Extracts covariates based on cohorts

Extracts covariates based on cohorts

Usage

createCohortCovariateSettings(
  cohortName,
  settingId,
  cohortDatabaseSchema = NULL,
  cohortTable = NULL,
  cohortId,
  startDay = -30,
  endDay = 0,
  count = FALSE,
  ageInteraction = FALSE,
  lnAgeInteraction = FALSE,
  analysisId = 456
)

Arguments

cohortName

Name for the cohort

settingId

A unique id for the covariate time and

cohortDatabaseSchema

The schema of the database with the cohort. If nothing is specified then the cohortDatabaseSchema from databaseDetails at runtime is used.

cohortTable

the table name that contains the covariate cohort. If nothing is specified then the cohortTable from databaseDetails at runtime is used.

cohortId

cohort id for the covariate cohort

startDay

The number of days prior to index to start observing the cohort

endDay

The number of days prior to index to stop observing the cohort

count

If FALSE the covariate value is binary (1 means cohort occurred between index+startDay and index+endDay, 0 means it did not) If TRUE then the covariate value is the number of unique cohort_start_dates between index+startDay and index+endDay

ageInteraction

If TRUE multiple covariate value by the patient's age in years

lnAgeInteraction

If TRUE multiple covariate value by the log of the patient's age in years

analysisId

The analysisId for the covariate

Value

An object of class covariateSettings specifying how to create the cohort covariate with the covariateId cohortId x 100000 + settingId x 1000 + analysisId

Details

The user specifies a cohort and time period and then a covariate is constructed whether they are in the cohort during the time periods relative to target population cohort index

Examples

createCohortCovariateSettings(cohortName="testCohort",
                              settingId=1,
                              cohortId=1,
                              cohortDatabaseSchema="cohorts",
                              cohortTable="cohort_table")
#> $covariateName
#> [1] "testCohort"
#> 
#> $covariateId
#> [1] 101456
#> 
#> $cohortDatabaseSchema
#> [1] "cohorts"
#> 
#> $cohortTable
#> [1] "cohort_table"
#> 
#> $cohortIds
#> [1] 1
#> 
#> $startDay
#> [1] -30
#> 
#> $endDays
#> [1] 0
#> 
#> $count
#> [1] FALSE
#> 
#> $ageInteraction
#> [1] FALSE
#> 
#> $lnAgeInteraction
#> [1] FALSE
#> 
#> $analysisId
#> [1] 456
#> 
#> attr(,"fun")
#> [1] "PatientLevelPrediction::getCohortCovariateData"
#> attr(,"class")
#> [1] "covariateSettings"