Package: FeatureExtraction 3.14.0

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_3.14.0.tar.gz
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manual.pdf |manual.html
DESCRIPTION |NEWS
card.svg |card.png
FeatureExtraction/json (API)

# Install 'FeatureExtraction' in R:
install.packages('FeatureExtraction', repos = c('https://ohdsi.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:

hadesopenjdk

10.75 score 72 stars 3 packages 292 scripts 1.2k downloads 32 exports 55 dependencies

Last updated from:53266f0233. Checks:7 WARNING, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64WARNING431
source / vignettesOK214
linux-release-x86_64WARNING374
macos-release-arm64WARNING308
macos-oldrel-arm64WARNING337
windows-develWARNING357
windows-releaseWARNING378
windows-oldrelWARNING341
wasm-releaseOK168

Exports:aggregateCovariatescomputeStandardizedDifferenceconvertPrespecSettingsToDetailedSettingscreateAnalysisDetailscreateCohortAttrCovariateSettingscreateCohortBasedCovariateSettingscreateCohortBasedTemporalCovariateSettingscreateCovariateSettingscreateDefaultCovariateSettingscreateDefaultTemporalCovariateSettingscreateDetailedCovariateSettingscreateDetailedTemporalCovariateSettingscreateEmptyCovariateDatacreateTable1createTable1CovariateSettingscreateTemporalCovariateSettingscreateTemporalSequenceCovariateSettingsfilterByCohortDefinitionIdfilterByRowIdgetDbCohortAttrCovariatesDatagetDbCohortBasedCovariatesDatagetDbCovariateDatagetDbDefaultCovariateDatagetDefaultTable1SpecificationsisAggregatedCovariateDataisCovariateDataisTemporalCovariateDataloadCovariateDatasaveCovariateDatashowsummarytidyCovariateData

Dependencies:Andromedabackportsbitbit64blobcachemcheckmateclicliprcpp11crayonDatabaseConnectorDBIdbplyrdigestdplyrduckdbfastmapgenericsgluehmsjsonlitelifecyclemagrittrmemoisememuseParallelLoggerpillarpkgconfigprettyunitsprogresspurrrR6RcppreadrrJavarlangRSQLiterstudioapisnowSqlRenderstringistringrtibbletidyrtidyselecttriebeardtzdburltoolsutf8vctrsvroomwithrxml2zip

Creating custom covariate builders
Introduction | Overview | Covariate settings function | Example function | Covariate construction function | Function inputs | Function outputs | Using the custom covariate builder

Last update: 2026-06-28
Started: 2016-03-25

Creating custom covariate builders (Korean)
서론 | 개요 | 공변량 설정 함수 | 함수 예제 | 공변량 구성 함수 | 함수 입력 | 함수 출력 | 사용자 지정 공변량 빌더 사용

Last update: 2026-06-28
Started: 2019-07-19

Using FeatureExtraction
Introduction | Covariate settings | Using the default set of covariates | Using prespecified analyses | Creating a set of custom covariates | Temporal covariates | Constructing covariates for a cohort of interest | Configuring the connection to the server | Creating a cohort of interest | Creating per-person covariates for a cohort of interest | Per-person covariate output format | Saving the data to file | Removing infrequent covariates, normalizing, and removing redundancy | Creating aggregated covariates for a cohort of interest | Aggregated covariate output format | Creating a table 1 | Comparing two cohorts

Last update: 2026-06-28
Started: 2017-10-05

Using FeatureExtraction (Korean)
서론 | 공변량 설정 | 기본 공변량 집합 사용하기 | 사전 지정된 분석 사용 | 사용자 공변량 집합을 생성 | 시간 공변량 | 관심 코호트에 대한 공변량 구성 | 서버 연결 설정 | 관심 코호트 생성 | 관심 코호트에 대한 1인당 공변량 생성 | 사용자 공변량 출력 형식 | 데이터를 파일로 저장 | 간헐적인 공변량 제거, 정규화 및 중복 제거 | 코호트에 대한 집계 공변량 생성 | 집계 공변량 출력 형식 | 테이블 만들기 1

Last update: 2026-06-28
Started: 2019-07-19

Creating covariates using cohort attributes
Introduction | Overview | Populating the cohort_attribute and attribute_definition tables | Example | Creating the cohort attributes and attributes definitions | Using the attributes as covariates

Last update: 2024-04-22
Started: 2016-03-25

Creating covariates based on other cohorts
Introduction | Overview | Populate a table with the cohorts to be used for covariate construction. | Example | Creating the cohort attributes and attributes definitions | Using the cohort as covariate

Last update: 2023-06-29
Started: 2023-06-29

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