getCohortCovariateData

Extracts covariates based on cohorts

A user friendly way to create patient level prediction models using
the Observational Medical Outcomes Partnership Common Data Model. Given a cohort
of interest and an outcome of interest, the package can use data in the Common
Data Model to build a large set of features. These features can then be used to
fit a predictive model with a number of machine learning algorithms. This is
further described in Reps (2017) <doi:10.1093/jamia/ocy032>.

Egill Fridgeirsson

PatientLevelPrediction

Develop Clinical Prediction Models Using the Common Data Model

Jenna Reps

Martijn Schuemie

Marc Suchard

Patrick Ryan

Peter Rijnbeek

Observational Health Data Science and Informatics 

getCohortCovariateData function

<dl><dt>connection</dt>
<dd>The database connection</dd>
<dt>tempEmulationSchema</dt>
<dd>The schema to use for temp tables</dd>
<dt>oracleTempSchema</dt>
<dd>DEPRECATED The temp schema if using oracle</dd>
<dt>cdmDatabaseSchema</dt>
<dd>The schema of the OMOP CDM data</dd>
<dt>cdmVersion</dt>
<dd>version of the OMOP CDM data</dd>
<dt>cohortTable</dt>
<dd>the table name that contains the target population cohort</dd>
<dt>rowIdField</dt>
<dd>string representing the unique identifier in the target population cohort</dd>
<dt>aggregated</dt>
<dd>whether the covariate should be aggregated</dd>
<dt>cohortIds</dt>
<dd>cohort id for the target cohort</dd>
<dt>covariateSettings</dt>
<dd>settings for the covariate cohorts and time periods</dd>
<dt>...</dt>
<dd>additional arguments from FeatureExtraction</dd></dl>

Arguments

Extracts covariates based on cohorts — getCohortCovariateData

<dl>

<dt>connection</dt>
<dd>The database connection</dd>


<dt>tempEmulationSchema</dt>
<dd>The schema to use for temp tables</dd>


<dt>oracleTempSchema</dt>
<dd>DEPRECATED The temp schema if using oracle</dd>


<dt>cdmDatabaseSchema</dt>
<dd>The schema of the OMOP CDM data</dd>


<dt>cdmVersion</dt>
<dd>version of the OMOP CDM data</dd>


<dt>cohortTable</dt>
<dd>the table name that contains the target population cohort</dd>


<dt>rowIdField</dt>
<dd>string representing the unique identifier in the target population cohort</dd>


<dt>aggregated</dt>
<dd>whether the covariate should be aggregated</dd>


<dt>cohortIds</dt>
<dd>cohort id for the target cohort</dd>


<dt>covariateSettings</dt>
<dd>settings for the covariate cohorts and time periods</dd>


<dt>...</dt>
<dd>additional arguments from FeatureExtraction</dd>

</dl>

getCohortCovariateData: Extracts covariates based on cohorts

Description

Usage

Value

Arguments

Details