Knowledge-Enhanced Electronic Profile Review (KEEPER)

KEEPER is part of HADES.

Introduction

An R package for reviewing patient profiles for phenotype validation.

Features

• Extracts patient level data for a) a random sample of patients in a cohort or b) patients in a user-specified list and formats it according to the KEEPER principles.
• Allows additional de-identification through replacing OMOP personId with a new random id.

Examples

keeper <- createKeeper(
  connectionDetails = connectionDetails,
  databaseId = "Synpuf",
  cdmDatabaseSchema = "dbo",
  cohortDatabaseSchema = "results",
  cohortTable = "cohort",
  cohortDefinitionId = 1234,
  cohortName = "DM type I",
  sampleSize = 100,
  assignNewId = TRUE,
  useAncestor = TRUE,
  doi = c(435216, 201254),
  symptoms = c(79936, 432454, 4232487, 4229881, 254761),
  comorbidities = c(141253, 432867, 436670, 433736, 255848),
  drugs = c(21600712, 21602728, 21603531),
  diagnosticProcedures = c(0),
  measurements  = c(3004410,3005131,3005673,3010084,3033819,4149519,4229110, 4020120),
  alternativeDiagnosis = c(192963,201826,441267,40443308),
  treatmentProcedures = c(4242748),
  complications =  c(201820,375545,380834,433968,442793,4016045,4209145,4299544)                             
)

Technology

Keeper is an R package.

Installation

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

2. Install Keeper from GitHub:

   install.packages("remotes")
   remotes::install_github("ohdsi/Keeper")

Technology

KEEPER is an R package.

System Requirements

Requires R (version 3.6.0 or higher).

User Documentation

Documentation can be found on the package website.

PDF versions of the documentation are also available:

• Vignette: Using Keeper with Large Language Models
• Vignette: Setting parameters for Keeper
• Package manual: Keeper manual

Support

• Developer questions/comments/feedback: OHDSI Forum
• We use the GitHub issue tracker for all bugs/issues/enhancements

Contributing

Read here how you can contribute to this package.

License

Keeper is licensed under Apache License 2.0.

Development

Keeper is being developed in R Studio.

Development status

Ready for testing. Interface may still change in future versions.

Acknowledgements

• None