getEunomiaPlpData: Create a plpData object from the Eunomia database'

In OHDSI/PatientLevelPrediction: Develop Clinical Prediction Models Using the Common Data Model

Create a plpData object from the Eunomia database'

Description

This function creates a plpData object from the Eunomia database. It gets the connection details, creates the cohorts, and extracts the data. The cohort is predicting GIbleed in new users of celecoxib.

Usage

getEunomiaPlpData(covariateSettings = NULL)

Arguments

covariateSettings

A list of covariateSettings objects created using the createCovariateSettings function in the FeatureExtraction package. If nothing is specified covariates with age, gender, conditions and drug era are used.

Value

An object of type plpData, containing information on the cohorts, their outcomes, and baseline covariates. Information about multiple outcomes can be captured at once for efficiency reasons. This object is a list with the following components:

outcomes

A data frame listing the outcomes per person, including the time to event, and the outcome id

cohorts

A data frame listing the persons in each cohort, listing their exposure status as well as the time to the end of the observation period and time to the end of the cohort

covariateData

An Andromeda object created with the FeatureExtraction package. This object contains the following items:

covariates

An Andromeda table listing the covariates per person in the two cohorts. This is done using a sparse representation: covariates with a value of 0 are omitted to save space. Usually has three columns, rowId, covariateId and covariateValue'.

covariateRef

An Andromeda table describing the covariates that have been extracted.

AnalysisRef

An Andromeda table with information about which analysisIds from 'FeatureExtraction' were used.

Examples

 
covariateSettings <- FeatureExtraction::createCovariateSettings(
  useDemographicsAge = TRUE,
  useDemographicsGender = TRUE,
  useConditionOccurrenceAnyTimePrior = TRUE
)
plpData <- getEunomiaPlpData(covariateSettings = covariateSettings)

OHDSI/PatientLevelPrediction documentation built on Feb. 14, 2025, 9:44 a.m.