Merge pull request #257 from OHDSI/develop

Release v3.5.2
OHDSI · May 2, 2024 · f4536fb · f4536fb
2 parents a93992b + f2a850c
commit f4536fb
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -13,3 +13,5 @@ deploy.sh
 compare_versions
 _pkgdown.yml
 nbactions.xml
+^CRAN-SUBMISSION$
+^cran-comments\.md$
diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION
@@ -0,0 +1,3 @@
+Version: 3.5.2
+Date: 2024-04-30 18:12:58 UTC
+SHA: fe1f8048024d84e8079e872e60c4623c9d0c5c5f
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,18 +1,19 @@
 Package: FeatureExtraction
 Type: Package
 Title: Generating Features for a Cohort
-Version: 3.5.1
-Date: 2024-04-22
+Version: 3.5.2
+Date: 2024-05-01
 Authors@R: c(
   person("Martijn", "Schuemie", , "schuemie@ohdsi.org", role = c("aut")),
   person("Marc", "Suchard", role = c("aut")),
   person("Patrick", "Ryan", role = c("aut")),
   person("Jenna", "Reps", role = c("aut")),
-  person("Anthony", "Sena", , "sena@ohdsi.org", role = c("aut", "cre")),
-  person("Ger", "Inberg", role = c("aut"))
+  person("Anthony", "Sena", , "sena@ohdsi.org", role = c("aut")),
+  person("Ger", "Inberg", , "g.inberg@erasmusmc.nl", role = c("aut", "cre")),
+  person("Observational Health Data Science and Informatics", role = c("cph"))
   )
-Maintainer: Anthony Sena <sena@ohdsi.org>
-Description: An R package for generating features (covariates) for a cohort using data in the Common Data Model.
+Maintainer: Ger Inberg <g.inberg@erasmusmc.nl>
+Description: An R interface for generating features for a cohort using data in the Common Data Model. Features can be constructed using default or custom made feature definitions. Furthermore it's possible to aggregate features and get the summary statistics.
 Depends:
   R (>= 3.2.2),
   DatabaseConnector (>= 3.0.0),
@@ -35,10 +36,10 @@ Suggests:
   testthat,
   knitr,
   rmarkdown,
-  Eunomia,
-  withr
-Remotes:
-  ohdsi/Eunomia
+  Eunomia (>= 2.0.0),
+  withr,
+  curl,
+  httr
 License: Apache License 2.0
 VignetteBuilder: knitr
 URL: https://github.com/OHDSI/FeatureExtraction

diff --git a/NAMESPACE b/NAMESPACE
@@ -13,6 +13,7 @@ export(createDefaultCovariateSettings)
 export(createDefaultTemporalCovariateSettings)
 export(createDetailedCovariateSettings)
 export(createDetailedTemporalCovariateSettings)
+export(createEmptyCovariateData)
 export(createTable1)
 export(createTable1CovariateSettings)
 export(createTemporalCovariateSettings)

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,8 @@
+FeatureExtraction 3.5.2
+=======================
+
+- Move FeatureExtraction to CRAN (#104)
+
 FeatureExtraction 3.5.1
 =======================
 

diff --git a/R/Aggregation.R b/R/Aggregation.R
@@ -24,8 +24,8 @@
 #' An object of class \code{covariateData}.
 #'
 #' @examples
-#' \dontrun{
-#' covariateData <- FeatureExtraction:::createEmptyCovariateData(
+#' \donttest{
+#' covariateData <- FeatureExtraction::createEmptyCovariateData(
 #'   cohortIds = 1,
 #'   aggregated = FALSE,
 #'   temporal = FALSE

diff --git a/R/CompareCohorts.R b/R/CompareCohorts.R
@@ -32,7 +32,7 @@
 #' of mean.
 #'
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' binaryCovDataFile <- system.file("testdata/binaryCovariateData.zip",
 #'   package = "FeatureExtraction"
 #' )

diff --git a/R/CovariateData.R b/R/CovariateData.R
@@ -52,9 +52,11 @@ setClass("CovariateData", contains = "Andromeda")
 #' @details
 #' The data will be written to a set of files in the folder specified by the user.
 #'
+#' @return No return value, called for side effects.
+#'
 #' @examples
-#' \dontrun{
-#' covariateData <- FeatureExtraction:::createEmptyCovariateData(
+#' \donttest{
+#' covariateData <- FeatureExtraction::createEmptyCovariateData(
 #'   cohortIds = 1,
 #'   aggregated = FALSE,
 #'   temporal = FALSE
@@ -96,7 +98,7 @@ saveCovariateData <- function(covariateData, file) {
 #' An object of class \code{CovariateData}.
 #'
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' binaryCovDataFile <- system.file("testdata/binaryCovariateData.zip",
 #'   package = "FeatureExtraction"
 #' )
@@ -183,7 +185,7 @@ print.summary.CovariateData <- function(x, ...) {
 #' A logical value.
 #'
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' binaryCovDataFile <- system.file("testdata/binaryCovariateData.zip",
 #'   package = "FeatureExtraction"
 #' )
@@ -204,8 +206,8 @@ isCovariateData <- function(x) {
 #' A logical value.
 #'
 #' @examples
-#' \dontrun{
-#' covariateData <- FeatureExtraction:::createEmptyCovariateData(
+#' \donttest{
+#' covariateData <- FeatureExtraction::createEmptyCovariateData(
 #'   cohortIds = 1,
 #'   aggregated = FALSE,
 #'   temporal = FALSE
@@ -232,8 +234,8 @@ isAggregatedCovariateData <- function(x) {
 #' A logical value.
 #'
 #' @examples
-#' \dontrun{
-#' covariateData <- FeatureExtraction:::createEmptyCovariateData(
+#' \donttest{
+#' covariateData <- FeatureExtraction::createEmptyCovariateData(
 #'   cohortIds = 1,
 #'   aggregated = FALSE,
 #'   temporal = FALSE
@@ -259,17 +261,19 @@ isTemporalCovariateData <- function(x) {
 #' @param temporal if the data is temporary
 #'
 #' @examples
-#' \dontrun{
-#' covariateData <- FeatureExtraction:::createEmptyCovariateData(
+#' \donttest{
+#' covariateData <- FeatureExtraction::createEmptyCovariateData(
 #'   cohortIds = 1,
 #'   aggregated = FALSE,
 #'   temporal = FALSE
 #' )
 #' }
-#' @return the empty CovariateData object
+#' @return an empty object of class \code{CovariateData}
 #'
+#' @export
 createEmptyCovariateData <- function(cohortIds, aggregated, temporal) {
   dummy <- tibble(
+    cohortDefinitionId = 1,
     covariateId = 1,
     covariateValue = 1
   )

diff --git a/R/DetailedCovariateSettings.R b/R/DetailedCovariateSettings.R
@@ -29,7 +29,7 @@
 #' An object of type \code{covariateSettings}, to be used in other functions.
 #'
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' analysisDetails <- createAnalysisDetails(
 #'   analysisId = 1,
 #'   sqlFileName = "DemographicsGender.sql",
@@ -78,7 +78,7 @@ createDetailedCovariateSettings <- function(analyses = list()) {
 #' An object of type \code{covariateSettings}, to be used in other functions.
 #'
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' analysisDetails <- createAnalysisDetails(
 #'   analysisId = 1,
 #'   sqlFileName = "DemographicsGender.sql",
@@ -193,7 +193,7 @@ createAnalysisDetails <- function(analysisId,
 #' An object of type \code{covariateSettings}, to be used in other functions.
 #'
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' covSettings <- createDefaultCovariateSettings()
 #' detailedSettings <- convertPrespecSettingsToDetailedSettings(covariateSettings = covSettings)
 #' }
@@ -225,7 +225,7 @@ convertPrespecSettingsToDetailedSettings <- function(covariateSettings) {
 #' An object of type \code{covariateSettings}, to be used in other functions.
 #'
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' covSettings <- createDefaultCovariateSettings(
 #'   includedCovariateConceptIds = c(1),
 #'   addDescendantsToInclude = FALSE,
@@ -273,7 +273,7 @@ createDefaultCovariateSettings <- function(includedCovariateConceptIds = c(),
 #' An object of type \code{covariateSettings}, to be used in other functions.
 #'
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' covSettings <- createDefaultTemporalCovariateSettings(
 #'   includedCovariateConceptIds = c(1),
 #'   addDescendantsToInclude = FALSE,

diff --git a/R/GetCovariates.R b/R/GetCovariates.R
@@ -67,7 +67,7 @@
 #' Returns an object of type \code{covariateData}, containing information on the covariates.
 #'
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' eunomiaConnectionDetails <- Eunomia::getEunomiaConnectionDetails()
 #' covSettings <- createDefaultCovariateSettings()
 #' Eunomia::createCohorts(

diff --git a/R/GetCovariatesFromCohortAttributes.R b/R/GetCovariatesFromCohortAttributes.R
@@ -25,7 +25,7 @@
 #' @template GetCovarParams
 #'
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' connectionDetails <- Eunomia::getEunomiaConnectionDetails()
 #' Eunomia::createCohorts(
 #'   connectionDetails = connectionDetails,
@@ -34,18 +34,6 @@
 #'   cohortTable = "cohort"
 #' )
 #' connection <- DatabaseConnector::connect(connectionDetails)
-#' sql <- "SELECT 1 AS attribute_definition_id, 'Length of observation in days' AS attribute_name
-#'        INTO @cohort_database_schema.@attribute_definition_table;"
-#' sql <- SqlRender::render(
-#'   sql,
-#'   cohort_database_schema = "main",
-#'   attribute_definition_table = "attribute_definition"
-#' )
-#' sql <- SqlRender::translate(
-#'   sql = sql,
-#'   targetDialect = attr(connection, "dbms")
-#' )
-#' DatabaseConnector::executeSql(connection, sql)
 #' covariateSettings <- createCohortAttrCovariateSettings(
 #'   attrDatabaseSchema = "main",
 #'   cohortAttrTable = "cohort_attribute",
@@ -196,7 +184,7 @@ getDbCohortAttrCovariatesData <- function(connection,
 #' An object of type \code{covariateSettings}, to be used in other functions.
 #'
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' covariateSettings <- createCohortAttrCovariateSettings(
 #'   analysisId = 1,
 #'   attrDatabaseSchema = "main",

diff --git a/R/GetDefaultCovariates.R b/R/GetDefaultCovariates.R
@@ -38,22 +38,25 @@
 #' @template GetCovarParams
 #'
 #' @examples
-#' \dontrun{
+#' \donttest{
+#' connectionDetails <- Eunomia::getEunomiaConnectionDetails()
+#' Eunomia::createCohorts(
+#'   connectionDetails = connectionDetails,
+#'   cdmDatabaseSchema = "main",
+#'   cohortDatabaseSchema = "main",
+#'   cohortTable = "cohort"
+#' )
 #' connection <- DatabaseConnector::connect(connectionDetails)
-#' Eunomia::createCohorts(connectionDetails)
 #'
 #' results <- getDbDefaultCovariateData(
 #'   connection = connection,
 #'   cdmDatabaseSchema = "main",
 #'   cohortTable = "cohort",
 #'   covariateSettings = createDefaultCovariateSettings(),
 #'   targetDatabaseSchema = "main",
-#'   targetCovariateTable = "ut_cov",
-#'   targetCovariateRefTable = "ut_cov_ref",
-#'   targetAnalysisRefTable = "ut_cov_analysis_ref"
+#'   targetCovariateTable = "ut_cov"
 #' )
 #' }
-#'
 #' @export
 getDbDefaultCovariateData <- function(connection,
                                       oracleTempSchema = NULL,

diff --git a/R/HelperFunctions.R b/R/HelperFunctions.R
@@ -23,8 +23,8 @@
 #' An object of type \code{covariateData}.
 #'
 #' @examples
-#' \dontrun{
-#' covariateData <- FeatureExtraction:::createEmptyCovariateData(
+#' \donttest{
+#' covariateData <- FeatureExtraction::createEmptyCovariateData(
 #'   cohortIds = 1,
 #'   aggregated = FALSE,
 #'   temporal = FALSE
@@ -72,10 +72,10 @@ filterByRowId <- function(covariateData, rowIds) {
 #' An object of type \code{covariateData}.
 #'
 #' @examples
-#' \dontrun{
-#' covariateData <- FeatureExtraction:::createEmptyCovariateData(
-#'   cohortIds = 1,
-#'   aggregated = FALSE,
+#' \donttest{
+#' covariateData <- FeatureExtraction::createEmptyCovariateData(
+#'   cohortIds = c(1, 2),
+#'   aggregated = TRUE,
 #'   temporal = FALSE
 #' )
 #'

diff --git a/R/Normalization.R b/R/Normalization.R
@@ -28,9 +28,11 @@
 #' @param normalize          Normalize the covariates? (dividing by the max).
 #' @param removeRedundancy   Should redundant covariates be removed?
 #'
+#' @return An object of class \code{CovariateData}.
+#'
 #' @examples
-#' \dontrun{
-#' covariateData <- FeatureExtraction:::createEmptyCovariateData(
+#' \donttest{
+#' covariateData <- FeatureExtraction::createEmptyCovariateData(
 #'   cohortIds = 1,
 #'   aggregated = FALSE,
 #'   temporal = FALSE

diff --git a/R/Table1.R b/R/Table1.R
@@ -24,7 +24,7 @@
 #' A specifications objects.
 #'
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' defaultTable1Specs <- getDefaultTable1Specifications()
 #' }
 #'
@@ -64,7 +64,7 @@ getDefaultTable1Specifications <- function() {
 #' A data frame, or, when \code{output = "list"} a list of two data frames.
 #'
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' eunomiaConnectionDetails <- Eunomia::getEunomiaConnectionDetails()
 #' covSettings <- createDefaultCovariateSettings()
 #' Eunomia::createCohorts(
@@ -680,7 +680,7 @@ createTable1 <- function(covariateData1,
 #' \code{\link{getDbCovariateData}} function.
 #'
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' table1CovSettings <- createTable1CovariateSettings(
 #'   specifications = getDefaultTable1Specifications(),
 #'   covariateSettings = createDefaultCovariateSettings(),

diff --git a/R/UnitTestHelperFunctions.R b/R/UnitTestHelperFunctions.R
@@ -23,11 +23,6 @@
 #' @return
 #' Returns an object of type \code{covariateSettings}, containing settings for the covariates.
 #'
-#' @examples
-#' \dontrun{
-#' looCovariateSettings <- .createLooCovariateSettings(useLengthOfObs = TRUE)
-#' }
-#'
 .createLooCovariateSettings <- function(useLengthOfObs = TRUE) {
   covariateSettings <- list(useLengthOfObs = useLengthOfObs)
   attr(covariateSettings, "fun") <- "FeatureExtraction:::.getDbLooCovariateData"
@@ -65,29 +60,6 @@
 #' @return
 #' Returns an object of type \code{covariateData}, containing information on the covariates.
 #'
-#' @examples
-#' \dontrun{
-#' eunomiaConnectionDetails <- Eunomia::getEunomiaConnectionDetails()
-#' covSettings <- .createLooCovariateSettings(useLengthOfObs = TRUE)
-#' Eunomia::createCohorts(
-#'   connectionDetails = eunomiaConnectionDetails,
-#'   cdmDatabaseSchema = "main",
-#'   cohortDatabaseSchema = "main",
-#'   cohortTable = "cohort"
-#' )
-#' connection <- DatabaseConnector::connect(connectionDetails)
-#' looCovariateData <- .getDbLooCovariateData(connection,
-#'   oracleTempSchema = NULL,
-#'   cdmDatabaseSchema = "main",
-#'   cohortTable = "cohort",
-#'   cohortId = 1,
-#'   cdmVersion = "5",
-#'   rowIdField = "subject_id",
-#'   covariateSettings = covSettings,
-#'   aggregated = FALSE
-#' )
-#' }
-#'
 .getDbLooCovariateData <- function(connection,
                                    oracleTempSchema = NULL,
                                    cdmDatabaseSchema,