KEEPER is part of HADES.
An R package for reviewing patient profiles for phenotype validation.
- 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.
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)
)Keeper is an R package.
-
See the instructions here for configuring your R environment, including Java.
-
Install
Keeperfrom GitHub:install.packages("remotes") remotes::install_github("ohdsi/Keeper")
KEEPER is an R package.
Requires R (version 3.6.0 or higher).
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
- Developer questions/comments/feedback: OHDSI Forum
- We use the GitHub issue tracker for all bugs/issues/enhancements
Read here how you can contribute to this package.
Keeper is licensed under Apache License 2.0.
Keeper is being developed in R Studio.
Ready for testing. Interface may still change in future versions.
- None