CreatingCovariatesBasedOnOtherCohorts.R
In FeatureExtraction: Generating Features for a Cohort

## ----echo=FALSE,message=FALSE,warning=FALSE,eval=TRUE-------------------------
library(FeatureExtraction)
vignetteFolder <- "s:/temp/vignetteFeatureExtractionCohortBased"

## ----tidy=FALSE,eval=FALSE----------------------------------------------------
#  library(SqlRender)
#  sql <- readSql("covariateCohorts.sql")
#  connection <- connect(connectionDetails)
#  renderTranslateExecuteSql(
#    connection = connection,
#    sql = sql,
#    cdm_database_schema = cdmDatabaseSchema,
#    cohort_database_schema = cohortDatabaseSchema,
#    cohort_table = cohortTable
#  )

## ----eval=FALSE---------------------------------------------------------------
#  sql <- paste(
#    "SELECT cohort_definition_id,
#                  COUNT(*) AS count",
#    "FROM @cohort_database_schema.@cohort_table",
#    "GROUP BY cohort_definition_id"
#  )
#  renderTranslateQuerySql(
#    connection = connection,
#    sql = sql,
#    cohort_database_schema = cohortDatabaseSchema,
#    cohort_table = cohortTable
#  )

## ----echo=FALSE,message=FALSE-------------------------------------------------
data.frame(cohort_concept_id = c(1, 2), count = c(954179, 979874))

## ----eval=FALSE---------------------------------------------------------------
#  covariateCohorts <- tibble(
#    cohortId = 2,
#    cohortName = "Type 2 diabetes"
#  )
#  
#  covariateSettings <- createCohortBasedCovariateSettings(
#    analysisId = 999,
#    covariateCohorts = covariateCohorts,
#    valueType = "binary",
#    startDay = -365,
#    endDay = 0
#  )

## ----eval=FALSE---------------------------------------------------------------
#  covariateData <- getDbCovariateData(
#    connectionDetails = connectionDetails,
#    cdmDatabaseSchema = cdmDatabaseSchema,
#    cohortDatabaseSchema = cohortDatabaseSchema,
#    cohortTable = cohortTable,
#    cohortId = 1,
#    rowIdField = "subject_id",
#    covariateSettings = covariateSettings
#  )
#  summary(covariateData)

## ----echo=FALSE,message=FALSE-------------------------------------------------
if (file.exists(file.path(vignetteFolder, "covariatesPerPerson"))) {
  covariateData <- loadCovariateData(file.path(vignetteFolder, "covariatesPerPerson"))
  summary(covariateData)
}

## ----eval=FALSE---------------------------------------------------------------
#  covariateData$covariateRef

## ----echo=FALSE,message=FALSE-------------------------------------------------
if (file.exists(file.path(vignetteFolder, "covariatesPerPerson"))) {
  covariateData$covariateRef
}

## ----eval=FALSE---------------------------------------------------------------
#  covariateSettings1 <- createCovariateSettings(
#    useDemographicsGender = TRUE,
#    useDemographicsAgeGroup = TRUE,
#    useDemographicsRace = TRUE,
#    useDemographicsEthnicity = TRUE,
#    useDemographicsIndexYear = TRUE,
#    useDemographicsIndexMonth = TRUE
#  )
#  
#  covariateCohorts <- tibble(
#    cohortId = 2,
#    cohortName = "Type 2 diabetes"
#  )
#  
#  covariateSettings2 <- createCohortBasedCovariateSettings(
#    analysisId = 999,
#    covariateCohorts = covariateCohorts,
#    valueType = "binary",
#    startDay = -365,
#    endDay = 0
#  )
#  
#  covariateSettingsList <- list(covariateSettings1, covariateSettings2)
#  
#  covariateData <- getDbCovariateData(
#    connectionDetails = connectionDetails,
#    cdmDatabaseSchema = cdmDatabaseSchema,
#    cohortDatabaseSchema = cohortDatabaseSchema,
#    cohortTable = cohortTable,
#    cohortId = 1,
#    rowIdField = "subject_id",
#    covariateSettings = covariateSettingsList,
#    aggregated = TRUE
#  )
#  summary(covariateData)

## ----echo=FALSE,message=FALSE-------------------------------------------------
if (file.exists(file.path(vignetteFolder, "covariatesAggregated"))) {
  covariateData <- loadCovariateData(file.path(vignetteFolder, "covariatesAggregated"))
  summary(covariateData)
}