (4.1.1): do not edit by hand +% Generated by roxygen2: do not edit by hand % Please edit documentation in R/exportToJson.R \name{exportConditionEraToJson} \alias{exportConditionEraToJson} \title{exportConditionEraToJson} \usage{ exportConditionEraToJson(connectionDetails, cdmDatabaseSchema, - resultsDatabaseSchema, outputPath = getwd(), cdmVersion = "4") + resultsDatabaseSchema, outputPath = getwd(), cdmVersion = "4", + vocabDatabaseSchema = cdmDatabaseSchema) } \arguments{ \item{connectionDetails}{An R object of type @@ -17,6 +18,10 @@ exportConditionEraToJson(connectionDetails, cdmDatabaseSchema, that contains the Achilles analysis files. Default is cdmDatabaseSchema} \item{outputPath}{A folder location to save the JSON files. Default is current working folder} + \item{vocabDatabaseSchema}{string name of database schema + that contains OMOP Vocabulary. Default is cdmDatabaseSchema. + On SQL Server, this should specifiy both the database and + the schema, so for example 'results.dbo'.} } \value{ none diff --git a/man/exportConditionToJson.Rd b/man/exportConditionToJson.Rd index bd09116e..b3f55437 100644 --- a/man/exportConditionToJson.Rd +++ b/man/exportConditionToJson.Rd @@ -1,11 +1,12 @@ -% Generated by roxygen2 (4.1.1): do not edit by hand +% Generated by roxygen2: do not edit by hand % Please edit documentation in R/exportToJson.R \name{exportConditionToJson} \alias{exportConditionToJson} \title{exportConditionToJson} \usage{ exportConditionToJson(connectionDetails, cdmDatabaseSchema, - resultsDatabaseSchema, outputPath = getwd(), cdmVersion = "4") + resultsDatabaseSchema, outputPath = getwd(), cdmVersion = "4", + vocabDatabaseSchema = cdmDatabaseSchema) } \arguments{ \item{connectionDetails}{An R object of type @@ -17,6 +18,10 @@ exportConditionToJson(connectionDetails, cdmDatabaseSchema, that contains the Achilles analysis files. Default is cdmDatabaseSchema} \item{outputPath}{A folder location to save the JSON files. Default is current working folder} + \item{vocabDatabaseSchema}{string name of database schema + that contains OMOP Vocabulary. Default is cdmDatabaseSchema. + On SQL Server, this should specifiy both the database and + the schema, so for example 'results.dbo'.} } \value{ none diff --git a/man/exportDashboardToJson.Rd b/man/exportDashboardToJson.Rd index ec30bece..07c43a81 100644 --- a/man/exportDashboardToJson.Rd +++ b/man/exportDashboardToJson.Rd @@ -1,11 +1,12 @@ -% Generated by roxygen2 (4.1.1): do not edit by hand +% Generated by roxygen2: do not edit by hand % Please edit documentation in R/exportToJson.R \name{exportDashboardToJson} \alias{exportDashboardToJson} \title{exportDashboardToJson} \usage{ exportDashboardToJson(connectionDetails, cdmDatabaseSchema, - resultsDatabaseSchema, outputPath = getwd(), cdmVersion = "4") + resultsDatabaseSchema, outputPath = getwd(), cdmVersion = "4", + vocabDatabaseSchema = cdmDatabaseSchema) } \arguments{ \item{connectionDetails}{An R object of type @@ -17,6 +18,10 @@ exportDashboardToJson(connectionDetails, cdmDatabaseSchema, that contains the Achilles analysis files. Default is cdmDatabaseSchema} \item{outputPath}{A folder location to save the JSON files. Default is current working folder} + \item{vocabDatabaseSchema}{string name of database schema + that contains OMOP Vocabulary. Default is cdmDatabaseSchema. + On SQL Server, this should specifiy both the database and + the schema, so for example 'results.dbo'.} } \value{ none diff --git a/man/exportDataDensityToJson.Rd b/man/exportDataDensityToJson.Rd index 8e17e993..af9110bc 100644 --- a/man/exportDataDensityToJson.Rd +++ b/man/exportDataDensityToJson.Rd @@ -1,11 +1,12 @@ -% Generated by roxygen2 (4.1.1): do not edit by hand +% Generated by roxygen2: do not edit by hand % Please edit documentation in R/exportToJson.R \name{exportDataDensityToJson} \alias{exportDataDensityToJson} \title{exportDataDensityToJson} \usage{ exportDataDensityToJson(connectionDetails, cdmDatabaseSchema, - resultsDatabaseSchema, outputPath = getwd(), cdmVersion = "4") + resultsDatabaseSchema, outputPath = getwd(), cdmVersion = "4", + vocabDatabaseSchema = cdmDatabaseSchema) } \arguments{ \item{connectionDetails}{An R object of type @@ -17,6 +18,10 @@ exportDataDensityToJson(connectionDetails, cdmDatabaseSchema, that contains the Achilles analysis files. Default is cdmDatabaseSchema} \item{outputPath}{A folder location to save the JSON files. Default is current working folder} + \item{vocabDatabaseSchema}{string name of database schema + that contains OMOP Vocabulary. Default is cdmDatabaseSchema. + On SQL Server, this should specifiy both the database and + the schema, so for example 'results.dbo'.} } \value{ none diff --git a/man/exportDeathToJson.Rd b/man/exportDeathToJson.Rd index de4163e0..e028ab8a 100644 --- a/man/exportDeathToJson.Rd +++ b/man/exportDeathToJson.Rd @@ -1,11 +1,12 @@ -% Generated by roxygen2 (4.1.1): do not edit by hand +% Generated by roxygen2: do not edit by hand % Please edit documentation in R/exportToJson.R \name{exportDeathToJson} \alias{exportDeathToJson} \title{exportDeathToJson} \usage{ exportDeathToJson(connectionDetails, cdmDatabaseSchema, resultsDatabaseSchema, - outputPath = getwd(), cdmVersion = "4") + outputPath = getwd(), cdmVersion = "4", + vocabDatabaseSchema = cdmDatabaseSchema) } \arguments{ \item{connectionDetails}{An R object of type @@ -17,6 +18,10 @@ exportDeathToJson(connectionDetails, cdmDatabaseSchema, resultsDatabaseSchema, that contains the Achilles analysis files. Default is cdmDatabaseSchema} \item{outputPath}{A folder location to save the JSON files. Default is current working folder} + \item{vocabDatabaseSchema}{string name of database schema + that contains OMOP Vocabulary. Default is cdmDatabaseSchema. + On SQL Server, this should specifiy both the database and + the schema, so for example 'results.dbo'.} } \value{ none diff --git a/man/exportDrugEraToJson.Rd b/man/exportDrugEraToJson.Rd index b97392c7..33b0cd03 100644 --- a/man/exportDrugEraToJson.Rd +++ b/man/exportDrugEraToJson.Rd @@ -1,11 +1,12 @@ -% Generated by roxygen2 (4.1.1): do not edit by hand +% Generated by roxygen2: do not edit by hand % Please edit documentation in R/exportToJson.R \name{exportDrugEraToJson} \alias{exportDrugEraToJson} \title{exportDrugEraToJson} \usage{ exportDrugEraToJson(connectionDetails, cdmDatabaseSchema, resultsDatabaseSchema, - outputPath = getwd(), cdmVersion = "4") + outputPath = getwd(), cdmVersion = "4", + vocabDatabaseSchema = cdmDatabaseSchema) } \arguments{ \item{connectionDetails}{An R object of type @@ -17,6 +18,10 @@ exportDrugEraToJson(connectionDetails, cdmDatabaseSchema, resultsDatabaseSchema, that contains the Achilles analysis files. Default is cdmDatabaseSchema} \item{outputPath}{A folder location to save the JSON files. Default is current working folder} + \item{vocabDatabaseSchema}{string name of database schema + that contains OMOP Vocabulary. Default is cdmDatabaseSchema. + On SQL Server, this should specifiy both the database and + the schema, so for example 'results.dbo'.} } \value{ none diff --git a/man/exportDrugToJson.Rd b/man/exportDrugToJson.Rd index f2df139b..3d6377a2 100644 --- a/man/exportDrugToJson.Rd +++ b/man/exportDrugToJson.Rd @@ -1,11 +1,12 @@ -% Generated by roxygen2 (4.1.1): do not edit by hand +% Generated by roxygen2: do not edit by hand % Please edit documentation in R/exportToJson.R \name{exportDrugToJson} \alias{exportDrugToJson} \title{exportDrugToJson} \usage{ exportDrugToJson(connectionDetails, cdmDatabaseSchema, resultsDatabaseSchema, - outputPath = getwd(), cdmVersion = "4") + outputPath = getwd(), cdmVersion = "4", + vocabDatabaseSchema = cdmDatabaseSchema) } \arguments{ \item{connectionDetails}{An R object of type @@ -17,6 +18,10 @@ exportDrugToJson(connectionDetails, cdmDatabaseSchema, resultsDatabaseSchema, that contains the Achilles analysis files. Default is cdmDatabaseSchema} \item{outputPath}{A folder location to save the JSON files. Default is current working folder} + \item{vocabDatabaseSchema}{string name of database schema + that contains OMOP Vocabulary. Default is cdmDatabaseSchema. + On SQL Server, this should specifiy both the database and + the schema, so for example 'results.dbo'.} } \value{ none diff --git a/man/exportHeelToJson.Rd b/man/exportHeelToJson.Rd index fb602591..870932ac 100644 --- a/man/exportHeelToJson.Rd +++ b/man/exportHeelToJson.Rd @@ -1,11 +1,12 @@ -% Generated by roxygen2 (4.1.1): do not edit by hand +% Generated by roxygen2: do not edit by hand % Please edit documentation in R/exportToJson.R \name{exportHeelToJson} \alias{exportHeelToJson} \title{exportHeelToJson} \usage{ exportHeelToJson(connectionDetails, cdmDatabaseSchema, resultsDatabaseSchema, - outputPath = getwd(), cdmVersion = "4") + outputPath = getwd(), cdmVersion = "4", + vocabDatabaseSchema = cdmDatabaseSchema) } \arguments{ \item{connectionDetails}{An R object of type @@ -17,6 +18,10 @@ exportHeelToJson(connectionDetails, cdmDatabaseSchema, resultsDatabaseSchema, that contains the Achilles analysis files. Default is cdmDatabaseSchema} \item{outputPath}{A folder location to save the JSON files. Default is current working folder} + \item{vocabDatabaseSchema}{string name of database schema + that contains OMOP Vocabulary. Default is cdmDatabaseSchema. + On SQL Server, this should specifiy both the database and + the schema, so for example 'results.dbo'.} } \value{ none diff --git a/man/exportMeasurementToJson.Rd b/man/exportMeasurementToJson.Rd index a9d6b5e9..991f21df 100644 --- a/man/exportMeasurementToJson.Rd +++ b/man/exportMeasurementToJson.Rd @@ -1,11 +1,12 @@ -% Generated by roxygen2 (4.1.1): do not edit by hand +% Generated by roxygen2: do not edit by hand % Please edit documentation in R/exportToJson.R \name{exportMeasurementToJson} \alias{exportMeasurementToJson} \title{exportMeasurementToJson} \usage{ exportMeasurementToJson(connectionDetails, cdmDatabaseSchema, - resultsDatabaseSchema, outputPath = getwd(), cdmVersion = "4") + resultsDatabaseSchema, outputPath = getwd(), cdmVersion = "4", + vocabDatabaseSchema = cdmDatabaseSchema) } \arguments{ \item{connectionDetails}{An R object of type @@ -17,6 +18,10 @@ exportMeasurementToJson(connectionDetails, cdmDatabaseSchema, that contains the Achilles analysis files. Default is cdmDatabaseSchema} \item{outputPath}{A folder location to save the JSON files. Default is current working folder} + \item{vocabDatabaseSchema}{string name of database schema + that contains OMOP Vocabulary. Default is cdmDatabaseSchema. + On SQL Server, this should specifiy both the database and + the schema, so for example 'results.dbo'.} } \value{ none diff --git a/man/exportObservationPeriodToJson.Rd b/man/exportObservationPeriodToJson.Rd index 616298d8..ee3c7580 100644 --- a/man/exportObservationPeriodToJson.Rd +++ b/man/exportObservationPeriodToJson.Rd @@ -1,11 +1,12 @@ -% Generated by roxygen2 (4.1.1): do not edit by hand +% Generated by roxygen2: do not edit by hand % Please edit documentation in R/exportToJson.R \name{exportObservationPeriodToJson} \alias{exportObservationPeriodToJson} \title{exportObservationPeriodToJson} \usage{ exportObservationPeriodToJson(connectionDetails, cdmDatabaseSchema, - resultsDatabaseSchema, outputPath = getwd(), cdmVersion = "4") + resultsDatabaseSchema, outputPath = getwd(), cdmVersion = "4", + vocabDatabaseSchema = cdmDatabaseSchema) } \arguments{ \item{connectionDetails}{An R object of type @@ -17,6 +18,10 @@ exportObservationPeriodToJson(connectionDetails, cdmDatabaseSchema, that contains the Achilles analysis files. Default is cdmDatabaseSchema} \item{outputPath}{A folder location to save the JSON files. Default is current working folder} + \item{vocabDatabaseSchema}{string name of database schema + that contains OMOP Vocabulary. Default is cdmDatabaseSchema. + On SQL Server, this should specifiy both the database and + the schema, so for example 'results.dbo'.} } \value{ none diff --git a/man/exportObservationToJson.Rd b/man/exportObservationToJson.Rd index 40fd9b95..70412b45 100644 --- a/man/exportObservationToJson.Rd +++ b/man/exportObservationToJson.Rd @@ -1,11 +1,12 @@ -% Generated by roxygen2 (4.1.1): do not edit by hand +% Generated by roxygen2: do not edit by hand % Please edit documentation in R/exportToJson.R \name{exportObservationToJson} \alias{exportObservationToJson} \title{exportObservationToJson} \usage{ exportObservationToJson(connectionDetails, cdmDatabaseSchema, - resultsDatabaseSchema, outputPath = getwd(), cdmVersion = "4") + resultsDatabaseSchema, outputPath = getwd(), cdmVersion = "4", + vocabDatabaseSchema = cdmDatabaseSchema) } \arguments{ \item{connectionDetails}{An R object of type @@ -17,6 +18,10 @@ exportObservationToJson(connectionDetails, cdmDatabaseSchema, that contains the Achilles analysis files. Default is cdmDatabaseSchema} \item{outputPath}{A folder location to save the JSON files. Default is current working folder} + \item{vocabDatabaseSchema}{string name of database schema + that contains OMOP Vocabulary. Default is cdmDatabaseSchema. + On SQL Server, this should specifiy both the database and + the schema, so for example 'results.dbo'.} } \value{ none diff --git a/man/exportPersonToJson.Rd b/man/exportPersonToJson.Rd index 8903088e..978bf0dd 100644 --- a/man/exportPersonToJson.Rd +++ b/man/exportPersonToJson.Rd @@ -1,11 +1,12 @@ -% Generated by roxygen2 (4.1.1): do not edit by hand +% Generated by roxygen2: do not edit by hand % Please edit documentation in R/exportToJson.R \name{exportPersonToJson} \alias{exportPersonToJson} \title{exportPersonToJson} \usage{ exportPersonToJson(connectionDetails, cdmDatabaseSchema, resultsDatabaseSchema, - outputPath = getwd(), cdmVersion = "4") + outputPath = getwd(), cdmVersion = "4", + vocabDatabaseSchema = cdmDatabaseSchema) } \arguments{ \item{connectionDetails}{An R object of type @@ -17,6 +18,10 @@ exportPersonToJson(connectionDetails, cdmDatabaseSchema, resultsDatabaseSchema, that contains the Achilles analysis files. Default is cdmDatabaseSchema} \item{outputPath}{A folder location to save the JSON files. Default is current working folder} + \item{vocabDatabaseSchema}{string name of database schema + that contains OMOP Vocabulary. Default is cdmDatabaseSchema. + On SQL Server, this should specifiy both the database and + the schema, so for example 'results.dbo'.} } \value{ none diff --git a/man/exportProcedureToJson.Rd b/man/exportProcedureToJson.Rd index 91cbdcc2..db8dee89 100644 --- a/man/exportProcedureToJson.Rd +++ b/man/exportProcedureToJson.Rd @@ -1,11 +1,12 @@ -% Generated by roxygen2 (4.1.1): do not edit by hand +% Generated by roxygen2: do not edit by hand % Please edit documentation in R/exportToJson.R \name{exportProcedureToJson} \alias{exportProcedureToJson} \title{exportProcedureToJson} \usage{ exportProcedureToJson(connectionDetails, cdmDatabaseSchema, - resultsDatabaseSchema, outputPath = getwd(), cdmVersion = "4") + resultsDatabaseSchema, outputPath = getwd(), cdmVersion = "4", + vocabDatabaseSchema = cdmDatabaseSchema) } \arguments{ \item{connectionDetails}{An R object of type @@ -17,6 +18,10 @@ exportProcedureToJson(connectionDetails, cdmDatabaseSchema, that contains the Achilles analysis files. Default is cdmDatabaseSchema} \item{outputPath}{A folder location to save the JSON files. Default is current working folder} + \item{vocabDatabaseSchema}{string name of database schema + that contains OMOP Vocabulary. Default is cdmDatabaseSchema. + On SQL Server, this should specifiy both the database and + the schema, so for example 'results.dbo'.} } \value{ none diff --git a/man/exportToJson.Rd b/man/exportToJson.Rd index e67f16c8..686cf131 100644 --- a/man/exportToJson.Rd +++ b/man/exportToJson.Rd @@ -1,25 +1,30 @@ -% Generated by roxygen2 (4.1.1): do not edit by hand +% Generated by roxygen2: do not edit by hand % Please edit documentation in R/exportToJson.R \name{exportToJson} \alias{exportToJson} \title{exportToJson} \usage{ exportToJson(connectionDetails, cdmDatabaseSchema, resultsDatabaseSchema, - outputPath = getwd(), reports = allReports, cdmVersion = "4") + outputPath = getwd(), reports = allReports, cdmVersion = "4", + vocabDatabaseSchema = cdmDatabaseSchema) } \arguments{ \item{connectionDetails}{An R object of type ConnectionDetail (details for the function that contains - server info, database type, optionally username/ - password, port)} \item{cdmDatabaseSchema}{Name of the - database schema that contains the vocabulary files} - \item{resultsDatabaseSchema}{Name of the database schema - that contains the Achilles analysis files. Default is - cdmDatabaseSchema} \item{outputPath}{A folder location - to save the JSON files. Default is current working - folder} \item{reports}{A character vector listing the - set of reports to generate. Default is all reports. See - \code{data(allReports)} for a list of all report types} + server info, database type, optionally username/password, + port)} \item{cdmDatabaseSchema}{Name of the database schema + that contains the OMOP CDM.} \item{resultsDatabaseSchema} + {Name of the database schema that contains the + Achilles analysis files. Default is cdmDatabaseSchema} + \item{outputPath}{A folder location to save the JSON + files. Default is current working folder} \item{reports} + {A character vector listing the set of reports to generate. + Default is all reports.} \item{vocabDatabaseSchema}{string + name of database schema that contains OMOP Vocabulary. + Default is cdmDatabaseSchema. On SQL Server, this should + specifiy both the database and the schema, so for example + 'results.dbo'. See \code{data(allReports)} for a list of all + report types} } \value{ none diff --git a/man/exportVisitToJson.Rd b/man/exportVisitToJson.Rd index d1228385..5468c364 100644 --- a/man/exportVisitToJson.Rd +++ b/man/exportVisitToJson.Rd @@ -1,11 +1,12 @@ -% Generated by roxygen2 (4.1.1): do not edit by hand +% Generated by roxygen2: do not edit by hand % Please edit documentation in R/exportToJson.R \name{exportVisitToJson} \alias{exportVisitToJson} \title{exportVisitToJson} \usage{ exportVisitToJson(connectionDetails, cdmDatabaseSchema, resultsDatabaseSchema, - outputPath = getwd(), cdmVersion = "4") + outputPath = getwd(), cdmVersion = "4", + vocabDatabaseSchema = cdmDatabaseSchema) } \arguments{ \item{connectionDetails}{An R object of type @@ -17,6 +18,10 @@ exportVisitToJson(connectionDetails, cdmDatabaseSchema, resultsDatabaseSchema, that contains the Achilles analysis files. Default is cdmDatabaseSchema} \item{outputPath}{A folder location to save the JSON files. Default is current working folder} + \item{vocabDatabaseSchema}{string name of database schema + that contains OMOP Vocabulary. Default is cdmDatabaseSchema. + On SQL Server, this should specifiy both the database and + the schema, so for example 'results.dbo'.} } \value{ none diff --git a/man/fetchAchillesAnalysisResults.Rd b/man/fetchAchillesAnalysisResults.Rd index 6ec70bad..53cd8c69 100644 --- a/man/fetchAchillesAnalysisResults.Rd +++ b/man/fetchAchillesAnalysisResults.Rd @@ -1,4 +1,4 @@ -% Generated by roxygen2 (4.1.1): do not edit by hand +% Generated by roxygen2: do not edit by hand % Please edit documentation in R/AchillesViewResults.R \name{fetchAchillesAnalysisResults} \alias{fetchAchillesAnalysisResults} diff --git a/man/fetchAchillesHeelResults.Rd b/man/fetchAchillesHeelResults.Rd index 2b849b3a..62f3214a 100644 --- a/man/fetchAchillesHeelResults.Rd +++ b/man/fetchAchillesHeelResults.Rd @@ -1,4 +1,4 @@ -% Generated by roxygen2 (4.1.1): do not edit by hand +% Generated by roxygen2: do not edit by hand % Please edit documentation in R/AchillesViewResults.R \name{fetchAchillesHeelResults} \alias{fetchAchillesHeelResults} diff --git a/man/getAnalysisDetails.Rd b/man/getAnalysisDetails.Rd index 4cf36af3..e3335f49 100644 --- a/man/getAnalysisDetails.Rd +++ b/man/getAnalysisDetails.Rd @@ -1,4 +1,4 @@ -% Generated by roxygen2 (4.1.1): do not edit by hand +% Generated by roxygen2: do not edit by hand % Please edit documentation in R/Achilles.R \name{getAnalysisDetails} \alias{getAnalysisDetails} diff --git a/man/showReportTypes.Rd b/man/showReportTypes.Rd index 260152ed..6a9321af 100644 --- a/man/showReportTypes.Rd +++ b/man/showReportTypes.Rd @@ -1,4 +1,4 @@ -% Generated by roxygen2 (4.1.1): do not edit by hand +% Generated by roxygen2: do not edit by hand % Please edit documentation in R/exportToJson.R \name{showReportTypes} \alias{showReportTypes}