inst/doc/CreatingCovariatesUsingCohortAttributes.R

In FeatureExtraction: Generating Features for a Cohort

## ----echo=FALSE,message=FALSE,warning=FALSE,eval=TRUE-------------------------
library(FeatureExtraction)

## ----tidy=FALSE,eval=FALSE----------------------------------------------------
# library(SqlRender)
# sql <- readSql("LengthOfObsCohortAttr.sql")
# sql <- render(sql,
#   cdm_database_schema = cdmDatabaseSchema,
#   cohort_database_schema = cohortDatabaseSchema,
#   cohort_table = "rehospitalization",
#   cohort_attribute_table = "loo_cohort_attr",
#   attribute_definition_table = "loo_attr_def",
#   cohort_definition_ids = c(1, 2)
# )
# sql <- translate(sql, targetDialect = connectionDetails$dbms)
# 
# connection <- connect(connectionDetails)
# executeSql(connection, sql)

## ----eval=FALSE---------------------------------------------------------------
# looCovSet <- createCohortAttrCovariateSettings(
#   attrDatabaseSchema = cohortDatabaseSchema,
#   cohortAttrTable = "loo_cohort_attr",
#   attrDefinitionTable = "loo_attr_def",
#   includeAttrIds = c(),
#   isBinary = FALSE,
#   missingMeansZero = FALSE
# )

## ----eval=FALSE---------------------------------------------------------------
# covariates <- getDbCovariateData(
#   connectionDetails = connectionDetails,
#   cdmDatabaseSchema = cdmDatabaseSchema,
#   cohortDatabaseSchema = cohortDatabaseSchema,
#   cohortTable = "rehospitalization",
#   cohortIds = c(1),
#   covariateSettings = looCovSet
# )

## ----eval=FALSE---------------------------------------------------------------
# covariateSettings <- createCovariateSettings(
#   useDemographicsGender = TRUE,
#   useDemographicsAgeGroup = TRUE,
#   useDemographicsRace = TRUE,
#   useDemographicsEthnicity = TRUE,
#   useDemographicsIndexYear = TRUE,
#   useDemographicsIndexMonth = TRUE
# )
# 
# looCovSet <- createCohortAttrCovariateSettings(
#   attrDatabaseSchema = cohortDatabaseSchema,
#   cohortAttrTable = "loo_cohort_attr",
#   attrDefinitionTable = "loo_attr_def",
#   includeAttrIds = c()
# )
# 
# covariateSettingsList <- list(covariateSettings, looCovSet)
# 
# covariates <- getDbCovariateData(
#   connectionDetails = connectionDetails,
#   cdmDatabaseSchema = cdmDatabaseSchema,
#   cohortDatabaseSchema = resultsDatabaseSchema,
#   cohortTable = "rehospitalization",
#   cohortIds = c(1),
#   covariateSettings = covariateSettingsList
# )