{ "_id": "6a12a909acfb0bcc41d1592e", "Package": "FeatureExtraction", "Type": "Package", "Title": "Generating Features for a Cohort", "Version": "3.13.0", "Date": "2026-03-05", "Authors@R": "c(\nperson(\"Martijn\", \"Schuemie\", , \"schuemie@ohdsi.org\", role = c(\"aut\")),\nperson(\"Marc\", \"Suchard\", role = c(\"aut\")),\nperson(\"Patrick\", \"Ryan\", role = c(\"aut\")),\nperson(\"Jenna\", \"Reps\", role = c(\"aut\")),\nperson(\"Anthony\", \"Sena\", , \"sena@ohdsi.org\", role = c(\"aut\")),\nperson(\"Ger\", \"Inberg\", , \"g.inberg@erasmusmc.nl\", role = c(\"aut\", \"cre\")),\nperson(\"Observational Health Data Science and Informatics\", role = c(\"cph\"))\n)", "Maintainer": "Ger Inberg ", "Description": "An R interface for generating features for a cohort using\ndata in the Common Data Model. Features can be constructed\nusing default or custom made feature definitions. Furthermore\nit's possible to aggregate features and get the summary\nstatistics.", "License": "Apache License 2.0", "VignetteBuilder": "knitr", "URL": "https://github.com/OHDSI/FeatureExtraction", "BugReports": "https://github.com/OHDSI/FeatureExtraction/issues", "NeedsCompilation": "no", "RoxygenNote": "7.3.3", "Encoding": "UTF-8", "Language": "en-US", "Config/pak/sysreqs": "make default-jdk libicu-dev libxml2-dev libx11-dev\nxz-utils", "Repository": "https://ohdsi.r-universe.dev", "Date/Publication": "2026-03-05 22:05:41 UTC", "RemoteUrl": "https://github.com/ohdsi/featureextraction", "RemoteRef": "HEAD", "RemoteSha": "2c9311e8b0706b22b28afc9a9e37cfeacf9b2111", "Packaged": { "Date": "2026-05-24 07:21:36 UTC", "User": "root" }, "Author": "Martijn Schuemie [aut],\nMarc Suchard [aut],\nPatrick Ryan [aut],\nJenna Reps [aut],\nAnthony Sena [aut],\nGer Inberg [aut, cre],\nObservational Health Data Science and Informatics [cph]", "MD5sum": "9a9cc05cd78baaefddfd3a47e4cacdc2", "_user": "ohdsi", "_type": "src", "_file": "FeatureExtraction_3.13.0.tar.gz", "_fileid": "b0d8dd25066624ecb1f0949404270d42cee265cb402517483b50b467b466cbd8", "_filesize": 7425492, "_sha256": "b0d8dd25066624ecb1f0949404270d42cee265cb402517483b50b467b466cbd8", "_created": "2026-05-24T07:21:36.000Z", "_published": "2026-05-24T07:30:17.881Z", "_distro": "noble", "_jobs": [ { "job": 77580125320, "time": 368, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "7183260756" }, { "job": 77580125314, "time": 383, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7183262141" }, { "job": 77580125317, "time": 237, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "7183257688" }, { "job": 77580125321, "time": 318, "config": "macos-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7183263726" }, { "job": 77579929354, "time": 211, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7183220754" }, { "job": 77580125312, "time": 140, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7183236402" }, { "job": 77580125358, "time": 158, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "7183238388" }, { "job": 77580125379, "time": 327, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "7183256425" }, { "job": 77580125368, "time": 479, "config": "windows-release", "r": "4.6.0", "check": "WARNING", "artifact": "7183271759" } ], "_buildurl": "https://github.com/r-universe/ohdsi/actions/runs/26354958647", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/ohdsi/featureextraction", "_commit": { "id": "2c9311e8b0706b22b28afc9a9e37cfeacf9b2111", "author": "Anthony Sena ", "committer": "GitHub ", "message": "Release v3.13", "time": 1772748341 }, "_maintainer": { "name": "Ger Inberg", "email": "g.inberg@erasmusmc.nl" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.2.2", "role": "Depends" }, { "package": "DatabaseConnector", "version": ">= 3.0.0", "role": "Depends" }, { "package": "Andromeda", "version": ">= 1.0.0", "role": "Depends" }, { "package": "methods", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "rJava", "role": "Imports" }, { "package": "jsonlite", "role": "Imports" }, { "package": "SqlRender", "version": ">= 1.18.0", "role": "Imports" }, { "package": "ParallelLogger", "version": ">= 2.0.2", "role": "Imports" }, { "package": "cli", "role": "Imports" }, { "package": "pillar", "role": "Imports" }, { "package": "readr", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "RSQLite", "role": "Imports" }, { "package": "DBI", "role": "Imports" }, { "package": "checkmate", "role": "Imports" }, { "package": "vroom", "role": "Imports" }, { "package": "testthat", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "Eunomia", "version": ">= 2.0.0", "role": "Suggests" }, { "package": "withr", "role": "Suggests" }, { "package": "curl", "role": "Suggests" }, { "package": "httr", "role": "Suggests" } ], "_owner": "ohdsi", "_selfowned": true, "_usedby": 3, "_updates": [ { "week": "2025-36", "n": 1 }, { "week": "2025-44", "n": 1 }, { "week": "2026-10", "n": 1 } ], "_tags": [ { "name": "v3.11.0", "date": "2025-09-02" }, { "name": "v3.12.0", "date": "2025-10-28" }, { "name": "v3.13.0", "date": "2026-03-05" } ], "_topics": [ "hades", "openjdk" ], "_stars": 71, "_contributors": [ { "user": "schuemie", "count": 210, "uuid": 6713328 }, { "user": "ginberg", "count": 202, "uuid": 7089667 }, { "user": "anthonysena", "count": 55, "uuid": 12902366 }, { "user": "msuchard", "count": 17, "uuid": 149039 }, { "user": "pavgra", "count": 6, "uuid": 10010071 }, { "user": "chandryou", "count": 6, "uuid": 18287430 }, { "user": "aperotte", "count": 5, "uuid": 77780 }, { "user": "chrisknoll", "count": 4, "uuid": 6818777 }, { "user": "tomwhite", "count": 4, "uuid": 85085 }, { "user": "wivern", "count": 4, "uuid": 1109753 }, { "user": "jpfairbanks", "count": 3, "uuid": 2753998 }, { "user": "sigfried", "count": 3, "uuid": 1586931 }, { "user": "gowthamrao", "count": 2, "uuid": 13936600 }, { "user": "oleg-odysseus", "count": 2, "uuid": 177556342 }, { "user": "fdefalco", "count": 2, "uuid": 6586384 }, { "user": "ablack3", "count": 2, "uuid": 10227522 }, { "user": "azimov", "count": 1, "uuid": 180659 }, { "user": "rbcavanaugh", "count": 1, "uuid": 46727239 }, { "user": "alondhe", "count": 1, "uuid": 8037742 }, { "user": "jreps", "count": 1, "uuid": 15040036 }, { "user": "mdlavallee92", "count": 1, "uuid": 44976592 }, { "user": "yuxitian", "count": 1, "uuid": 7904590 } ], "_userbio": { "uuid": 6570077, "type": "organization", "name": "Observational Health Data Sciences and Informatics" }, "_downloads": { "count": 1182, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/FeatureExtraction" }, "_devurl": "https://github.com/ohdsi/featureextraction", "_searchresults": 258, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/FeatureExtraction.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/ohdsi/featureextraction", "_realowner": "ohdsi", "_cranurl": true, "_releases": [ { "version": "3.5.2", "date": "2024-05-01" }, { "version": "3.6.0", "date": "2024-07-15" }, { "version": "3.7.0", "date": "2024-09-03" }, { "version": "3.7.1", "date": "2024-09-12" }, { "version": "3.7.2", "date": "2024-10-18" }, { "version": "3.8.0", "date": "2025-03-22" }, { "version": "3.9.0", "date": "2025-04-20" }, { "version": "3.10.0", "date": "2025-05-08" }, { "version": "3.11.0", "date": "2025-09-01" }, { "version": "3.12.0", "date": "2025-10-28" }, { "version": "3.13.0", "date": "2026-03-06" } ], "_exports": [ "aggregateCovariates", "computeStandardizedDifference", "convertPrespecSettingsToDetailedSettings", "createAnalysisDetails", "createCohortAttrCovariateSettings", "createCohortBasedCovariateSettings", "createCohortBasedTemporalCovariateSettings", "createCovariateSettings", "createDefaultCovariateSettings", "createDefaultTemporalCovariateSettings", "createDetailedCovariateSettings", "createDetailedTemporalCovariateSettings", "createEmptyCovariateData", "createTable1", "createTable1CovariateSettings", "createTemporalCovariateSettings", "createTemporalSequenceCovariateSettings", "filterByCohortDefinitionId", "filterByRowId", "getDbCohortAttrCovariatesData", "getDbCohortBasedCovariatesData", "getDbCovariateData", "getDbDefaultCovariateData", "getDefaultTable1Specifications", "isAggregatedCovariateData", "isCovariateData", "isTemporalCovariateData", "loadCovariateData", "saveCovariateData", "show", "summary", "tidyCovariateData" ], "_help": [ { "page": "dot-createLooCovariateSettings", "title": "Get covariate settings", "topics": [ ".createLooCovariateSettings" ] }, { "page": "dot-getDbLooCovariateData", "title": "Get covariate information from the database", "topics": [ ".getDbLooCovariateData" ] }, { "page": "aggregateCovariates", "title": "Aggregate covariate data", "topics": [ "aggregateCovariates" ] }, { "page": "computeStandardizedDifference", "title": "Compute standardized difference of mean for all covariates.", "topics": [ "computeStandardizedDifference" ] }, { "page": "convertPrespecSettingsToDetailedSettings", "title": "Convert prespecified covariate settings into detailed covariate settings", "topics": [ "convertPrespecSettingsToDetailedSettings" ] }, { "page": "CovariateData-class", "title": "Covariate Data", "topics": [ "CovariateData", "CovariateData-class", "show,CovariateData-method", "summary,CovariateData-method" ] }, { "page": "createAnalysisDetails", "title": "Create detailed covariate settings", "topics": [ "createAnalysisDetails" ] }, { "page": "createCohortAttrCovariateSettings", "title": "Create cohort attribute covariate settings", "topics": [ "createCohortAttrCovariateSettings" ] }, { "page": "createCohortBasedCovariateSettings", "title": "Create settings for covariates based on other cohorts", "topics": [ "createCohortBasedCovariateSettings" ] }, { "page": "createCohortBasedTemporalCovariateSettings", "title": "Create settings for temporal covariates based on other cohorts", "topics": [ "createCohortBasedTemporalCovariateSettings" ] }, { "page": "createCovariateSettings", "title": "Create covariate settings", "topics": [ "createCovariateSettings" ] }, { "page": "createDefaultCovariateSettings", "title": "Create default covariate settings", "topics": [ "createDefaultCovariateSettings" ] }, { "page": "createDefaultTemporalCovariateSettings", "title": "Create default covariate settings", "topics": [ "createDefaultTemporalCovariateSettings" ] }, { "page": "createDetailedCovariateSettings", "title": "Create detailed covariate settings", "topics": [ "createDetailedCovariateSettings" ] }, { "page": "createDetailedTemporalCovariateSettings", "title": "Create detailed temporal covariate settings", "topics": [ "createDetailedTemporalCovariateSettings" ] }, { "page": "createEmptyCovariateData", "title": "Creates an empty covariate data object", "topics": [ "createEmptyCovariateData" ] }, { "page": "createTable1", "title": "Create a table 1", "topics": [ "createTable1" ] }, { "page": "createTable1CovariateSettings", "title": "Create covariate settings for a table 1", "topics": [ "createTable1CovariateSettings" ] }, { "page": "createTemporalCovariateSettings", "title": "Create covariate settings", "topics": [ "createTemporalCovariateSettings" ] }, { "page": "createTemporalSequenceCovariateSettings", "title": "Create covariate settings", "topics": [ "createTemporalSequenceCovariateSettings" ] }, { "page": "filterByCohortDefinitionId", "title": "Filter covariates by cohort definition IDs", "topics": [ "filterByCohortDefinitionId" ] }, { "page": "filterByRowId", "title": "Filter covariates by row ID", "topics": [ "filterByRowId" ] }, { "page": "getDbCohortAttrCovariatesData", "title": "Getcovariate information from the database through the cohort_attribute table", "topics": [ "getDbCohortAttrCovariatesData" ] }, { "page": "getDbCohortBasedCovariatesData", "title": "Get covariate information from the database based on other cohorts", "topics": [ "getDbCohortBasedCovariatesData" ] }, { "page": "getDbCovariateData", "title": "Get covariate information from the database", "topics": [ "getDbCovariateData" ] }, { "page": "getDbDefaultCovariateData", "title": "Get default covariate information from the database", "topics": [ "getDbDefaultCovariateData" ] }, { "page": "getDefaultTable1Specifications", "title": "Get the default table 1 specifications", "topics": [ "getDefaultTable1Specifications" ] }, { "page": "isAggregatedCovariateData", "title": "Check whether covariate data is aggregated", "topics": [ "isAggregatedCovariateData" ] }, { "page": "isCovariateData", "title": "Check whether an object is a CovariateData object", "topics": [ "isCovariateData" ] }, { "page": "isTemporalCovariateData", "title": "Check whether covariate data is temporal", "topics": [ "isTemporalCovariateData" ] }, { "page": "loadCovariateData", "title": "Load the covariate data from a folder", "topics": [ "loadCovariateData" ] }, { "page": "replaceCovariateSettingsCohortSchemaTable", "title": "Utility function to set the cohort table & schema on createCohortBasedCovariateSettings with information from the execution settings", "topics": [ "replaceCovariateSettingsCohortSchemaTable" ] }, { "page": "saveCovariateData", "title": "Save the covariate data to folder", "topics": [ "saveCovariateData" ] }, { "page": "tidyCovariateData", "title": "Tidy covariate data", "topics": [ "tidyCovariateData" ] } ], "_readme": "https://github.com/ohdsi/featureextraction/raw/HEAD/README.md", "_rundeps": [ "Andromeda", "backports", "bit", "bit64", "blob", "cachem", "checkmate", "cli", "clipr", "cpp11", "crayon", "DatabaseConnector", "DBI", "dbplyr", "digest", "dplyr", "duckdb", "fastmap", "generics", "glue", "hms", "jsonlite", "lifecycle", "magrittr", "memoise", "memuse", "ParallelLogger", "pillar", "pkgconfig", "prettyunits", "progress", "purrr", "R6", "Rcpp", "readr", "rJava", "rlang", "RSQLite", "rstudioapi", "snow", "SqlRender", "stringi", "stringr", "tibble", "tidyr", "tidyselect", "triebeard", "tzdb", "urltools", "utf8", "vctrs", "vroom", "withr", "xml2", "zip" ], "_sysdeps": [ { "shlib": "libjvm", "package": "openjdk-21-jre-headless", "headers": "openjdk-21-jre-headless", "source": "openjdk", "version": "21.0.10+7-1~24.04", "name": "openjdk", "homepage": "https://openjdk.java.net/", "description": "OpenJDK Java runtime, using Hotspot JIT (headless)" } ], "_vignettes": [ { "source": "CreatingCovariatesBasedOnOtherCohorts.Rmd", "filename": "CreatingCovariatesBasedOnOtherCohorts.html", "title": "Creating covariates based on other cohorts", "author": "Martijn J. Schuemie", "engine": "knitr::rmarkdown", "headings": [ "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" ], "created": "2023-06-29 21:49:38", "modified": "2023-06-29 21:49:38", "commits": 1 }, { "source": "CreatingCovariatesUsingCohortAttributes.Rmd", "filename": "CreatingCovariatesUsingCohortAttributes.html", "title": "Creating covariates using cohort attributes", "author": "Martijn J. Schuemie", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Overview", "Populating the cohort_attribute and attribute_definition tables", "Example", "Creating the cohort attributes and attributes definitions", "Using the attributes as covariates" ], "created": "2016-03-25 12:48:15", "modified": "2024-04-22 19:00:41", "commits": 12 }, { "source": "CreatingCustomCovariateBuilders.Rmd", "filename": "CreatingCustomCovariateBuilders.html", "title": "Creating custom covariate builders", "author": "Martijn J. Schuemie", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Overview", "Covariate settings function", "Example function", "Covariate construction function", "Function inputs", "Function outputs", "Using the custom covariate builder" ], "created": "2016-03-25 12:48:15", "modified": "2025-04-22 05:24:47", "commits": 13 }, { "source": "CreatingCustomCovariateBuildersKorean.Rmd", "filename": "CreatingCustomCovariateBuildersKorean.html", "title": "Creating custom covariate builders (Korean)", "author": "Jeon Ga Bin & Martijn J. Schuemie", "engine": "knitr::rmarkdown", "headings": [ "서론", "개요", "공변량 설정 함수", "함수 예제", "공변량 구성 함수", "함수 입력", "함수 출력", "사용자 지정 공변량 빌더 사용" ], "created": "2019-07-19 15:00:43", "modified": "2024-04-22 19:00:41", "commits": 4 }, { "source": "UsingFeatureExtraction.Rmd", "filename": "UsingFeatureExtraction.html", "title": "Using FeatureExtraction", "author": "Martijn J. Schuemie", "engine": "knitr::rmarkdown", "headings": [ "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" ], "created": "2017-10-05 15:06:04", "modified": "2024-05-02 16:38:18", "commits": 17 }, { "source": "UsingFeatureExtractionKorean.Rmd", "filename": "UsingFeatureExtractionKorean.html", "title": "Using FeatureExtraction (Korean)", "author": "Jeon Ga Bin & Martijn J. Schuemie", "engine": "knitr::rmarkdown", "headings": [ "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" ], "created": "2019-07-19 08:22:55", "modified": "2024-05-02 16:38:18", "commits": 9 } ], "_score": 10.566199844840112, "_indexed": true, "_nocasepkg": "featureextraction", "_universes": [ "ohdsi" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "3.13.0", "date": "2026-05-24T07:24:16.000Z", "distro": "noble", "commit": "2c9311e8b0706b22b28afc9a9e37cfeacf9b2111", "fileid": "d65fc8ea8966476cc974d7e5f1731645e1b56592b11e823554b48040d728f8f8", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/ohdsi/actions/runs/26354958647" }, { "r": "4.6.0", "os": "linux", "version": "3.13.0", "date": "2026-05-24T07:24:20.000Z", "distro": "noble", "commit": "2c9311e8b0706b22b28afc9a9e37cfeacf9b2111", "fileid": "3707acf25e74953c64b7b7cc793ac996e176003bdfeb58f9fca30b72b6cb3c8d", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/ohdsi/actions/runs/26354958647" }, { "r": "4.5.3", "os": "mac", "version": "3.13.0", "date": "2026-05-24T07:25:04.000Z", "commit": "2c9311e8b0706b22b28afc9a9e37cfeacf9b2111", "fileid": "76ffd92ece9d33d4d091d157a60ee4cfe3d504415bb6e5df79daacc39f7aadca", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/ohdsi/actions/runs/26354958647" }, { "r": "4.6.0", "os": "mac", "version": "3.13.0", "date": "2026-05-24T07:25:04.000Z", "commit": "2c9311e8b0706b22b28afc9a9e37cfeacf9b2111", "fileid": "717839eddd279c89322eed4762b745dbb238743f3087496ace56676eec617f3a", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/ohdsi/actions/runs/26354958647" }, { "r": "4.6.0", "os": "wasm", "version": "3.13.0", "date": "2026-05-24T07:24:22.000Z", "commit": "2c9311e8b0706b22b28afc9a9e37cfeacf9b2111", "fileid": "8b13f1a8a428535bf44727762b8f2679dafb6f1c9d240416b402f175cd3724d1", "status": "success", "buildurl": "https://github.com/r-universe/ohdsi/actions/runs/26354958647" }, { "r": "4.7.0", "os": "win", "version": "3.13.0", "date": "2026-05-24T07:23:15.000Z", "commit": "2c9311e8b0706b22b28afc9a9e37cfeacf9b2111", "fileid": "b71213ef3c7bf2983f90e54ec2273d5128cb66eb7496ad5a6186192c19e18580", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/ohdsi/actions/runs/26354958647" }, { "r": "4.5.3", "os": "win", "version": "3.13.0", "date": "2026-05-24T07:23:07.000Z", "commit": "2c9311e8b0706b22b28afc9a9e37cfeacf9b2111", "fileid": "c662b8d68ae799e1c49143a92793e65b055b4b7d4aabdfb9284c3276940517af", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/ohdsi/actions/runs/26354958647" }, { "r": "4.6.0", "os": "win", "version": "3.13.0", "date": "2026-05-24T07:25:13.000Z", "commit": "2c9311e8b0706b22b28afc9a9e37cfeacf9b2111", "fileid": "b0fc97651a34aad8415fbeedc3a5d6946608c1f19fe5777760a2f184280d9293", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/ohdsi/actions/runs/26354958647" } ] }