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featureextraction

An R package for generating features (covariates) for a cohort using data in the Common Data Model.

https://github.com/ohdsi/featureextraction

Science Score: 36.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    3 of 36 committers (8.3%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (13.9%) to scientific vocabulary

Keywords

hades

Keywords from Contributors

chart genomics interactive projection serializer cycles packaging network-simulation shellcodes hacking
Last synced: 6 months ago · JSON representation

Repository

An R package for generating features (covariates) for a cohort using data in the Common Data Model.

Basic Info
Statistics
  • Stars: 65
  • Watchers: 28
  • Forks: 61
  • Open Issues: 52
  • Releases: 18
Topics
hades
Created almost 10 years ago · Last pushed 6 months ago
Metadata Files
Readme Changelog

README.md

FeatureExtraction

Build Status codecov.io CRAN status

FeatureExtraction is part of HADES.

Introduction

An R package for generating features (covariates) for a cohort using data in the Common Data Model.

Features

  • Takes a cohort as input.
  • Generates baseline features for that cohort.
  • Default covariates include all drugs, diagnoses, procedures, as well as age, comorbidity indexes, etc.
  • Support for creating custom covariates.
  • Generate paper-ready summary table of select population characteristics.

Technology

FeatureExtraction is an R package, with some functions implemented in C++.

System Requirements

Requires R (version 3.2.2 or higher). Installation on Windows requires RTools. FeatureExtraction require Java.

Getting Started

  1. See the instructions here for configuring your R environment, including RTools and Java.

  2. In R, use the following commands to download and install FeatureExtraction:

r install.packages("drat") drat::addRepo("OHDSI") install.packages("FeatureExtraction")

User Documentation

The documentation website can be found at https://ohdsi.github.io/FeatureExtraction/. PDF versions of the vignettes and package manual are here:

These vignettes are also available in Korean:

Support

Contributing

Read here how you can contribute to this package.

License

FeatureExtraction is licensed under Apache License 2.0

Development

FeatureExtraction is being developed in R Studio.

Development status

Ready for use

Acknowledgements

  • This project is supported in part through the National Science Foundation grant IIS 1251151.

Owner

  • Name: Observational Health Data Sciences and Informatics
  • Login: OHDSI
  • Kind: organization

GitHub Events

Total
  • Create event: 13
  • Issues event: 25
  • Release event: 5
  • Watch event: 6
  • Delete event: 1
  • Issue comment event: 24
  • Push event: 48
  • Pull request review comment event: 5
  • Pull request review event: 13
  • Pull request event: 28
  • Fork event: 4
Last Year
  • Create event: 13
  • Issues event: 25
  • Release event: 5
  • Watch event: 6
  • Delete event: 1
  • Issue comment event: 24
  • Push event: 48
  • Pull request review comment event: 5
  • Pull request review event: 13
  • Pull request event: 28
  • Fork event: 4

Committers

Last synced: 10 months ago

All Time
  • Total Commits: 468
  • Total Committers: 36
  • Avg Commits per committer: 13.0
  • Development Distribution Score (DDS): 0.635
Past Year
  • Commits: 74
  • Committers: 9
  • Avg Commits per committer: 8.222
  • Development Distribution Score (DDS): 0.189
Top Committers
Name Email Commits
schuemie s****e@o****g 171
Ger Inberg g****g@g****m 137
Anthony Sena a****5@i****m 38
Schuemie M****I@i****m 30
Marc Suchard m****d@g****m 14
chandryou a****a@g****m 6
PGrafkin p****a@g****m 6
Adler Perotte a****0@c****u 5
alex-odysseus a****o@o****m 5
Cornelius Raths c****s@n****m 5
Vitaly Koulakov v****v@f****m 4
Chris Knoll c****l@o****g 4
Tom White t****m@c****m 4
Sigfried Gold s****d@s****g 3
James Fairbanks j****s@g****u 3
alpivonka a****a@q****m 3
Ryan P****4@i****m 3
Admin_mschuemi A****i@i****m 2
git v****v@o****m 2
Edwin Cruz e****n@u****g 2
Adam Black a****3 2
Frank DeFalco f****o@o****g 2
Gowtham Rao g****o 2
oleg-odysseus o****f@g****m 2
dependabot[bot] 4****] 2
Rob Cavanaugh 4****h 1
ymolodkov y****v@e****m 1
molodkov yaroslav y****v@o****m 1
Melissa Rost m****t@g****u 1
Londhe A****2@i****m 1
and 6 more...
Committer Domains (Top 20 + Academic)
its.jnj.com: 6 odysseusinc.com: 4 ohdsi.org: 3 gtri.gatech.edu: 2 amgen.com: 1 epam.com: 1 unitedprospects.org: 1 quintiles.com: 1 sigfried.org: 1 cloudera.com: 1 firstlinesoftware.com: 1 nantmobile.com: 1 cumc.columbia.edu: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 37
  • Total pull requests: 45
  • Average time to close issues: 2 months
  • Average time to close pull requests: about 2 months
  • Total issue authors: 15
  • Total pull request authors: 9
  • Average comments per issue: 1.05
  • Average comments per pull request: 1.09
  • Merged pull requests: 35
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 16
  • Pull requests: 23
  • Average time to close issues: about 1 month
  • Average time to close pull requests: 4 days
  • Issue authors: 9
  • Pull request authors: 3
  • Average comments per issue: 0.69
  • Average comments per pull request: 0.13
  • Merged pull requests: 21
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • anthonysena (9)
  • ginberg (7)
  • schuemie (4)
  • gowthamrao (4)
  • jreps (4)
  • dimshitc (2)
  • haleyhuston1 (2)
  • sgasmanjj (2)
  • javier-gracia-tabuenca-tuni (2)
  • azimov (2)
  • pavgra (1)
  • conovermitch (1)
  • chrisknoll (1)
  • egillax (1)
  • fdefalco (1)
Pull Request Authors
  • ginberg (44)
  • schuemie (4)
  • anthonysena (3)
  • YaroslavTir (2)
  • alex-odysseus (2)
  • gowthamrao (2)
  • fdefalco (1)
  • sfortin1 (1)
  • dependabot[bot] (1)
  • chrisknoll (1)
  • cukarthik (1)
Top Labels
Issue Labels
bug (3) help wanted (1) good first issue (1) enhancement (1)
Pull Request Labels
dependencies (1) github_actions (1)

Packages

  • Total packages: 1
  • Total downloads:
    • cran 1,074 last-month
  • Total docker downloads: 245
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 9
  • Total maintainers: 1
cran.r-project.org: FeatureExtraction

Generating Features for a Cohort

  • Versions: 9
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 1,074 Last month
  • Docker Downloads: 245
Rankings
Dependent packages count: 27.8%
Dependent repos count: 35.7%
Average: 49.5%
Downloads: 84.9%
Maintainers (1)
g.inberg@erasmusmc.nl
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • Andromeda * depends
  • DatabaseConnector >= 3.0.0 depends
  • R >= 3.2.2 depends
  • DBI * imports
  • ParallelLogger >= 2.0.2 imports
  • RSQLite * imports
  • SqlRender >= 1.6.0 imports
  • cli * imports
  • dplyr * imports
  • jsonlite * imports
  • methods * imports
  • pillar * imports
  • rJava * imports
  • readr * imports
  • rlang * imports
  • Eunomia * suggests
  • knitr * suggests
  • rmarkdown * suggests
  • testthat * suggests
  • withr * suggests
pom.xml maven
  • org.json:json 20170516
  • org.ohdsi.sql:SqlRender 1.7.0
.github/workflows/R_CMD_check_Hades.yaml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • actions/create-release v1 composite
  • actions/download-artifact v2 composite
  • actions/upload-artifact v2 composite
  • r-lib/actions/setup-pandoc v1 composite
  • r-lib/actions/setup-r v1 composite
  • r-lib/actions/setup-tinytex v1 composite
.github/workflows/nightly_cleanup_Hades.yml actions
  • c-hive/gha-remove-artifacts v1 composite