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Merge pull request #272 from OHDSI/develop
Release v3.7.0
2 parents a0bbc9b + 725aee8 commit eabfb42

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‎CRAN-SUBMISSION‎

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Version: 3.5.2
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Date: 2024-04-30 18:12:58 UTC
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SHA: fe1f8048024d84e8079e872e60c4623c9d0c5c5f
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Version: 3.7.0
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Date: 2024-09-03 08:24:46 UTC
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SHA: efa425b67203564c5a581de9180a87d14c28767e

‎DESCRIPTION‎

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Package: FeatureExtraction
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Type: Package
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Title: Generating Features for a Cohort
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Version: 3.6.0
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Date: 2024-07-15
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Version: 3.7.0
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Date: 2024-09-02
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Authors@R: c(
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person("Martijn", "Schuemie", , "schuemie@ohdsi.org", role = c("aut")),
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person("Marc", "Suchard", role = c("aut")),
@@ -45,6 +45,6 @@ VignetteBuilder: knitr
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URL: https://github.com/OHDSI/FeatureExtraction
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BugReports: https://github.com/OHDSI/FeatureExtraction/issues
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NeedsCompilation: no
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RoxygenNote: 7.3.1
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RoxygenNote: 7.3.2
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Encoding: UTF-8
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Language: en-US

‎NEWS.md‎

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FeatureExtraction 3.7.0
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=======================
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- Deprecate oracleTempSchema param, add tempEmulationSchema param (#126)
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- Filter binary covariates server side (#255)
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- Limit tests that are run on CRAN (#267)
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FeatureExtraction 3.6.0
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=======================
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‎R/DefaultCovariateSettings.R‎

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#' useMeasurementValueAsConceptAnyTimePrior = FALSE,
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#' useMeasurementValueAsConceptLongTerm = TRUE,
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#' useMeasurementValueAsConceptMediumTerm = FALSE,
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#' useMeasurementValueAsConceptShortTerm = TRUE,
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#' useMeasurementValueAsConceptShortTerm = TRUE,
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#' useObservationAnyTimePrior = FALSE,
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#' useObservationLongTerm = TRUE,
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#' useObservationMediumTerm = FALSE,
@@ -617,7 +617,7 @@ createCovariateSettings <- function(useDemographicsGender = FALSE,
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useObservationValueAsConceptAnyTimePrior = FALSE,
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useObservationValueAsConceptLongTerm = FALSE,
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useObservationValueAsConceptMediumTerm = FALSE,
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useObservationValueAsConceptShortTerm = FALSE,
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useObservationValueAsConceptShortTerm = FALSE,
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useCharlsonIndex = FALSE,
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useDcsi = FALSE,
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useChads2 = FALSE,

‎R/GetCovariates.R‎

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#' \code{connect} function in the \code{DatabaseConnector} package.
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#' Either the \code{connection} or \code{connectionDetails} argument
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#' should be specified.
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#' @param oracleTempSchema A schema where temp tables can be created in Oracle.
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#' @param oracleTempSchema DEPRECATED: use \code{tempEmulationSchema} instead.
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#' @param cdmDatabaseSchema The name of the database schema that contains the OMOP CDM instance.
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#' Requires read permissions to this database. On SQL Server, this should
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#' specify both the database and the schema, so for example
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#' @param minCharacterizationMean The minimum mean value for characterization output. Values below this will be cut off from output. This
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#' will help reduce the file size of the characterization output, but will remove information
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#' on covariates that have very low values. The default is 0.
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#' @param tempEmulationSchema Some database platforms like Oracle and Impala do not truly support
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#' temp tables. To emulate temp tables, provide a schema with write
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#' privileges where temp tables can be created.
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#'
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#' @return
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#' Returns an object of type \code{covariateData}, containing information on the covariates.
@@ -82,7 +85,7 @@
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#' )
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#' covData <- getDbCovariateData(
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#' connectionDetails = eunomiaConnectionDetails,
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#' oracleTempSchema = NULL,
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#' tempEmulationSchema = NULL,
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#' cdmDatabaseSchema = "main",
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#' cdmVersion = "5",
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#' cohortTable = "cohort",
@@ -109,7 +112,8 @@ getDbCovariateData <- function(connectionDetails = NULL,
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rowIdField = "subject_id",
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covariateSettings,
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aggregated = FALSE,
112-
minCharacterizationMean = 0) {
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minCharacterizationMean = 0,
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tempEmulationSchema = NULL) {
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if (is.null(connectionDetails) && is.null(connection)) {
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stop("Need to provide either connectionDetails or connection")
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}
@@ -123,6 +127,13 @@ getDbCovariateData <- function(connectionDetails = NULL,
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warning("cohortId argument has been deprecated, please use cohortIds")
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cohortIds <- cohortId
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}
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if (!is.null(oracleTempSchema) && oracleTempSchema != "") {
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rlang::warn("The 'oracleTempSchema' argument is deprecated. Use 'tempEmulationSchema' instead.",
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.frequency = "regularly",
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.frequency_id = "oracleTempSchema"
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)
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tempEmulationSchema <- oracleTempSchema
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}
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errorMessages <- checkmate::makeAssertCollection()
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minCharacterizationMean <- utils::type.convert(minCharacterizationMean, as.is = TRUE)
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checkmate::assertNumeric(x = minCharacterizationMean, lower = 0, upper = 1, add = errorMessages)
@@ -149,7 +160,7 @@ getDbCovariateData <- function(connectionDetails = NULL,
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sql <- SqlRender::translate(
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sql = sql,
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targetDialect = attr(connection, "dbms"),
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oracleTempSchema = oracleTempSchema
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tempEmulationSchema = tempEmulationSchema
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)
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temp <- DatabaseConnector::querySql(connection, sql, snakeCaseToCamelCase = TRUE)
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if (aggregated) {
@@ -174,7 +185,7 @@ getDbCovariateData <- function(connectionDetails = NULL,
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fun <- attr(covariateSettings[[i]], "fun")
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args <- list(
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connection = connection,
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oracleTempSchema = oracleTempSchema,
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tempEmulationSchema = tempEmulationSchema,
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cdmDatabaseSchema = cdmDatabaseSchema,
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cohortTable = cohortDatabaseSchemaTable,
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cohortIds = cohortIds,

‎R/GetCovariatesFromCohortAttributes.R‎

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#'
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#' covData <- getDbCohortAttrCovariatesData(
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#' connection = connection,
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#' oracleTempSchema = NULL,
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#' tempEmulationSchema = NULL,
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#' cdmDatabaseSchema = "main",
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#' cdmVersion = "5",
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#' cohortTable = "cohort",
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cdmVersion = "5",
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rowIdField = "subject_id",
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covariateSettings,
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aggregated = FALSE) {
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aggregated = FALSE,
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tempEmulationSchema = NULL) {
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if (aggregated) {
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stop("Aggregation not implemented for covariates from cohort attributes.")
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}
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warning("cohortId argument has been deprecated, please use cohortIds")
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cohortIds <- cohortId
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}
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if (!is.null(oracleTempSchema) && oracleTempSchema != "") {
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rlang::warn("The 'oracleTempSchema' argument is deprecated. Use 'tempEmulationSchema' instead.",
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.frequency = "regularly",
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.frequency_id = "oracleTempSchema"
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)
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tempEmulationSchema <- oracleTempSchema
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}
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start <- Sys.time()
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writeLines("Constructing covariates from cohort attributes table")
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dropTableIfExists = TRUE,
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createTable = TRUE,
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tempTable = TRUE,
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oracleTempSchema = oracleTempSchema
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tempEmulationSchema = tempEmulationSchema
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)
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}
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sql <- SqlRender::readSql(system.file("sql/sql_server/GetAttrCovariates.sql", package = "FeatureExtraction"))
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renderedSql <- SqlRender::translate(
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sql = renderedSql,
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targetDialect = attr(connection, "dbms"),
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oracleTempSchema = oracleTempSchema
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tempEmulationSchema = tempEmulationSchema
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)
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# renderedSql <- SqlRender::loadRenderTranslateSql("GetAttrCovariates.sql",
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# packageName = "FeatureExtraction",
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# dbms = attr(connection, "dbms"),
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# oracleTempSchema = oracleTempSchema,
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# tempEmulationSchema = tempEmulationSchema,
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# attr_database_schema = covariateSettings$attrDatabaseSchema,
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# cohort_table = cohortTable,
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# row_id_field = rowIdField,
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covariateRefSql <- SqlRender::translate(
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sql = covariateRefSql,
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targetDialect = attr(connection, "dbms"),
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oracleTempSchema = oracleTempSchema
140+
tempEmulationSchema = tempEmulationSchema
133141
)
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covariateRef <- DatabaseConnector::querySql(connection, covariateRefSql, snakeCaseToCamelCase = TRUE)
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covariateRef$analysisId <- rep(as.numeric(covariateSettings$analysisId), length = nrow(covariateRef))

‎R/GetCovariatesFromOtherCohorts.R‎

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@@ -38,10 +38,12 @@ getDbCohortBasedCovariatesData <- function(connection,
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rowIdField = "subject_id",
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covariateSettings,
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aggregated = FALSE,
41-
minCharacterizationMean = 0) {
41+
minCharacterizationMean = 0,
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tempEmulationSchema = NULL) {
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errorMessages <- checkmate::makeAssertCollection()
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checkmate::assertClass(connection, "DatabaseConnectorConnection", add = errorMessages)
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checkmate::assertCharacter(oracleTempSchema, len = 1, null.ok = TRUE, add = errorMessages)
46+
checkmate::assertCharacter(tempEmulationSchema, len = 1, null.ok = TRUE, add = errorMessages)
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checkmate::assertCharacter(cdmDatabaseSchema, len = 1, null.ok = TRUE, add = errorMessages)
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checkmate::assertCharacter(cohortTable, len = 1, add = errorMessages)
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checkmate::assertIntegerish(cohortId, add = errorMessages)
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5658
warning("cohortId argument has been deprecated, please use cohortIds")
5759
cohortIds <- cohortId
5860
}
61+
if (!is.null(oracleTempSchema) && oracleTempSchema != "") {
62+
rlang::warn("The 'oracleTempSchema' argument is deprecated. Use 'tempEmulationSchema' instead.",
63+
.frequency = "regularly",
64+
.frequency_id = "oracleTempSchema"
65+
)
66+
tempEmulationSchema <- oracleTempSchema
67+
}
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6069
start <- Sys.time()
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message("Constructing covariates from other cohorts")
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dropTableIfExists = TRUE,
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createTable = TRUE,
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tempTable = TRUE,
72-
oracleTempSchema = oracleTempSchema,
81+
tempEmulationSchema = tempEmulationSchema,
7382
camelCaseToSnakeCase = TRUE
7483
)
7584
if (is.null(covariateSettings$covariateCohortTable)) {
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137146
}
138147
result <- getDbDefaultCovariateData(
139148
connection = connection,
140-
oracleTempSchema = oracleTempSchema,
149+
tempEmulationSchema = tempEmulationSchema,
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cdmDatabaseSchema = cdmDatabaseSchema,
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cohortTable = cohortTable,
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cohortIds = cohortIds,
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sql = sql,
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progressBar = FALSE,
156165
reportOverallTime = FALSE,
157-
oracleTempSchema = oracleTempSchema
166+
tempEmulationSchema = tempEmulationSchema
158167
)
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return(result)
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}

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