inst/doc/UsingFeatureExtractionKorean.R

In FeatureExtraction: Generating Features for a Cohort

## ----set-options,echo=FALSE,message=FALSE,warning=FALSE,eval=TRUE-------------------------------------------------------------------------------------------------------------------------------------
old <- options(width = 200)
library(FeatureExtraction)
vignetteFolder <- "c:/temp/vignetteFeatureExtraction"

## -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
settings <- createDefaultCovariateSettings()

## -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
settings <- createDefaultCovariateSettings(
  excludedCovariateConceptIds = 1124300,
  addDescendantsToExclude = TRUE
)

## -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
settings <- createCovariateSettings(
  useDemographicsGender = TRUE,
  useDemographicsAgeGroup = TRUE,
  useConditionOccurrenceAnyTimePrior = TRUE
)

## -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
settings <- createCovariateSettings(
  useConditionEraLongTerm = TRUE,
  useConditionEraShortTerm = TRUE,
  useDrugEraLongTerm = TRUE,
  useDrugEraShortTerm = TRUE,
  longTermStartDays = -180,
  shortTermStartDays = -14,
  endDays = -1
)

## -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
settings <- createCovariateSettings(
  useConditionEraLongTerm = TRUE,
  useConditionEraShortTerm = TRUE,
  useDrugEraLongTerm = TRUE,
  useDrugEraShortTerm = TRUE,
  longTermStartDays = -180,
  shortTermStartDays = -14,
  endDays = -1,
  excludedCovariateConceptIds = 1124300,
  addDescendantsToExclude = TRUE
)

## -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
settings <- createCovariateSettings(useConditionEraLongTerm = TRUE)
settings2 <- convertPrespecSettingsToDetailedSettings(settings)
settings2$analyses[[1]]

## -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
analysisDetails <- createAnalysisDetails(
  analysisId = 1,
  sqlFileName = "DemographicsGender.sql",
  parameters = list(
    analysisId = 1,
    analysisName = "Gender",
    domainId = "Demographics"
  ),
  includedCovariateConceptIds = c(),
  addDescendantsToInclude = FALSE,
  excludedCovariateConceptIds = c(),
  addDescendantsToExclude = FALSE,
  includedCovariateIds = c()
)

settings <- createDetailedCovariateSettings(list(analysisDetails))

## -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
settings <- createDefaultTemporalCovariateSettings()

## -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
settings <- createTemporalCovariateSettings(
  useConditionOccurrence = TRUE,
  useMeasurementValue = TRUE
)

## -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
settings <- createTemporalCovariateSettings(
  useConditionOccurrence = TRUE,
  useMeasurementValue = TRUE,
  temporalStartDays = seq(-364, -7, by = 7),
  temporalEndDays = seq(-358, -1, by = 7)
)

## -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
analysisDetails <- createAnalysisDetails(
  analysisId = 1,
  sqlFileName = "MeasurementValue.sql",
  parameters = list(
    analysisId = 1,
    analysisName = "MeasurementValue",
    domainId = "Measurement"
  ),
  includedCovariateConceptIds = c(),
  addDescendantsToInclude = FALSE,
  excludedCovariateConceptIds = c(),
  addDescendantsToExclude = FALSE,
  includedCovariateIds = c()
)

settings <- createDetailedTemporalCovariateSettings(list(analysisDetails))

## ----tidy=FALSE,eval=FALSE----------------------------------------------------------------------------------------------------------------------------------------------------------------------------
#  connectionDetails <- createConnectionDetails(
#    dbms = "postgresql",
#    server = "localhost/ohdsi",
#    user = "joe",
#    password = "supersecret"
#  )
#  
#  cdmDatabaseSchema <- "my_cdm_data"
#  resultsDatabaseSchema <- "my_results"

## ----tidy=FALSE,eval=FALSE----------------------------------------------------------------------------------------------------------------------------------------------------------------------------
#  library(SqlRender)
#  sql <- readSql("cohortsOfInterest.sql")
#  sql <- render(sql,
#    cdmDatabaseSchema = cdmDatabaseSchema,
#    resultsDatabaseSchema = resultsDatabaseSchema
#  )
#  sql <- translate(sql, targetDialect = connectionDetails$dbms)
#  
#  connection <- connect(connectionDetails)
#  executeSql(connection, sql)

## ----tidy=FALSE,eval=FALSE----------------------------------------------------------------------------------------------------------------------------------------------------------------------------
#  sql <- paste(
#    "SELECT cohort_definition_id, COUNT(*) AS count",
#    "FROM @resultsDatabaseSchema.cohorts_of_interest",
#    "GROUP BY cohort_definition_id"
#  )
#  sql <- render(sql, resultsDatabaseSchema = resultsDatabaseSchema)
#  sql <- translate(sql, targetDialect = connectionDetails$dbms)
#  
#  querySql(connection, sql)

## ----echo=FALSE,message=FALSE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------
data.frame(cohort_concept_id = c(1124300, 1118084), count = c(240761, 47293))

## ----eval=FALSE---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
#  covariateSettings <- createDefaultCovariateSettings()
#  
#  covariateData <- getDbCovariateData(
#    connectionDetails = connectionDetails,
#    cdmDatabaseSchema = cdmDatabaseSchema,
#    cohortDatabaseSchema = resultsDatabaseSchema,
#    cohortTable = "cohorts_of_interest",
#    cohortIds = c(1118084),
#    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$covariates

## ----echo=FALSE,message=FALSE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------
if (file.exists(file.path(vignetteFolder, "covariatesPerPerson"))) {
  covariateData$covariates %>%
    mutate(rowId = row_number())
}

## ----eval=FALSE---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
#  saveCovariateData(covariateData, "covariates")

## ----eval=FALSE---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
#  tidyCovariates <- tidyCovariateData(covariateData,
#    minFraction = 0.001,
#    normalize = TRUE,
#    removeRedundancy = TRUE
#  )

## ----eval=FALSE---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
#  deletedCovariateIds <- tidyCovariates$metaData$deletedInfrequentCovariateIds
#  head(deletedCovariateIds)

## ----echo=FALSE,message=FALSE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------
if (file.exists(file.path(vignetteFolder, "deletedInfrequentCovariateIds.rds"))) {
  deletedCovariateIds <- readRDS(file.path(vignetteFolder, "deletedInfrequentCovariateIds.rds"))
  head(deletedCovariateIds)
}

## ----eval=FALSE---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
#  deletedCovariateIds <- tidyCovariates$metaData$deletedRedundantCovariateIds
#  head(deletedCovariateIds)

## ----echo=FALSE,message=FALSE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------
if (file.exists(file.path(vignetteFolder, "deletedRedundantCovariateIds.rds"))) {
  deletedCovariateIds <- readRDS(file.path(vignetteFolder, "deletedRedundantCovariateIds.rds"))
  head(deletedCovariateIds)
}

## ----eval=FALSE---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
#  covariateData2 <- aggregateCovariates(covariateData)

## ----eval=FALSE---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
#  covariateSettings <- createDefaultCovariateSettings()
#  
#  covariateData2 <- getDbCovariateData(
#    connectionDetails = connectionDetails,
#    cdmDatabaseSchema = cdmDatabaseSchema,
#    cohortDatabaseSchema = resultsDatabaseSchema,
#    cohortTable = "cohorts_of_interest",
#    cohortIds = c(1118084),
#    covariateSettings = covariateSettings,
#    aggregated = TRUE
#  )
#  summary(covariateData2)

## ----echo=FALSE,message=FALSE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------
if (file.exists(file.path(vignetteFolder, "aggregatedCovariates"))) {
  covariateData2 <- loadCovariateData(file.path(vignetteFolder, "aggregatedCovariates"))
  summary(covariateData2)
}

## ----eval=FALSE---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
#  covariateData2$covariates

## ----echo=FALSE,message=FALSE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------
if (file.exists(file.path(vignetteFolder, "aggregatedCovariates"))) {
  covariateData2$covariates
}

## ----eval=FALSE---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
#  covariateData2$covariatesContinuous

## ----echo=FALSE,message=FALSE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------
if (file.exists(file.path(vignetteFolder, "aggregatedCovariates"))) {
  covariateData2$covariatesContinuous
}

## ----eval=FALSE---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
#  result <- createTable1(
#    covariateData1 = covariateData2,
#    output = "one column"
#  )
#  print(result, row.names = FALSE, right = FALSE)

## ----comment=NA,echo=FALSE,message=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------
if (file.exists(file.path(vignetteFolder, "aggregatedCovariates"))) {
  result <- createTable1(
    covariateData1 = covariateData2,
    output = "one column"
  )
  print(result, row.names = FALSE, right = FALSE)
}

## ----eval=FALSE---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
#  covariateSettings <- createTable1CovariateSettings()
#  
#  covariateData2b <- getDbCovariateData(
#    connectionDetails = connectionDetails,
#    cdmDatabaseSchema = cdmDatabaseSchema,
#    cohortDatabaseSchema = resultsDatabaseSchema,
#    cohortTable = "cohorts_of_interest",
#    cohortIds = c(1118084),
#    covariateSettings = covariateSettings,
#    aggregated = TRUE
#  )
#  summary(covariateData2b)

## ----echo=FALSE,message=FALSE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------
if (file.exists(file.path(vignetteFolder, "table1Covariates"))) {
  covariateData2b <- loadCovariateData(file.path(vignetteFolder, "table1Covariates"))
  summary(covariateData2b)
}

## ----eval=FALSE---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
#  settings <- createTable1CovariateSettings(
#    excludedCovariateConceptIds = c(1118084, 1124300),
#    addDescendantsToExclude = TRUE
#  )
#  
#  covCelecoxib <- getDbCovariateData(
#    connectionDetails = connectionDetails,
#    cdmDatabaseSchema = cdmDatabaseSchema,
#    cohortDatabaseSchema = resultsDatabaseSchema,
#    cohortTable = "cohorts_of_interest",
#    cohortIds = c(1118084),
#    covariateSettings = settings,
#    aggregated = TRUE
#  )
#  
#  covDiclofenac <- getDbCovariateData(
#    connectionDetails = connectionDetails,
#    cdmDatabaseSchema = cdmDatabaseSchema,
#    cohortDatabaseSchema = resultsDatabaseSchema,
#    cohortTable = "cohorts_of_interest",
#    cohortIds = c(1124300),
#    covariateSettings = settings,
#    aggregated = TRUE
#  )
#  std <- computeStandardizedDifference(covCelecoxib, covDiclofenac)

## ----eval=FALSE---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
#  head(std)

## ----echo=FALSE,message=FALSE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------
if (file.exists(file.path(vignetteFolder, "covDiclofenac"))) {
  covCelecoxib <- loadCovariateData(file.path(vignetteFolder, "covCelecoxib"))
  covDiclofenac <- loadCovariateData(file.path(vignetteFolder, "covDiclofenac"))
  std <- computeStandardizedDifference(covCelecoxib, covDiclofenac)
  truncRight <- function(x, n) {
    nc <- nchar(x)
    x[nc > (n - 3)] <- paste("...", substr(x[nc > (n - 3)], nc[nc > (n - 3)] - n + 1, nc[nc > (n - 3)]), sep = "")
    x
  }
  std$covariateName <- truncRight(as.character(std$covariateName), 30)
  head(std)
}

## ----eval=FALSE---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
#  result <- createTable1(
#    covariateData1 = covCelecoxib,
#    covariateData2 = covDiclofenac,
#    output = "two columns"
#  )
#  print(result, row.names = FALSE, right = FALSE)

## ----comment=NA,echo=FALSE,message=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------
if (file.exists(file.path(vignetteFolder, "covDiclofenac"))) {
  result <- createTable1(
    covariateData1 = covCelecoxib,
    covariateData2 = covDiclofenac,
    output = "one column"
  )
  print(result, row.names = FALSE, right = FALSE)
}

## ----reset-options,echo=FALSE,message=FALSE,warning=FALSE,eval=TRUE-----------
options(old)