Package: FeatureExtraction 3.13.0

Ger Inberg

FeatureExtraction: Generating Features for a Cohort

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.

Authors:Martijn Schuemie [aut], Marc Suchard [aut], Patrick Ryan [aut], Jenna Reps [aut], Anthony Sena [aut], Ger Inberg [aut, cre], Observational Health Data Science and Informatics [cph]

FeatureExtraction_3.13.0.tar.gz
FeatureExtraction_3.13.0.tar.gz(r-4.7-any)FeatureExtraction_3.13.0.tar.gz(r-4.6-any)
FeatureExtraction_3.13.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
FeatureExtraction/json (API)
NEWS

# Install 'FeatureExtraction' in R:
install.packages('FeatureExtraction', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/ohdsi/featureextraction/issues

Uses libs:
  • openjdk– OpenJDK Java runtime, using Hotspot JIT

On CRAN:

Conda:

openjdk

6.35 score 3 packages 250 scripts 1.1k downloads 32 exports 55 dependencies

Last updated from:d836133d5f. Checks:2 WARNING, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-x86_64WARNING343
source / vignettesOK216
linux-release-x86_64WARNING338
wasm-releaseOK139

Exports:aggregateCovariatescomputeStandardizedDifferenceconvertPrespecSettingsToDetailedSettingscreateAnalysisDetailscreateCohortAttrCovariateSettingscreateCohortBasedCovariateSettingscreateCohortBasedTemporalCovariateSettingscreateCovariateSettingscreateDefaultCovariateSettingscreateDefaultTemporalCovariateSettingscreateDetailedCovariateSettingscreateDetailedTemporalCovariateSettingscreateEmptyCovariateDatacreateTable1createTable1CovariateSettingscreateTemporalCovariateSettingscreateTemporalSequenceCovariateSettingsfilterByCohortDefinitionIdfilterByRowIdgetDbCohortAttrCovariatesDatagetDbCohortBasedCovariatesDatagetDbCovariateDatagetDbDefaultCovariateDatagetDefaultTable1SpecificationsisAggregatedCovariateDataisCovariateDataisTemporalCovariateDataloadCovariateDatasaveCovariateDatashowsummarytidyCovariateData

Dependencies:Andromedabackportsbitbit64blobcachemcheckmateclicliprcpp11crayonDatabaseConnectorDBIdbplyrdigestdplyrduckdbfastmapgenericsgluehmsjsonlitelifecyclemagrittrmemoisememuseParallelLoggerpillarpkgconfigprettyunitsprogresspurrrR6RcppreadrrJavarlangRSQLiterstudioapisnowSqlRenderstringistringrtibbletidyrtidyselecttriebeardtzdburltoolsutf8vctrsvroomwithrxml2zip

Creating covariates based on other cohorts

Martijn J. Schuemie

Rendered fromCreatingCovariatesBasedOnOtherCohorts.Rmdusingknitr::rmarkdownon Jun 04 2026.

Last update: 2024-05-02
Started: 2024-05-02

Creating covariates using cohort attributes

Martijn J. Schuemie

Rendered fromCreatingCovariatesUsingCohortAttributes.Rmdusingknitr::rmarkdownon Jun 04 2026.

Last update: 2024-05-02
Started: 2024-05-02

Creating custom covariate builders

Martijn J. Schuemie

Rendered fromCreatingCustomCovariateBuilders.Rmdusingknitr::rmarkdownon Jun 04 2026.

Last update: 2025-04-20
Started: 2024-05-02

Creating custom covariate builders (Korean)

Jeon Ga Bin & Martijn J. Schuemie

Rendered fromCreatingCustomCovariateBuildersKorean.Rmdusingknitr::rmarkdownon Jun 04 2026.

Last update: 2024-05-02
Started: 2024-05-02

Using FeatureExtraction

Martijn J. Schuemie

Rendered fromUsingFeatureExtraction.Rmdusingknitr::rmarkdownon Jun 04 2026.

Last update: 2024-05-02
Started: 2024-05-02

Using FeatureExtraction (Korean)

Jeon Ga Bin & Martijn J. Schuemie

Rendered fromUsingFeatureExtractionKorean.Rmdusingknitr::rmarkdownon Jun 04 2026.

Last update: 2024-05-02
Started: 2024-05-02

Readme and manuals

Help Manual

Help pageTopics
Get covariate settings.createLooCovariateSettings
Get covariate information from the database.getDbLooCovariateData
Aggregate covariate dataaggregateCovariates
Compute standardized difference of mean for all covariates.computeStandardizedDifference
Convert prespecified covariate settings into detailed covariate settingsconvertPrespecSettingsToDetailedSettings
Covariate DataCovariateData CovariateData-class show,CovariateData-method summary,CovariateData-method
Create detailed covariate settingscreateAnalysisDetails
Create cohort attribute covariate settingscreateCohortAttrCovariateSettings
Create settings for covariates based on other cohortscreateCohortBasedCovariateSettings
Create settings for temporal covariates based on other cohortscreateCohortBasedTemporalCovariateSettings
Create covariate settingscreateCovariateSettings
Create default covariate settingscreateDefaultCovariateSettings
Create default covariate settingscreateDefaultTemporalCovariateSettings
Create detailed covariate settingscreateDetailedCovariateSettings
Create detailed temporal covariate settingscreateDetailedTemporalCovariateSettings
Creates an empty covariate data objectcreateEmptyCovariateData
Create a table 1createTable1
Create covariate settings for a table 1createTable1CovariateSettings
Create covariate settingscreateTemporalCovariateSettings
Create covariate settingscreateTemporalSequenceCovariateSettings
Filter covariates by cohort definition IDsfilterByCohortDefinitionId
Filter covariates by row IDfilterByRowId
Getcovariate information from the database through the cohort_attribute tablegetDbCohortAttrCovariatesData
Get covariate information from the database based on other cohortsgetDbCohortBasedCovariatesData
Get covariate information from the databasegetDbCovariateData
Get default covariate information from the databasegetDbDefaultCovariateData
Get the default table 1 specificationsgetDefaultTable1Specifications
Check whether covariate data is aggregatedisAggregatedCovariateData
Check whether an object is a CovariateData objectisCovariateData
Check whether covariate data is temporalisTemporalCovariateData
Load the covariate data from a folderloadCovariateData
Utility function to set the cohort table & schema on createCohortBasedCovariateSettings with information from the execution settingsreplaceCovariateSettingsCohortSchemaTable
Save the covariate data to foldersaveCovariateData
Tidy covariate datatidyCovariateData