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Merge pull request #257 from OHDSI/develop
Release v3.5.2
2 parents a93992b + f2a850c commit f4536fb

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‎.Rbuildignore‎

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compare_versions
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_pkgdown.yml
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nbactions.xml
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^CRAN-SUBMISSION$
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^cran-comments\.md$

‎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

‎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: 3.5.1
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Date: 2024-04-22
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Version: 3.5.2
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Date: 2024-05-01
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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")),
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person("Patrick", "Ryan", role = c("aut")),
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person("Jenna", "Reps", role = c("aut")),
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person("Anthony", "Sena", , "sena@ohdsi.org", role = c("aut", "cre")),
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person("Ger", "Inberg", role = c("aut"))
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person("Anthony", "Sena", , "sena@ohdsi.org", role = c("aut")),
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person("Ger", "Inberg", , "g.inberg@erasmusmc.nl", role = c("aut", "cre")),
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person("Observational Health Data Science and Informatics", role = c("cph"))
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)
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Maintainer: Anthony Sena <sena@ohdsi.org>
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Description: An R package for generating features (covariates) for a cohort using data in the Common Data Model.
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Maintainer: Ger Inberg <g.inberg@erasmusmc.nl>
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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.
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Depends:
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R (>= 3.2.2),
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DatabaseConnector (>= 3.0.0),
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testthat,
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knitr,
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rmarkdown,
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Eunomia,
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withr
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Remotes:
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ohdsi/Eunomia
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Eunomia (>= 2.0.0),
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withr,
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curl,
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httr
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License: Apache License 2.0
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VignetteBuilder: knitr
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URL: https://github.com/OHDSI/FeatureExtraction

‎NAMESPACE‎

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export(createDefaultTemporalCovariateSettings)
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export(createDetailedCovariateSettings)
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export(createDetailedTemporalCovariateSettings)
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export(createEmptyCovariateData)
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export(createTable1)
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export(createTable1CovariateSettings)
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export(createTemporalCovariateSettings)

‎NEWS.md‎

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FeatureExtraction 3.5.2
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=======================
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- Move FeatureExtraction to CRAN (#104)
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FeatureExtraction 3.5.1
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=======================
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‎R/Aggregation.R‎

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#' An object of class \code{covariateData}.
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#'
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#' @examples
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#' \dontrun{
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#' covariateData <- FeatureExtraction:::createEmptyCovariateData(
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#' \donttest{
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#' covariateData <- FeatureExtraction::createEmptyCovariateData(
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#' cohortIds = 1,
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#' aggregated = FALSE,
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#' temporal = FALSE

‎R/CompareCohorts.R‎

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#' of mean.
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#'
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#' @examples
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#' \dontrun{
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#' \donttest{
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#' binaryCovDataFile <- system.file("testdata/binaryCovariateData.zip",
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#' package = "FeatureExtraction"
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#' )

‎R/CovariateData.R‎

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#' @details
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#' The data will be written to a set of files in the folder specified by the user.
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#'
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#' @return No return value, called for side effects.
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#'
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#' @examples
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#' \dontrun{
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#' covariateData <- FeatureExtraction:::createEmptyCovariateData(
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#' \donttest{
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#' covariateData <- FeatureExtraction::createEmptyCovariateData(
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#' cohortIds = 1,
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#' aggregated = FALSE,
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#' temporal = FALSE
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#' An object of class \code{CovariateData}.
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#'
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#' @examples
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#' \dontrun{
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#' \donttest{
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#' binaryCovDataFile <- system.file("testdata/binaryCovariateData.zip",
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#' package = "FeatureExtraction"
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#' )
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#' A logical value.
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#'
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#' @examples
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#' \dontrun{
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#' \donttest{
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#' binaryCovDataFile <- system.file("testdata/binaryCovariateData.zip",
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#' package = "FeatureExtraction"
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#' )
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#' A logical value.
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#'
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#' @examples
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#' \dontrun{
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#' covariateData <- FeatureExtraction:::createEmptyCovariateData(
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#' \donttest{
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#' covariateData <- FeatureExtraction::createEmptyCovariateData(
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#' cohortIds = 1,
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#' aggregated = FALSE,
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#' temporal = FALSE
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#' A logical value.
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#'
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#' @examples
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#' \dontrun{
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#' covariateData <- FeatureExtraction:::createEmptyCovariateData(
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#' \donttest{
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#' covariateData <- FeatureExtraction::createEmptyCovariateData(
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#' cohortIds = 1,
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#' aggregated = FALSE,
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#' temporal = FALSE
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#' @param temporal if the data is temporary
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#'
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#' @examples
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#' \dontrun{
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#' covariateData <- FeatureExtraction:::createEmptyCovariateData(
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#' \donttest{
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#' covariateData <- FeatureExtraction::createEmptyCovariateData(
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#' cohortIds = 1,
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#' aggregated = FALSE,
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#' temporal = FALSE
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#' )
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#' }
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#' @return the empty CovariateData object
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#' @return an empty object of class \code{CovariateData}
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#'
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#' @export
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createEmptyCovariateData <- function(cohortIds, aggregated, temporal) {
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dummy <- tibble(
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cohortDefinitionId = 1,
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covariateId = 1,
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covariateValue = 1
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)

‎R/DetailedCovariateSettings.R‎

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#' An object of type \code{covariateSettings}, to be used in other functions.
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#'
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#' @examples
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#' \dontrun{
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#' \donttest{
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#' analysisDetails <- createAnalysisDetails(
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#' analysisId = 1,
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#' sqlFileName = "DemographicsGender.sql",
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#' An object of type \code{covariateSettings}, to be used in other functions.
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#'
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#' @examples
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#' \dontrun{
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#' \donttest{
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#' analysisDetails <- createAnalysisDetails(
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#' analysisId = 1,
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#' sqlFileName = "DemographicsGender.sql",
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#' An object of type \code{covariateSettings}, to be used in other functions.
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#'
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#' @examples
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#' \dontrun{
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#' \donttest{
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#' covSettings <- createDefaultCovariateSettings()
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#' detailedSettings <- convertPrespecSettingsToDetailedSettings(covariateSettings = covSettings)
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#' }
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#' An object of type \code{covariateSettings}, to be used in other functions.
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#'
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#' @examples
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#' \dontrun{
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#' \donttest{
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#' covSettings <- createDefaultCovariateSettings(
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#' includedCovariateConceptIds = c(1),
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#' addDescendantsToInclude = FALSE,
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#' An object of type \code{covariateSettings}, to be used in other functions.
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#'
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#' @examples
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#' \dontrun{
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#' \donttest{
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#' covSettings <- createDefaultTemporalCovariateSettings(
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#' includedCovariateConceptIds = c(1),
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#' addDescendantsToInclude = FALSE,

‎R/GetCovariates.R‎

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#' Returns an object of type \code{covariateData}, containing information on the covariates.
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#'
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#' @examples
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#' \dontrun{
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#' \donttest{
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#' eunomiaConnectionDetails <- Eunomia::getEunomiaConnectionDetails()
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#' covSettings <- createDefaultCovariateSettings()
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#' Eunomia::createCohorts(

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