diff --git a/DESCRIPTION b/DESCRIPTION
index ec8a067..8f7a543 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: Characterization
 Type: Package
 Title: Characterizations of Cohorts
-Version: 0.1.4
-Date: 2024-02-26
+Version: 0.1.5
+Date: 2024-04-03
 Authors@R: c(
 	person("Jenna", "Reps", , "reps@ohdsi.org", role = c("aut", "cre")),
 	person("Patrick", "Ryan", , "ryan@ohdsi.org", role = c("aut"))
@@ -42,6 +42,6 @@ Remotes:
 	ohdsi/ShinyAppBuilder,
 	ohdsi/DatabaseConnector
 NeedsCompilation: no
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Encoding: UTF-8
 VignetteBuilder: knitr
diff --git a/NEWS.md b/NEWS.md
index dc879bf..acf123e 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,7 @@
+Characterization 0.1.5
+======================
+Changed export to csv approach to use batch export from SQLite (#41)
+
 Characterization 0.1.4
 ======================
 Added extra error logging
@@ -21,7 +25,7 @@ Fixing bug where cohort_counts were not being saved in the database
 Characterization 0.1.0
 ======================
 
-- added support to enable target cohorts with multiple cohort entries for the aggregate covariate analysis by restructing to first cohort entry and ensuring the subject has a user specified minPriorObservation days observation in the database at first entry and also perform analysis on first outcomes and any outcome that is recorded during TAR.
+- added support to enable target cohorts with multiple cohort entries for the aggregate covariate analysis by restricting to first cohort entry and ensuring the subject has a user specified minPriorObservation days observation in the database at first entry and also perform analysis on first outcomes and any outcome that is recorded during TAR.
 - added shiny app
 
 
diff --git a/R/AggregateCovariates.R b/R/AggregateCovariates.R
index 02e17ac..bad74ec 100644
--- a/R/AggregateCovariates.R
+++ b/R/AggregateCovariates.R
@@ -1,4 +1,4 @@
-# Copyright 2022 Observational Health Data Sciences and Informatics
+# Copyright 2024 Observational Health Data Sciences and Informatics
 #
 # This file is part of Characterization
 #
@@ -27,27 +27,25 @@
 #'
 #' @export
 createAggregateCovariateSettings <- function(
-  targetIds,
-  outcomeIds,
-  minPriorObservation = 0,
-  riskWindowStart = 1,
-  startAnchor = 'cohort start',
-  riskWindowEnd = 365,
-  endAnchor = 'cohort start',
-  covariateSettings
-){
-
+    targetIds,
+    outcomeIds,
+    minPriorObservation = 0,
+    riskWindowStart = 1,
+    startAnchor = "cohort start",
+    riskWindowEnd = 365,
+    endAnchor = "cohort start",
+    covariateSettings) {
   errorMessages <- checkmate::makeAssertCollection()
   # check targetIds is a vector of int/double
   .checkCohortIds(
     cohortIds = targetIds,
-    type = 'target',
+    type = "target",
     errorMessages = errorMessages
   )
   # check outcomeIds is a vector of int/double
   .checkCohortIds(
     cohortIds = outcomeIds,
-    type = 'outcome',
+    type = "outcome",
     errorMessages = errorMessages
   )
 
@@ -81,12 +79,12 @@ createAggregateCovariateSettings <- function(
     minPriorObservation = minPriorObservation,
     riskWindowStart = riskWindowStart,
     startAnchor = startAnchor,
-    riskWindowEnd = riskWindowEnd ,
+    riskWindowEnd = riskWindowEnd,
     endAnchor = endAnchor,
     covariateSettings = covariateSettings
   )
 
-  class(result) <- 'aggregateCovariateSettings'
+  class(result) <- "aggregateCovariateSettings"
   return(result)
 }
 
@@ -106,19 +104,17 @@ createAggregateCovariateSettings <- function(
 #'
 #' @export
 computeAggregateCovariateAnalyses <- function(
-  connectionDetails = NULL,
-  cdmDatabaseSchema,
-  cdmVersion = 5,
-  targetDatabaseSchema,
-  targetTable,
-  outcomeDatabaseSchema = targetDatabaseSchema, # remove
-  outcomeTable =  targetTable,  # remove
-  tempEmulationSchema = getOption("sqlRenderTempEmulationSchema"),
-  aggregateCovariateSettings,
-  databaseId = 'database 1',
-  runId = 1
-) {
-
+    connectionDetails = NULL,
+    cdmDatabaseSchema,
+    cdmVersion = 5,
+    targetDatabaseSchema,
+    targetTable,
+    outcomeDatabaseSchema = targetDatabaseSchema, # remove
+    outcomeTable = targetTable, # remove
+    tempEmulationSchema = getOption("sqlRenderTempEmulationSchema"),
+    aggregateCovariateSettings,
+    databaseId = "database 1",
+    runId = 1) {
   # check inputs
 
   start <- Sys.time()
@@ -128,7 +124,7 @@ computeAggregateCovariateAnalyses <- function(
   )
   on.exit(
     DatabaseConnector::disconnect(connection)
-    )
+  )
 
   # select T, O, create TnO, TnOc, Onprior T
   # into temp table #agg_cohorts
@@ -145,11 +141,11 @@ computeAggregateCovariateAnalyses <- function(
   )
 
   ## get counts
-  sql <- 'select cohort_definition_id, count(*) row_count, count(distinct subject_id) person_count from #agg_cohorts group by cohort_definition_id;'
+  sql <- "select cohort_definition_id, count(*) row_count, count(distinct subject_id) person_count from #agg_cohorts group by cohort_definition_id;"
   sql <- SqlRender::translate(
     sql = sql,
     targetDialect = connectionDetails$dbms
-    )
+  )
   counts <- DatabaseConnector::querySql(
     connection = connection,
     sql = sql,
@@ -162,7 +158,7 @@ computeAggregateCovariateAnalyses <- function(
     connection = connection,
     oracleTempSchema = tempEmulationSchema,
     cdmDatabaseSchema = cdmDatabaseSchema,
-    cohortTable = '#agg_cohorts',
+    cohortTable = "#agg_cohorts",
     cohortTableIsTemp = T,
     cohortId = -1,
     covariateSettings = aggregateCovariateSettings$covariateSettings,
@@ -176,7 +172,7 @@ computeAggregateCovariateAnalyses <- function(
   # could add settings table with this and just have setting id
   # as single extra column?
 
-  for(tableName in names(result)){
+  for (tableName in names(result)) {
     result[[tableName]] <- result[[tableName]] %>%
       dplyr::mutate(
         runId = !!runId,
@@ -185,16 +181,16 @@ computeAggregateCovariateAnalyses <- function(
       dplyr::relocate(
         "databaseId",
         "runId"
-        )
+      )
   }
 
-# cohort details:
+  # cohort details:
 
   result$cohortDetails <- DatabaseConnector::querySql(
     connection = connection,
     sql = SqlRender::translate(
-    sql = " select * from #cohort_details;",
-    targetDialect = connectionDetails$dbms
+      sql = " select * from #cohort_details;",
+      targetDialect = connectionDetails$dbms
     ),
     snakeCaseToCamelCase = T
   ) %>%
@@ -218,14 +214,14 @@ computeAggregateCovariateAnalyses <- function(
   )
 
   result$settings <- data.frame(
-      runId = runId,
-      databaseId = databaseId,
-      covariateSettingJson = covariateSettingsJson,
-      riskWindowStart = aggregateCovariateSettings$riskWindowStart,
-      startAnchor = aggregateCovariateSettings$startAnchor,
-      riskWindowEnd = aggregateCovariateSettings$riskWindowEnd ,
-      endAnchor = aggregateCovariateSettings$endAnchor
-    )
+    runId = runId,
+    databaseId = databaseId,
+    covariateSettingJson = covariateSettingsJson,
+    riskWindowStart = aggregateCovariateSettings$riskWindowStart,
+    startAnchor = aggregateCovariateSettings$startAnchor,
+    riskWindowEnd = aggregateCovariateSettings$riskWindowEnd,
+    endAnchor = aggregateCovariateSettings$endAnchor
+  )
 
   sql <- SqlRender::loadRenderTranslateSql(
     sqlFilename = "DropAggregateCovariate.sql",
@@ -245,17 +241,15 @@ computeAggregateCovariateAnalyses <- function(
 
 
 createCohortsOfInterest <- function(
-  connection,
-  cdmDatabaseSchema,
-  dbms,
-  aggregateCovariateSettings,
-  targetDatabaseSchema,
-  targetTable,
-  outcomeDatabaseSchema,
-  outcomeTable,
-  tempEmulationSchema
-){
-
+    connection,
+    cdmDatabaseSchema,
+    dbms,
+    aggregateCovariateSettings,
+    targetDatabaseSchema,
+    targetTable,
+    outcomeDatabaseSchema,
+    outcomeTable,
+    tempEmulationSchema) {
   sql <- SqlRender::loadRenderTranslateSql(
     sqlFilename = "createTargetOutcomeCombinations.sql",
     packageName = "Characterization",
@@ -266,21 +260,21 @@ createCohortsOfInterest <- function(
     target_table = targetTable,
     outcome_database_schema = outcomeDatabaseSchema,
     outcome_table = outcomeTable,
-    target_ids = paste(aggregateCovariateSettings$targetIds, collapse = ',', sep = ','),
-    outcome_ids = paste(aggregateCovariateSettings$outcomeIds, collapse = ',', sep = ','),
+    target_ids = paste(aggregateCovariateSettings$targetIds, collapse = ",", sep = ","),
+    outcome_ids = paste(aggregateCovariateSettings$outcomeIds, collapse = ",", sep = ","),
     min_prior_observation = aggregateCovariateSettings$minPriorObservation,
     tar_start = aggregateCovariateSettings$riskWindowStart,
     tar_start_anchor = ifelse(
-      aggregateCovariateSettings$startAnchor == 'cohort start',
-      'cohort_start_date',
-      'cohort_end_date'
-      ),
+      aggregateCovariateSettings$startAnchor == "cohort start",
+      "cohort_start_date",
+      "cohort_end_date"
+    ),
     tar_end = aggregateCovariateSettings$riskWindowEnd,
     tar_end_anchor = ifelse(
-      aggregateCovariateSettings$endAnchor == 'cohort start',
-      'cohort_start_date',
-      'cohort_end_date'
-      )
+      aggregateCovariateSettings$endAnchor == "cohort start",
+      "cohort_start_date",
+      "cohort_end_date"
+    )
   )
 
   DatabaseConnector::executeSql(
@@ -289,5 +283,4 @@ createCohortsOfInterest <- function(
     progressBar = FALSE,
     reportOverallTime = FALSE
   )
-
 }
diff --git a/R/Characterization.R b/R/Characterization.R
index 3885f20..9c47bbb 100644
--- a/R/Characterization.R
+++ b/R/Characterization.R
@@ -1,4 +1,4 @@
-# Copyright 2022 Observational Health Data Sciences and Informatics
+# Copyright 2024 Observational Health Data Sciences and Informatics
 #
 # This file is part of Characterization
 #
diff --git a/R/Database.R b/R/Database.R
index 592ec33..249d761 100644
--- a/R/Database.R
+++ b/R/Database.R
@@ -1,6 +1,6 @@
 # @file Database.R
 #
-# Copyright 2022 Observational Health Data Sciences and Informatics
+# Copyright 2024 Observational Health Data Sciences and Informatics
 #
 # This file is part of Characterization
 #
@@ -30,15 +30,13 @@
 #'
 #' @export
 createSqliteDatabase <- function(
-    sqliteLocation = tempdir()
-){
-
+    sqliteLocation = tempdir()) {
   sqliteLocation <- file.path(
     sqliteLocation,
-    'sqliteCharacterization'
+    "sqliteCharacterization"
   )
 
-  if(!dir.exists(sqliteLocation )){
+  if (!dir.exists(sqliteLocation)) {
     dir.create(
       path = sqliteLocation,
       recursive = T
@@ -46,8 +44,8 @@ createSqliteDatabase <- function(
   }
 
   connectionDetails <- DatabaseConnector::createConnectionDetails(
-    dbms = 'sqlite',
-    server = file.path(sqliteLocation, 'sqlite.sqlite')
+    dbms = "sqlite",
+    server = file.path(sqliteLocation, "sqlite.sqlite")
   )
   connection <- DatabaseConnector::connect(
     connectionDetails = connectionDetails
@@ -64,10 +62,9 @@ insertAndromedaToDatabase <- function(
     andromedaObject,
     tempEmulationSchema,
     bulkLoad = T,
-    tablePrefix = 'c_',
+    tablePrefix = "c_",
     minCellCount = 0,
-    minCellCountColumns = list()
-){
+    minCellCountColumns = list()) {
   errorMessages <- checkmate::makeAssertCollection()
   .checkTablePrefix(
     tablePrefix = tablePrefix,
@@ -75,12 +72,11 @@ insertAndromedaToDatabase <- function(
   )
   checkmate::reportAssertions(errorMessages)
 
-  message('Inserting Andromeda table into database table ', tablePrefix, tableName)
+  message("Inserting Andromeda table into database table ", tablePrefix, tableName)
 
   Andromeda::batchApply(
     tbl = andromedaObject,
-    fun = function(x){
-
+    fun = function(x) {
       data <- as.data.frame(x %>% dplyr::collect()) # apply minCellCount
       data <- removeMinCell(
         data = data,
@@ -91,7 +87,7 @@ insertAndromedaToDatabase <- function(
       DatabaseConnector::insertTable(
         connection = connection,
         databaseSchema = databaseSchema,
-        tableName = paste0(tablePrefix,tableName),
+        tableName = paste0(tablePrefix, tableName),
         data = data,
         dropTableIfExists = F,
         createTable = F,
@@ -108,22 +104,21 @@ insertAndromedaToDatabase <- function(
 removeMinCell <- function(
     data,
     minCellCount = 0,
-    minCellCountColumns = list()
-){
-  for(columns in minCellCountColumns){
+    minCellCountColumns = list()) {
+  for (columns in minCellCountColumns) {
     ind <- apply(
-      X = data[,columns, drop = FALSE],
+      X = data[, columns, drop = FALSE],
       MARGIN = 1,
-      FUN = function(x) sum(x < minCellCount)>0
+      FUN = function(x) sum(x < minCellCount) > 0
     )
 
-    if(sum(ind) > 0 ){
+    if (sum(ind) > 0) {
       ParallelLogger::logInfo(
         paste0(
-          'Removing values less than ',
+          "Removing values less than ",
           minCellCount,
-          ' from ',
-          paste(columns, collapse = ' and ')
+          " from ",
+          paste(columns, collapse = " and ")
         )
       )
       data[ind, columns] <- -1
@@ -158,12 +153,11 @@ removeMinCell <- function(
 createCharacterizationTables <- function(
     conn,
     resultSchema,
-    targetDialect = 'postgresql',
+    targetDialect = "postgresql",
     deleteExistingTables = T,
     createTables = T,
-    tablePrefix = 'c_',
-    tempEmulationSchema = getOption("sqlRenderTempEmulationSchema")
-){
+    tablePrefix = "c_",
+    tempEmulationSchema = getOption("sqlRenderTempEmulationSchema")) {
   errorMessages <- checkmate::makeAssertCollection()
   .checkTablePrefix(
     tablePrefix = tablePrefix,
@@ -172,8 +166,8 @@ createCharacterizationTables <- function(
   checkmate::reportAssertions(errorMessages)
 
 
-  if(deleteExistingTables){
-    message('Deleting existing tables')
+  if (deleteExistingTables) {
+    message("Deleting existing tables")
     tables <- getResultTables()
     tables <- paste0(tablePrefix, tables)
 
@@ -184,9 +178,9 @@ createCharacterizationTables <- function(
       )
     )
 
-    for(tb in tables){
-      if(tb %in% alltables){
-        sql <- 'DELETE FROM @my_schema.@table'
+    for (tb in tables) {
+      if (tb %in% alltables) {
+        sql <- "DELETE FROM @my_schema.@table"
         sql <- SqlRender::render(
           sql = sql,
           my_schema = resultSchema,
@@ -202,7 +196,7 @@ createCharacterizationTables <- function(
           sql = sql
         )
 
-        sql <- 'DROP TABLE @my_schema.@table'
+        sql <- "DROP TABLE @my_schema.@table"
         sql <- SqlRender::render(
           sql = sql,
           my_schema = resultSchema,
@@ -218,13 +212,11 @@ createCharacterizationTables <- function(
           sql = sql
         )
       }
-
     }
-
   }
 
-  if(createTables){
-    ParallelLogger::logInfo('Creating characterization results tables')
+  if (createTables) {
+    ParallelLogger::logInfo("Creating characterization results tables")
     renderedSql <- SqlRender::loadRenderTranslateSql(
       sqlFilename = "ResultTables.sql",
       packageName = "Characterization",
@@ -241,7 +233,6 @@ createCharacterizationTables <- function(
 
     # add database migration here in the future
   }
-
 }
 
 #' Exports all tables in the result database to csv files
@@ -274,11 +265,9 @@ exportDatabaseToCsv <- function(
     targetDialect = NULL,
     tablePrefix = "c_",
     filePrefix = NULL,
-    tempEmulationSchema = NULL,
+    tempEmulationSchema = getOption("sqlRenderTempEmulationSchema"),
     saveDirectory,
-    minMeanCovariateValue = 0.001
-){
-
+    minMeanCovariateValue = 0.001) {
   errorMessages <- checkmate::makeAssertCollection()
   .checkConnectionDetails(connectionDetails, errorMessages)
   .checkTablePrefix(
@@ -291,7 +280,7 @@ exportDatabaseToCsv <- function(
   }
 
   if (is.null(filePrefix)) {
-    filePrefix = ''
+    filePrefix <- ""
   }
 
   # connect to result database
@@ -303,7 +292,7 @@ exportDatabaseToCsv <- function(
   )
 
   # create the folder to save the csv files
-  if(!dir.exists(saveDirectory)){
+  if (!dir.exists(saveDirectory)) {
     dir.create(
       path = saveDirectory,
       recursive = T
@@ -317,55 +306,116 @@ exportDatabaseToCsv <- function(
   tables <- getResultTables()
 
   # extract result per table
-  for(table in tables){
-    message(paste0("Exporting ", table))
-    sql <- "select * from @resultSchema.@appendtotable@tablename;"
+  for (table in tables) {
+    ParallelLogger::logInfo(paste0("Exporting rows from ", table, " to csv file"))
+    # get row count and figure out number of loops
+    sql <- "select count(*) as N from @resultSchema.@appendtotable@tablename;"
     sql <- SqlRender::render(
       sql = sql,
       resultSchema = resultSchema,
       appendtotable = tablePrefix,
       tablename = table
     )
-    resultSet <- DatabaseConnector::dbSendQuery(connection, sql)
-    tryCatch({
-      i <- 1
-      while (i == 1 || !DatabaseConnector::dbHasCompleted(resultSet)) {
-        start <- format(x = (i-1)*maxRowCount+1, scientific = F, big.mark = ",")
-        end <- format(x = maxRowCount*i, scientific = F, big.mark = ",")
-        message(paste0("  -- Rows ", start, " to ", end))
-        result <- DatabaseConnector::dbFetch(resultSet, n = maxRowCount)
-        if (table == "covariates" && minMeanCovariateValue > 0) {
-          result <- result %>%
-            dplyr::filter(.data$average_value >= minMeanCovariateValue)
-        }
-        result <- formatDouble(result)
-        # save the results as a csv
-        readr::write_csv(
-          x = result,
-          file = file.path(saveDirectory, paste0(tolower(filePrefix), table,'.csv')),
-          append = (i > 1)
-        )
-        i <- i + 1
+    sql <- SqlRender::translate(
+      sql = sql,
+      targetDialect = connectionDetails$dbms,
+      tempEmulationSchema = tempEmulationSchema
+    )
+    countN <- DatabaseConnector::querySql(
+      connection = connection,
+      sql = sql,
+      snakeCaseToCamelCase = F
+    )$N
+
+    # get column names
+    sql <- "select * from @resultSchema.@appendtotable@tablename where 1=0;"
+    sql <- SqlRender::render(
+      sql = sql,
+      resultSchema = resultSchema,
+      appendtotable = tablePrefix,
+      tablename = table
+    )
+    sql <- SqlRender::translate(
+      sql = sql,
+      targetDialect = connectionDetails$dbms,
+      tempEmulationSchema = tempEmulationSchema
+    )
+    cnames <- colnames(DatabaseConnector::querySql(
+      connection = connection,
+      sql = sql,
+      snakeCaseToCamelCase = F
+    ))
+
+    inds <- floor(countN / maxRowCount)
+    tableAppend <- F
+    # NOTE: If the table has 0 rows (countN == 0),
+    # then setting the txtProgressBar will fail since
+    # min < max. So, setting max = countN+1 for this
+    # reason.
+    pb <- utils::txtProgressBar(min = 0, max = countN + 1, initial = 0)
+
+    for (i in 1:length(inds)) {
+      startRow <- (i - 1) * maxRowCount + 1
+      endRow <- min(i * maxRowCount, countN)
+
+      sql <- "select @cnames from
+    (select *,
+    ROW_NUMBER() OVER(ORDER BY @cnames) AS row
+    from @resultSchema.@appendtotable@tablename
+    ) temp
+    where
+    temp.row >= @start_row and
+    temp.row <= @end_row;"
+      sql <- SqlRender::render(
+        sql = sql,
+        resultSchema = resultSchema,
+        appendtotable = tablePrefix,
+        tablename = table,
+        cnames = paste(cnames, collapse = ","),
+        start_row = startRow,
+        end_row = endRow
+      )
+      sql <- SqlRender::translate(
+        sql = sql,
+        targetDialect = connectionDetails$dbms,
+        tempEmulationSchema = tempEmulationSchema
+      )
+      result <- DatabaseConnector::querySql(
+        connection = connection,
+        sql = sql,
+        snakeCaseToCamelCase = F
+      )
+      result <- formatDouble(result)
+
+      # save the results as a csv
+      readr::write_csv(
+        x = result,
+        file = file.path(saveDirectory, paste0(tolower(filePrefix), table, ".csv")),
+        append = tableAppend
+      )
+      tableAppend <- T
+      # NOTE: Handling progresss bar per note on txtProgressBar
+      # above. Otherwise the progress bar doesn't show that it completed.
+      if (endRow == countN) {
+        utils::setTxtProgressBar(pb, countN + 1)
+      } else {
+        utils::setTxtProgressBar(pb, endRow)
       }
-    },
-    error = function(e) {
-      message(paste0("ERROR in export to csv: ", e$message));
-    },
-    finally = {
-      DatabaseConnector::dbClearResult(resultSet)
-    })
+    }
+    close(pb)
   }
+
   invisible(saveDirectory)
 }
 
-getResultTables <- function(){
+getResultTables <- function() {
   return(
     unique(
       readr::read_csv(
         file = system.file(
-          'settings',
-          'resultsDataModelSpecification.csv',
-          package = 'Characterization'
+          "settings",
+          "resultsDataModelSpecification.csv",
+          package = "Characterization"
         ),
         show_col_types = FALSE
       )$table_name
@@ -384,4 +434,3 @@ formatDouble <- function(x, scientific = F, ...) {
 
   return(x)
 }
-
diff --git a/R/DechallengeRechallenge.R b/R/DechallengeRechallenge.R
index 24bf0b7..4ad299b 100644
--- a/R/DechallengeRechallenge.R
+++ b/R/DechallengeRechallenge.R
@@ -1,4 +1,4 @@
-# Copyright 2022 Observational Health Data Sciences and Informatics
+# Copyright 2024 Observational Health Data Sciences and Informatics
 #
 # This file is part of Characterization
 #
@@ -26,23 +26,21 @@
 #'
 #' @export
 createDechallengeRechallengeSettings <- function(
-  targetIds,
-  outcomeIds,
-  dechallengeStopInterval = 30,
-  dechallengeEvaluationWindow = 30
-){
-
+    targetIds,
+    outcomeIds,
+    dechallengeStopInterval = 30,
+    dechallengeEvaluationWindow = 30) {
   errorMessages <- checkmate::makeAssertCollection()
   # check targetIds is a vector of int/double
   .checkCohortIds(
     cohortIds = targetIds,
-    type = 'target',
+    type = "target",
     errorMessages = errorMessages
-    )
+  )
   # check outcomeIds is a vector of int/double
   .checkCohortIds(
     cohortIds = outcomeIds,
-    type = 'outcome',
+    type = "outcome",
     errorMessages = errorMessages
   )
 
@@ -53,7 +51,7 @@ createDechallengeRechallengeSettings <- function(
     finite = TRUE,
     any.missing = FALSE,
     len = 1,
-    .var.name = 'dechallengeStopInterval',
+    .var.name = "dechallengeStopInterval",
     add = errorMessages
   )
 
@@ -64,7 +62,7 @@ createDechallengeRechallengeSettings <- function(
     finite = TRUE,
     any.missing = FALSE,
     len = 1,
-    .var.name = 'dechallengeEvaluationWindow',
+    .var.name = "dechallengeEvaluationWindow",
     add = errorMessages
   )
 
@@ -78,7 +76,7 @@ createDechallengeRechallengeSettings <- function(
     dechallengeEvaluationWindow = dechallengeEvaluationWindow
   )
 
-  class(result) <- 'dechallengeRechallengeSettings'
+  class(result) <- "dechallengeRechallengeSettings"
   return(result)
 }
 
@@ -95,45 +93,43 @@ createDechallengeRechallengeSettings <- function(
 #'
 #' @export
 computeDechallengeRechallengeAnalyses <- function(
-  connectionDetails = NULL,
-  targetDatabaseSchema,
-  targetTable,
-  outcomeDatabaseSchema = targetDatabaseSchema,
-  outcomeTable =  targetTable,
-  tempEmulationSchema = getOption("sqlRenderTempEmulationSchema"),
-  dechallengeRechallengeSettings,
-  databaseId = 'database 1'
-) {
-
+    connectionDetails = NULL,
+    targetDatabaseSchema,
+    targetTable,
+    outcomeDatabaseSchema = targetDatabaseSchema,
+    outcomeTable = targetTable,
+    tempEmulationSchema = getOption("sqlRenderTempEmulationSchema"),
+    dechallengeRechallengeSettings,
+    databaseId = "database 1") {
   # check inputs
   errorMessages <- checkmate::makeAssertCollection()
   .checkConnectionDetails(connectionDetails, errorMessages)
   .checkCohortDetails(
     cohortDatabaseSchema = targetDatabaseSchema,
     cohortTable = targetTable,
-    type = 'target',
-    errorMessages =  errorMessages
-    )
+    type = "target",
+    errorMessages = errorMessages
+  )
   .checkCohortDetails(
     cohortDatabaseSchema = outcomeDatabaseSchema,
     cohortTable = outcomeTable,
-    type = 'outcome',
-    errorMessages =  errorMessages
+    type = "outcome",
+    errorMessages = errorMessages
   )
   .checkTempEmulationSchema(
     tempEmulationSchema = tempEmulationSchema,
-    errorMessages =  errorMessages
+    errorMessages = errorMessages
   )
   .checkDechallengeRechallengeSettings(
     settings = dechallengeRechallengeSettings,
-    errorMessages =  errorMessages
-    )
+    errorMessages = errorMessages
+  )
 
   valid <- checkmate::reportAssertions(
     collection = errorMessages
-    )
+  )
 
-  if(valid){
+  if (valid) {
     # inputs all pass if getting here
     message("Inputs checked")
 
@@ -144,7 +140,7 @@ computeDechallengeRechallengeAnalyses <- function(
     )
     on.exit(
       DatabaseConnector::disconnect(connection)
-      )
+    )
 
     message("Computing dechallenge rechallenge results")
     sql <- SqlRender::loadRenderTranslateSql(
@@ -157,8 +153,8 @@ computeDechallengeRechallengeAnalyses <- function(
       target_table = targetTable,
       outcome_database_schema = outcomeDatabaseSchema,
       outcome_table = outcomeTable,
-      target_ids = paste(dechallengeRechallengeSettings$targetCohortDefinitionIds, sep='', collapse = ','),
-      outcome_ids = paste(dechallengeRechallengeSettings$outcomeCohortDefinitionIds, sep='', collapse = ','),
+      target_ids = paste(dechallengeRechallengeSettings$targetCohortDefinitionIds, sep = "", collapse = ","),
+      outcome_ids = paste(dechallengeRechallengeSettings$outcomeCohortDefinitionIds, sep = "", collapse = ","),
       dechallenge_stop_interval = dechallengeRechallengeSettings$dechallengeStopInterval,
       dechallenge_evaluation_window = dechallengeRechallengeSettings$dechallengeEvaluationWindow
     )
@@ -167,17 +163,17 @@ computeDechallengeRechallengeAnalyses <- function(
       sql = sql
     )
 
-    sql <- 'select * from #challenge;'
+    sql <- "select * from #challenge;"
     sql <- SqlRender::translate(
       sql = sql,
-      targetDialect =  connection@dbms,
+      targetDialect = connection@dbms,
       tempEmulationSchema = tempEmulationSchema
     )
 
     result <- DatabaseConnector::querySqlToAndromeda(
       connection = connection,
       andromeda = Andromeda::andromeda(),
-      andromedaTableName = 'dechallengeRechallenge',
+      andromedaTableName = "dechallengeRechallenge",
       sql = sql,
       snakeCaseToCamelCase = TRUE
     )
@@ -200,7 +196,7 @@ computeDechallengeRechallengeAnalyses <- function(
       paste0(
         "Computing dechallenge rechallenge for ",
         length(dechallengeRechallengeSettings$targetCohortDefinitionIds), " target ids and ",
-        length(dechallengeRechallengeSettings$outcomeCohortDefinitionIds),"outcome ids took ",
+        length(dechallengeRechallengeSettings$outcomeCohortDefinitionIds), "outcome ids took ",
         signif(delta, 3), " ",
         attr(delta, "units")
       )
@@ -225,44 +221,42 @@ computeDechallengeRechallengeAnalyses <- function(
 #'
 #' @export
 computeRechallengeFailCaseSeriesAnalyses <- function(
-  connectionDetails = NULL,
-  targetDatabaseSchema,
-  targetTable,
-  outcomeDatabaseSchema = targetDatabaseSchema,
-  outcomeTable =  targetTable,
-  tempEmulationSchema = getOption("sqlRenderTempEmulationSchema"),
-  dechallengeRechallengeSettings,
-  databaseId = 'database 1',
-  showSubjectId = F
-) {
-
+    connectionDetails = NULL,
+    targetDatabaseSchema,
+    targetTable,
+    outcomeDatabaseSchema = targetDatabaseSchema,
+    outcomeTable = targetTable,
+    tempEmulationSchema = getOption("sqlRenderTempEmulationSchema"),
+    dechallengeRechallengeSettings,
+    databaseId = "database 1",
+    showSubjectId = F) {
   # check inputs
   errorMessages <- checkmate::makeAssertCollection()
   .checkConnectionDetails(connectionDetails, errorMessages)
   .checkCohortDetails(
     cohortDatabaseSchema = targetDatabaseSchema,
     cohortTable = targetTable,
-    type = 'target',
-    errorMessages =  errorMessages
+    type = "target",
+    errorMessages = errorMessages
   )
   .checkCohortDetails(
     cohortDatabaseSchema = outcomeDatabaseSchema,
     cohortTable = outcomeTable,
-    type = 'outcome',
-    errorMessages =  errorMessages
+    type = "outcome",
+    errorMessages = errorMessages
   )
   .checkTempEmulationSchema(
     tempEmulationSchema = tempEmulationSchema,
-    errorMessages =  errorMessages
+    errorMessages = errorMessages
   )
   .checkDechallengeRechallengeSettings(
     settings = dechallengeRechallengeSettings,
-    errorMessages =  errorMessages
+    errorMessages = errorMessages
   )
 
   valid <- checkmate::reportAssertions(errorMessages)
 
-  if(valid){
+  if (valid) {
     # inputs all pass if getting here
     message("Inputs checked")
 
@@ -273,7 +267,7 @@ computeRechallengeFailCaseSeriesAnalyses <- function(
     )
     on.exit(
       DatabaseConnector::disconnect(connection)
-      )
+    )
 
     message("Computing dechallenge rechallenge results")
     sql <- SqlRender::loadRenderTranslateSql(
@@ -286,8 +280,8 @@ computeRechallengeFailCaseSeriesAnalyses <- function(
       target_table = targetTable,
       outcome_database_schema = outcomeDatabaseSchema,
       outcome_table = outcomeTable,
-      target_ids = paste(dechallengeRechallengeSettings$targetCohortDefinitionIds, sep='', collapse = ','),
-      outcome_ids = paste(dechallengeRechallengeSettings$outcomeCohortDefinitionIds, sep='', collapse = ','),
+      target_ids = paste(dechallengeRechallengeSettings$targetCohortDefinitionIds, sep = "", collapse = ","),
+      outcome_ids = paste(dechallengeRechallengeSettings$outcomeCohortDefinitionIds, sep = "", collapse = ","),
       dechallenge_stop_interval = dechallengeRechallengeSettings$dechallengeStopInterval,
       dechallenge_evaluation_window = dechallengeRechallengeSettings$dechallengeEvaluationWindow,
       show_subject_id = showSubjectId
@@ -297,17 +291,17 @@ computeRechallengeFailCaseSeriesAnalyses <- function(
       sql = sql
     )
 
-    sql <- 'select * from #fail_case_series;'
+    sql <- "select * from #fail_case_series;"
     sql <- SqlRender::translate(
       sql = sql,
-      targetDialect =  connection@dbms,
+      targetDialect = connection@dbms,
       tempEmulationSchema = tempEmulationSchema
     )
 
     result <- DatabaseConnector::querySqlToAndromeda(
       connection = connection,
       andromeda = Andromeda::andromeda(),
-      andromedaTableName = 'rechallengeFailCaseSeries',
+      andromedaTableName = "rechallengeFailCaseSeries",
       sql = sql,
       snakeCaseToCamelCase = TRUE
     )
@@ -330,7 +324,7 @@ computeRechallengeFailCaseSeriesAnalyses <- function(
       paste0(
         "Computing dechallenge failed case series for ",
         length(dechallengeRechallengeSettings$targetCohortDefinitionIds), " target IDs and ",
-        length(dechallengeRechallengeSettings$outcomeCohortDefinitionIds)," outcome IDs took ",
+        length(dechallengeRechallengeSettings$outcomeCohortDefinitionIds), " outcome IDs took ",
         signif(delta, 3), " ",
         attr(delta, "units")
       )
diff --git a/R/HelperFunctions.R b/R/HelperFunctions.R
index 26eb408..973ec25 100644
--- a/R/HelperFunctions.R
+++ b/R/HelperFunctions.R
@@ -1,4 +1,4 @@
-# Copyright 2022 Observational Health Data Sciences and Informatics
+# Copyright 2024 Observational Health Data Sciences and Informatics
 #
 # This file is part of Characterization
 #
@@ -15,25 +15,23 @@
 # limitations under the License.
 
 .checkConnection <- function(
-  connection,
-  errorMessages
-  ) {
+    connection,
+    errorMessages) {
   checkmate::assertClass(
     x = connection,
     classes = "DatabaseConnectorConnection",
     add = errorMessages
-    )
+  )
 }
 
 .checkConnectionDetails <- function(
-  connectionDetails,
-  errorMessages
-  ) {
+    connectionDetails,
+    errorMessages) {
   if (inherits(connectionDetails, "connectionDetails")) {
-  checkmate::assertClass(
-    x = connectionDetails,
-    classes = "connectionDetails",
-    add = errorMessages
+    checkmate::assertClass(
+      x = connectionDetails,
+      classes = "connectionDetails",
+      add = errorMessages
     )
   } else {
     checkmate::assertClass(
@@ -41,48 +39,42 @@
       classes = "ConnectionDetails",
       add = errorMessages
     )
-
   }
 }
 
 .checkDechallengeRechallengeSettings <- function(
-  settings,
-  errorMessages
-  ) {
+    settings,
+    errorMessages) {
   checkmate::assertClass(
     x = settings,
     classes = "dechallengeRechallengeSettings",
     add = errorMessages
-    )
+  )
 }
 
 .checkDechallengeRechallengeSettingsList <- function(
-  settings,
-  errorMessages
-) {
-
-  if(is.null(settings)){
+    settings,
+    errorMessages) {
+  if (is.null(settings)) {
     return()
   }
 
-  if(inherits(settings, 'dechallengeRechallengeSettings')){
+  if (inherits(settings, "dechallengeRechallengeSettings")) {
     settings <- list(settings)
   }
 
-  lapply(settings, function(x){
+  lapply(settings, function(x) {
     checkmate::assertClass(
       x = x,
       classes = "dechallengeRechallengeSettings",
       add = errorMessages
     )
-  }
-  )
+  })
 }
 
 .checkTimeToEventSettings <- function(
-  settings,
-  errorMessages
-) {
+    settings,
+    errorMessages) {
   checkmate::assertClass(
     x = settings,
     classes = "timeToEventSettings",
@@ -91,32 +83,28 @@
 }
 
 .checkTimeToEventSettingsList <- function(
-  settings,
-  errorMessages
-) {
-
-  if(is.null(settings)){
+    settings,
+    errorMessages) {
+  if (is.null(settings)) {
     return()
   }
 
-  if(inherits(settings,'timeToEventSettings')){
+  if (inherits(settings, "timeToEventSettings")) {
     settings <- list(settings)
   }
 
-  lapply(settings, function(x){
+  lapply(settings, function(x) {
     checkmate::assertClass(
       x = x,
       classes = "timeToEventSettings",
       add = errorMessages
     )
-  }
-  )
+  })
 }
 
 .checkAggregateCovariateSettings <- function(
-  settings,
-  errorMessages
-) {
+    settings,
+    errorMessages) {
   checkmate::assertClass(
     x = settings,
     classes = "aggregateCovariateSettings",
@@ -125,32 +113,28 @@
 }
 
 .checkAggregateCovariateSettingsList <- function(
-  settings,
-  errorMessages
-) {
-
-  if(is.null(settings)){
+    settings,
+    errorMessages) {
+  if (is.null(settings)) {
     return()
   }
 
-  if(inherits(settings,'aggregateCovariateSettings')){
+  if (inherits(settings, "aggregateCovariateSettings")) {
     settings <- list(settings)
   }
 
-  lapply(settings, function(x){
+  lapply(settings, function(x) {
     checkmate::assertClass(
       x = x,
       classes = "aggregateCovariateSettings",
       add = errorMessages
     )
-  }
-  )
+  })
 }
 
 .checkCharacterizationSettings <- function(
-  settings,
-  errorMessages
-) {
+    settings,
+    errorMessages) {
   checkmate::assertClass(
     x = settings,
     classes = "characterizationSettings",
@@ -158,45 +142,42 @@
   )
 }
 
-.checkCohortDetails<- function(
-  cohortDatabaseSchema,
-  cohortTable,
-  type = 'cohort',
-  errorMessages
-  ) {
+.checkCohortDetails <- function(
+    cohortDatabaseSchema,
+    cohortTable,
+    type = "cohort",
+    errorMessages) {
   checkmate::assertCharacter(
     x = cohortDatabaseSchema,
     len = 1,
     add = errorMessages,
-    .var.name = paste0(type, 'DatabaseSchema')
-    )
+    .var.name = paste0(type, "DatabaseSchema")
+  )
   checkmate::assertCharacter(
     x = cohortTable,
     len = 1,
     add = errorMessages,
-    .var.name = paste0(type, 'Table')
-    )
+    .var.name = paste0(type, "Table")
+  )
 }
 
 .checkCohortIds <- function(
-  cohortIds,
-  type = 'cohort',
-  errorMessages
-) {
+    cohortIds,
+    type = "cohort",
+    errorMessages) {
   checkmate::assertNumeric(
     x = cohortIds,
     add = errorMessages,
-    .var.name = paste0(type, 'Id')
+    .var.name = paste0(type, "Id")
   )
 }
 
 .checkTimeAtRisk <- function(
-  riskWindowStart,
-  startAnchor,
-  riskWindowEnd,
-  endAnchor,
-  errorMessages
-) {
+    riskWindowStart,
+    startAnchor,
+    riskWindowEnd,
+    endAnchor,
+    errorMessages) {
   checkmate::assertInt(riskWindowStart, add = errorMessages)
   checkmate::assertChoice(startAnchor, c("cohort start", "cohort end"), add = errorMessages)
   checkmate::assertInt(riskWindowEnd, add = errorMessages)
@@ -204,22 +185,20 @@
 }
 
 .checkTempEmulationSchema <- function(
-  tempEmulationSchema,
-  errorMessages
-  ) {
+    tempEmulationSchema,
+    errorMessages) {
   checkmate::assertCharacter(
     x = tempEmulationSchema,
     len = 1,
     null.ok = TRUE,
     add = errorMessages
-    )
+  )
 }
 
 
 .checkTablePrefix <- function(
     tablePrefix,
-    errorMessages
-) {
+    errorMessages) {
   checkmate::assertCharacter(
     pattern = "[a-zA-Z]_$",
     x = tablePrefix,
@@ -234,27 +213,29 @@
 .checkCovariateSettings <- function(covariateSettings,
                                     errorMessages) {
   if (class(covariateSettings) == "covariateSettings") {
-    checkmate::assertClass(x = covariateSettings,
-                           classes = "covariateSettings",
-                           add = errorMessages)
+    checkmate::assertClass(
+      x = covariateSettings,
+      classes = "covariateSettings",
+      add = errorMessages
+    )
   } else {
     for (j in (1:length(covariateSettings))) {
-      checkmate::assertClass(x = covariateSettings[[j]],
-                             classes = "covariateSettings",
-                             add = errorMessages)
+      checkmate::assertClass(
+        x = covariateSettings[[j]],
+        classes = "covariateSettings",
+        add = errorMessages
+      )
     }
   }
-
 }
 
 .checkMinPriorObservation <- function(
     minPriorObservation,
-  errorMessages
-) {
+    errorMessages) {
   checkmate::assertCount(
     x = minPriorObservation,
     null.ok = F,
-    .var.name = 'minPriorObservation',
+    .var.name = "minPriorObservation",
     add = errorMessages
   )
 }
diff --git a/R/RunCharacterization.R b/R/RunCharacterization.R
index 531631c..94bc488 100644
--- a/R/RunCharacterization.R
+++ b/R/RunCharacterization.R
@@ -16,9 +16,7 @@
 createCharacterizationSettings <- function(
     timeToEventSettings = NULL,
     dechallengeRechallengeSettings = NULL,
-    aggregateCovariateSettings = NULL
-)
-{
+    aggregateCovariateSettings = NULL) {
   errorMessages <- checkmate::makeAssertCollection()
   .checkTimeToEventSettingsList(
     settings = timeToEventSettings,
@@ -67,13 +65,12 @@ createCharacterizationSettings <- function(
 #' @param fileName  The location to save the json settings
 #'
 #' @return
-#' Returns the location of the drectory containing the json settings
+#' Returns the location of the directory containing the json settings
 #'
 #' @export
 saveCharacterizationSettings <- function(
     settings,
-    fileName
-) {
+    fileName) {
   ParallelLogger::saveSettingsToJson(
     object = settings,
     fileName = fileName
@@ -96,9 +93,7 @@ saveCharacterizationSettings <- function(
 #'
 #' @export
 loadCharacterizationSettings <- function(
-    fileName
-) {
-
+    fileName) {
   settings <- ParallelLogger::loadSettingsFromJson(
     fileName = fileName
   )
@@ -122,7 +117,7 @@ loadCharacterizationSettings <- function(
 #' @param characterizationSettings The study settings created using \code{createCharacterizationSettings}
 #' @param saveDirectory The location to save the results to
 #' @param tablePrefix A string to append the tables in the results
-#' @param databaseId The unqiue identifier for the cdm database
+#' @param databaseId The unique identifier for the cdm database
 #' @param showSubjectId  Whether to include subjectId of failed rechallenge case series or hide
 #' @param minCellCount  The minimum count value that is calculated
 #'
@@ -144,8 +139,7 @@ runCharacterizationAnalyses <- function(
     tablePrefix = "c_",
     databaseId = "1",
     showSubjectId = F,
-    minCellCount = 0
-) {
+    minCellCount = 0) {
   # inputs checks
   errorMessages <- checkmate::makeAssertCollection()
   .checkCharacterizationSettings(
@@ -155,10 +149,10 @@ runCharacterizationAnalyses <- function(
   .checkTablePrefix(
     tablePrefix = tablePrefix,
     errorMessages = errorMessages
-    )
+  )
   checkmate::reportAssertions(
     errorMessages
-    )
+  )
 
   # create the Database
   conn <- createSqliteDatabase(
@@ -166,7 +160,7 @@ runCharacterizationAnalyses <- function(
   )
   on.exit(
     DatabaseConnector::disconnect(conn)
-    )
+  )
 
   createCharacterizationTables(
     conn = conn,
@@ -179,7 +173,6 @@ runCharacterizationAnalyses <- function(
 
   if (!is.null(characterizationSettings$timeToEventSettings)) {
     for (i in 1:length(characterizationSettings$timeToEventSettings)) {
-
       message("Running time to event analysis ", i)
 
       result <- tryCatch(
@@ -197,7 +190,7 @@ runCharacterizationAnalyses <- function(
           )
         },
         error = function(e) {
-          message(paste0("ERROR in time-to-event analysis: ", e$message));
+          message(paste0("ERROR in time-to-event analysis: ", e$message))
           return(NULL)
         }
       )
@@ -222,10 +215,9 @@ runCharacterizationAnalyses <- function(
           andromedaObject = result$timeToEvent,
           tablePrefix = tablePrefix,
           minCellCount = minCellCount,
-          minCellCountColumns = list('numEvents')
+          minCellCountColumns = list("numEvents")
         )
       }
-
     }
   }
 
@@ -247,7 +239,7 @@ runCharacterizationAnalyses <- function(
           )
         },
         error = function(e) {
-          message(paste0("ERROR in dechallenge rechallenge analysis: ", e$message));
+          message(paste0("ERROR in dechallenge rechallenge analysis: ", e$message))
           return(NULL)
         }
       )
@@ -273,12 +265,12 @@ runCharacterizationAnalyses <- function(
           tablePrefix = tablePrefix,
           minCellCount = minCellCount,
           minCellCountColumns = list(
-              c('numCases'),
-              c('dechallengeAttempt'),
-              c('dechallengeFail', 'dechallengeSuccess'),
-              c('rechallengeAttempt'),
-              c('rechallengeFail', 'rechallengeSuccess')
-              )
+            c("numCases"),
+            c("dechallengeAttempt"),
+            c("dechallengeFail", "dechallengeSuccess"),
+            c("rechallengeAttempt"),
+            c("rechallengeFail", "rechallengeSuccess")
+          )
         )
       }
 
@@ -300,7 +292,7 @@ runCharacterizationAnalyses <- function(
           )
         },
         error = function(e) {
-          message(paste0("ERROR in rechallenge failed case analysis: ", e$message));
+          message(paste0("ERROR in rechallenge failed case analysis: ", e$message))
           return(NULL)
         }
       )
@@ -350,8 +342,8 @@ runCharacterizationAnalyses <- function(
           )
         },
         error = function(e) {
-          message(paste0("ERROR in aggregate covariate analyses: ", e$message));
-          message(e);
+          message(paste0("ERROR in aggregate covariate analyses: ", e$message))
+          message(e)
           return(NULL)
         }
       )
@@ -417,7 +409,7 @@ runCharacterizationAnalyses <- function(
             tablePrefix = tablePrefix,
             minCellCount = minCellCount,
             minCellCountColumns = list(
-              c('sumValue') #c('SUM_VALUE') #AVERAGE_VALUE
+              c("sumValue") # c('SUM_VALUE') #AVERAGE_VALUE
             )
           )
         }
@@ -431,7 +423,7 @@ runCharacterizationAnalyses <- function(
             tablePrefix = tablePrefix,
             minCellCount = minCellCount,
             minCellCountColumns = list(
-              c('countValue')
+              c("countValue")
             )
           )
         }
diff --git a/R/SaveLoad.R b/R/SaveLoad.R
index f6c2e23..af7bb4e 100644
--- a/R/SaveLoad.R
+++ b/R/SaveLoad.R
@@ -1,4 +1,4 @@
-# Copyright 2022 Observational Health Data Sciences and Informatics
+# Copyright 2024 Observational Health Data Sciences and Informatics
 #
 # This file is part of Characterization
 #
@@ -32,8 +32,7 @@ colnamesLower <- function(data) {
 #' @export
 saveTimeToEventAnalyses <- function(
     result,
-    fileName
-) {
+    fileName) {
   Andromeda::saveAndromeda(
     andromeda = result,
     fileName = fileName,
@@ -56,19 +55,17 @@ saveTimeToEventAnalyses <- function(
 exportTimeToEventToCsv <- function(
     result,
     saveDirectory,
-    minCellCount = 0
-) {
+    minCellCount = 0) {
   if (!dir.exists(saveDirectory)) {
     dir.create(
       path = saveDirectory,
       recursive = T
-      )
+    )
   }
 
   Andromeda::batchApply(
     tbl = result$timeToEvent,
     fun = function(x) {
-
       append <- file.exists(
         file.path(
           saveDirectory,
@@ -79,14 +76,14 @@ exportTimeToEventToCsv <- function(
       dat <- as.data.frame(
         x %>%
           dplyr::collect()
-        )
+      )
 
       colnames(dat) <- SqlRender::camelCaseToSnakeCase(
         string = colnames(dat)
       )
 
-      if(sum(dat$NUM_EVENTS < minCellCount)>0){
-        ParallelLogger::logInfo(paste0('Removing NUM_EVENTS less than ', minCellCount))
+      if (sum(dat$NUM_EVENTS < minCellCount) > 0) {
+        ParallelLogger::logInfo(paste0("Removing NUM_EVENTS less than ", minCellCount))
         dat$NUM_EVENTS[dat$NUM_EVENTS < minCellCount] <- -1
       }
 
@@ -95,10 +92,9 @@ exportTimeToEventToCsv <- function(
         file = file.path(
           saveDirectory,
           "time_to_event.csv"
-          ),
+        ),
         append = append
       )
-
     }
   )
 
@@ -134,8 +130,7 @@ loadTimeToEventAnalyses <- function(fileName) {
 #' @export
 saveDechallengeRechallengeAnalyses <- function(
     result,
-    fileName
-) {
+    fileName) {
   Andromeda::saveAndromeda(
     andromeda = result,
     fileName = fileName,
@@ -157,8 +152,7 @@ saveDechallengeRechallengeAnalyses <- function(
 #' @export
 saveRechallengeFailCaseSeriesAnalyses <- function(
     result,
-    fileName
-) {
+    fileName) {
   Andromeda::saveAndromeda(
     andromeda = result,
     fileName = fileName,
@@ -178,8 +172,7 @@ saveRechallengeFailCaseSeriesAnalyses <- function(
 #'
 #' @export
 loadDechallengeRechallengeAnalyses <- function(
-    fileName
-) {
+    fileName) {
   result <- Andromeda::loadAndromeda(fileName)
   return(result)
 }
@@ -193,8 +186,7 @@ loadDechallengeRechallengeAnalyses <- function(
 #'
 #' @export
 loadRechallengeFailCaseSeriesAnalyses <- function(
-    fileName
-) {
+    fileName) {
   result <- Andromeda::loadAndromeda(fileName)
   return(result)
 }
@@ -212,9 +204,7 @@ loadRechallengeFailCaseSeriesAnalyses <- function(
 exportDechallengeRechallengeToCsv <- function(
     result,
     saveDirectory,
-    minCellCount = 0
-) {
-
+    minCellCount = 0) {
   countN <- dplyr::pull(
     dplyr::count(result$dechallengeRechallenge)
   )
@@ -232,49 +222,49 @@ exportDechallengeRechallengeToCsv <- function(
       dat <- as.data.frame(
         x %>%
           dplyr::collect()
-        )
+      )
 
       colnames(dat) <- SqlRender::camelCaseToSnakeCase(
         string = colnames(dat)
       )
 
       removeInd <- dat$NUM_EVENTS < minCellCount
-      if(sum(removeInd) > 0){
-        ParallelLogger::logInfo(paste0('Removing NUM_EVENTS counts less than ', minCellCount))
-        if(sum(removeInd) > 0){
-            dat$NUM_CASES[removeInd] <- -1
-          }
+      if (sum(removeInd) > 0) {
+        ParallelLogger::logInfo(paste0("Removing NUM_EVENTS counts less than ", minCellCount))
+        if (sum(removeInd) > 0) {
+          dat$NUM_CASES[removeInd] <- -1
+        }
       }
 
       removeInd <- dat$DECHALLENGE_ATTEMPT < minCellCount
-      if(sum(removeInd) > 0){
-        ParallelLogger::logInfo(paste0('Removing DECHALLENGE_ATTEMPT counts less than ', minCellCount))
-        if(sum(removeInd) > 0){
+      if (sum(removeInd) > 0) {
+        ParallelLogger::logInfo(paste0("Removing DECHALLENGE_ATTEMPT counts less than ", minCellCount))
+        if (sum(removeInd) > 0) {
           dat$DECHALLENGE_ATTEMPT[removeInd] <- -1
         }
       }
 
       removeInd <- dat$DECHALLENGE_FAIL < minCellCount | dat$DECHALLENGE_SUCCESS < minCellCount
-      if(sum(removeInd) > 0){
-        ParallelLogger::logInfo(paste0('Removing DECHALLENGE FAIL or SUCCESS counts less than ', minCellCount))
-        if(sum(removeInd) > 0){
+      if (sum(removeInd) > 0) {
+        ParallelLogger::logInfo(paste0("Removing DECHALLENGE FAIL or SUCCESS counts less than ", minCellCount))
+        if (sum(removeInd) > 0) {
           dat$DECHALLENGE_FAIL[removeInd] <- -1
           dat$DECHALLENGE_SUCCESS[removeInd] <- -1
         }
       }
 
       removeInd <- dat$RECHALLENGE_ATTEMPT < minCellCount
-      if(sum(removeInd) > 0){
-        ParallelLogger::logInfo(paste0('Removing RECHALLENGE_ATTEMPT counts less than ', minCellCount))
-        if(sum(removeInd) > 0){
+      if (sum(removeInd) > 0) {
+        ParallelLogger::logInfo(paste0("Removing RECHALLENGE_ATTEMPT counts less than ", minCellCount))
+        if (sum(removeInd) > 0) {
           dat$RECHALLENGE_ATTEMPT[removeInd] <- -1
         }
       }
 
       removeInd <- dat$RECHALLENGE_FAIL < minCellCount | dat$RECHALLENGE_SUCCESS < minCellCount
-      if(sum(removeInd) > 0){
-        ParallelLogger::logInfo(paste0('Removing RECHALLENGE FAIL or SUCCESS counts less than ', minCellCount))
-        if(sum(removeInd) > 0){
+      if (sum(removeInd) > 0) {
+        ParallelLogger::logInfo(paste0("Removing RECHALLENGE FAIL or SUCCESS counts less than ", minCellCount))
+        if (sum(removeInd) > 0) {
           dat$RECHALLENGE_FAIL[removeInd] <- -1
           dat$RECHALLENGE_SUCCESS[removeInd] <- -1
         }
@@ -288,7 +278,6 @@ exportDechallengeRechallengeToCsv <- function(
         ),
         append = append
       )
-
     }
   )
 
@@ -311,8 +300,7 @@ exportDechallengeRechallengeToCsv <- function(
 #' @export
 exportRechallengeFailCaseSeriesToCsv <- function(
     result,
-    saveDirectory
-) {
+    saveDirectory) {
   if (!dir.exists(saveDirectory)) {
     dir.create(
       path = saveDirectory,
@@ -322,39 +310,37 @@ exportRechallengeFailCaseSeriesToCsv <- function(
 
   countN <- dplyr::pull(
     dplyr::count(result$rechallengeFailCaseSeries)
-    )
+  )
 
   message("Writing ", countN, " rows to csv")
 
   Andromeda::batchApply(
     tbl = result$rechallengeFailCaseSeries,
     fun = function(x) {
-
       append <- file.exists(
         file.path(
           saveDirectory,
           "rechallenge_fail_case_series.csv"
-          )
         )
+      )
 
       dat <- as.data.frame(
         x %>%
           dplyr::collect()
-        )
+      )
 
       colnames(dat) <- SqlRender::camelCaseToSnakeCase(
         string = colnames(dat)
-        )
+      )
 
       readr::write_csv(
         x = dat,
         file = file.path(
           saveDirectory,
           "rechallenge_fail_case_series.csv"
-          ),
+        ),
         append = append
       )
-
     }
   )
 
@@ -377,8 +363,7 @@ exportRechallengeFailCaseSeriesToCsv <- function(
 #' @export
 saveAggregateCovariateAnalyses <- function(
     result,
-    fileName
-) {
+    fileName) {
   Andromeda::saveAndromeda(
     andromeda = result,
     fileName = fileName,
@@ -397,8 +382,7 @@ saveAggregateCovariateAnalyses <- function(
 #'
 #' @export
 loadAggregateCovariateAnalyses <- function(
-    fileName
-) {
+    fileName) {
   result <- Andromeda::loadAndromeda(
     fileName = fileName
   )
@@ -419,8 +403,7 @@ loadAggregateCovariateAnalyses <- function(
 exportAggregateCovariateToCsv <- function(
     result,
     saveDirectory,
-    minCellCount = 0
-) {
+    minCellCount = 0) {
   if (!dir.exists(saveDirectory)) {
     dir.create(saveDirectory, recursive = T)
   }
@@ -429,7 +412,6 @@ exportAggregateCovariateToCsv <- function(
   Andromeda::batchApply(
     tbl = result$settings,
     fun = function(x) {
-
       append <- file.exists(
         file.path(
           saveDirectory,
@@ -454,14 +436,12 @@ exportAggregateCovariateToCsv <- function(
         ),
         append = append
       )
-
     }
   )
   # cohort details
   Andromeda::batchApply(
     tbl = result$cohortCounts,
     fun = function(x) {
-
       append <- file.exists(
         file.path(
           saveDirectory,
@@ -486,7 +466,6 @@ exportAggregateCovariateToCsv <- function(
         ),
         append = append
       )
-
     }
   )
 
@@ -494,7 +473,6 @@ exportAggregateCovariateToCsv <- function(
   Andromeda::batchApply(
     tbl = result$cohortDetails,
     fun = function(x) {
-
       append <- file.exists(
         file.path(
           saveDirectory,
@@ -519,7 +497,6 @@ exportAggregateCovariateToCsv <- function(
         ),
         append = append
       )
-
     }
   )
 
@@ -527,7 +504,6 @@ exportAggregateCovariateToCsv <- function(
   Andromeda::batchApply(
     tbl = result$analysisRef,
     fun = function(x) {
-
       append <- file.exists(
         file.path(
           saveDirectory,
@@ -538,7 +514,7 @@ exportAggregateCovariateToCsv <- function(
       dat <- as.data.frame(
         x %>%
           dplyr::collect()
-        )
+      )
 
       colnames(dat) <- SqlRender::camelCaseToSnakeCase(
         string = colnames(dat)
@@ -552,7 +528,6 @@ exportAggregateCovariateToCsv <- function(
         ),
         append = append
       )
-
     }
   )
 
@@ -560,7 +535,6 @@ exportAggregateCovariateToCsv <- function(
   Andromeda::batchApply(
     tbl = result$covariateRef,
     fun = function(x) {
-
       append <- file.exists(
         file.path(
           saveDirectory,
@@ -571,7 +545,7 @@ exportAggregateCovariateToCsv <- function(
       dat <- as.data.frame(
         x %>%
           dplyr::collect()
-        )
+      )
 
       colnames(dat) <- SqlRender::camelCaseToSnakeCase(
         string = colnames(dat)
@@ -585,7 +559,6 @@ exportAggregateCovariateToCsv <- function(
         ),
         append = append
       )
-
     }
   )
 
@@ -593,27 +566,26 @@ exportAggregateCovariateToCsv <- function(
   Andromeda::batchApply(
     tbl = result$covariates,
     fun = function(x) {
-
       append <- file.exists(
         file.path(
           saveDirectory,
           "covariates.csv"
-          )
         )
+      )
 
       dat <- as.data.frame(
         x %>%
           dplyr::collect()
-        )
+      )
 
       colnames(dat) <- SqlRender::camelCaseToSnakeCase(
         string = colnames(dat)
       )
 
       removeInd <- dat$SUM_VALUE < minCellCount
-      if(sum(removeInd) > 0){
-        ParallelLogger::logInfo(paste0('Removing SUM_VALUE counts less than ', minCellCount))
-        if(sum(removeInd) > 0){
+      if (sum(removeInd) > 0) {
+        ParallelLogger::logInfo(paste0("Removing SUM_VALUE counts less than ", minCellCount))
+        if (sum(removeInd) > 0) {
           dat$SUM_VALUE[removeInd] <- -1
           dat$AVERAGE_VALUE[removeInd] <- -1
         }
@@ -627,7 +599,6 @@ exportAggregateCovariateToCsv <- function(
         ),
         append = append
       )
-
     }
   )
 
@@ -635,7 +606,6 @@ exportAggregateCovariateToCsv <- function(
   Andromeda::batchApply(
     tbl = result$covariatesContinuous,
     fun = function(x) {
-
       append <- file.exists(
         file.path(
           saveDirectory,
@@ -646,16 +616,16 @@ exportAggregateCovariateToCsv <- function(
       dat <- as.data.frame(
         x %>%
           dplyr::collect()
-        )
+      )
 
       colnames(dat) <- SqlRender::camelCaseToSnakeCase(
         string = colnames(dat)
       )
 
       removeInd <- dat$COUNT_VALUE < minCellCount
-      if(sum(removeInd) > 0){
-        ParallelLogger::logInfo(paste0('Removing COUNT_VALUE counts less than ', minCellCount))
-        if(sum(removeInd) > 0){
+      if (sum(removeInd) > 0) {
+        ParallelLogger::logInfo(paste0("Removing COUNT_VALUE counts less than ", minCellCount))
+        if (sum(removeInd) > 0) {
           dat$COUNT_VALUE[removeInd] <- -1
         }
       }
@@ -668,13 +638,13 @@ exportAggregateCovariateToCsv <- function(
         ),
         append = append
       )
-
     }
   )
   invisible(
     file.path(
       saveDirectory,
-      c("cohort_details.csv",
+      c(
+        "cohort_details.csv",
         "settings.csv",
         "analysis_ref.csv",
         "covariate_ref.csv",
diff --git a/R/TimeToEvent.R b/R/TimeToEvent.R
index 3c9d7b9..5affa92 100644
--- a/R/TimeToEvent.R
+++ b/R/TimeToEvent.R
@@ -1,4 +1,4 @@
-# Copyright 2022 Observational Health Data Sciences and Informatics
+# Copyright 2024 Observational Health Data Sciences and Informatics
 #
 # This file is part of Characterization
 #
@@ -24,22 +24,20 @@
 #'
 #' @export
 createTimeToEventSettings <- function(
-  targetIds,
-  outcomeIds
-){
-
+    targetIds,
+    outcomeIds) {
   # check indicationIds
   errorMessages <- checkmate::makeAssertCollection()
   # check targetIds is a vector of int/double
   .checkCohortIds(
     cohortIds = targetIds,
-    type = 'target',
+    type = "target",
     errorMessages = errorMessages
   )
   # check outcomeIds is a vector of int/double
   .checkCohortIds(
     cohortIds = outcomeIds,
-    type = 'outcome',
+    type = "outcome",
     errorMessages = errorMessages
   )
   checkmate::reportAssertions(errorMessages)
@@ -51,7 +49,7 @@ createTimeToEventSettings <- function(
     outcomeIds = outcomeIds
   )
 
-  class(result) <- 'timeToEventSettings'
+  class(result) <- "timeToEventSettings"
   return(result)
 }
 
@@ -69,35 +67,33 @@ createTimeToEventSettings <- function(
 #'
 #' @export
 computeTimeToEventAnalyses <- function(
-  connectionDetails = NULL,
-  targetDatabaseSchema,
-  targetTable,
-  outcomeDatabaseSchema = targetDatabaseSchema,
-  outcomeTable = targetTable,
-  tempEmulationSchema = getOption("sqlRenderTempEmulationSchema"),
-  cdmDatabaseSchema,
-  timeToEventSettings,
-  databaseId = 'database 1'
-) {
-
+    connectionDetails = NULL,
+    targetDatabaseSchema,
+    targetTable,
+    outcomeDatabaseSchema = targetDatabaseSchema,
+    outcomeTable = targetTable,
+    tempEmulationSchema = getOption("sqlRenderTempEmulationSchema"),
+    cdmDatabaseSchema,
+    timeToEventSettings,
+    databaseId = "database 1") {
   # check inputs
   errorMessages <- checkmate::makeAssertCollection()
   .checkConnectionDetails(connectionDetails, errorMessages)
   .checkCohortDetails(
     cohortDatabaseSchema = targetDatabaseSchema,
     cohortTable = targetTable,
-    type = 'target',
-    errorMessages =  errorMessages
+    type = "target",
+    errorMessages = errorMessages
   )
   .checkCohortDetails(
     cohortDatabaseSchema = outcomeDatabaseSchema,
     cohortTable = outcomeTable,
-    type = 'outcome',
-    errorMessages =  errorMessages
+    type = "outcome",
+    errorMessages = errorMessages
   )
   .checkTempEmulationSchema(
     tempEmulationSchema = tempEmulationSchema,
-    errorMessages =  errorMessages
+    errorMessages = errorMessages
   )
   .checkTimeToEventSettings(
     settings = timeToEventSettings,
@@ -106,7 +102,7 @@ computeTimeToEventAnalyses <- function(
 
   valid <- checkmate::reportAssertions(errorMessages)
 
-  if(valid){
+  if (valid) {
     start <- Sys.time()
 
     connection <- DatabaseConnector::connect(
@@ -114,7 +110,7 @@ computeTimeToEventAnalyses <- function(
     )
     on.exit(
       DatabaseConnector::disconnect(connection)
-      )
+    )
 
     # upload table to #cohort_settings
     message("Uploading #cohort_settings")
@@ -155,10 +151,10 @@ computeTimeToEventAnalyses <- function(
       sql = sql
     )
 
-    sql <- 'select * from #two_tte_summary;'
+    sql <- "select * from #two_tte_summary;"
     sql <- SqlRender::translate(
       sql = sql,
-      targetDialect =  connection@dbms,
+      targetDialect = connection@dbms,
       tempEmulationSchema = tempEmulationSchema
     )
 
@@ -166,7 +162,7 @@ computeTimeToEventAnalyses <- function(
       connection = connection,
       sql = sql,
       andromeda = Andromeda::andromeda(),
-      andromedaTableName = 'timeToEvent',
+      andromedaTableName = "timeToEvent",
       snakeCaseToCamelCase = TRUE
     )
 
diff --git a/R/ViewShiny.R b/R/ViewShiny.R
index a9c3290..3eea909 100644
--- a/R/ViewShiny.R
+++ b/R/ViewShiny.R
@@ -12,9 +12,7 @@
 #' @export
 viewCharacterization <- function(
     resultLocation,
-    cohortDefinitionSet = NULL
-    ) {
-
+    cohortDefinitionSet = NULL) {
   databaseSettings <- prepareCharacterizationShiny(
     resultLocation = resultLocation,
     cohortDefinitionSet = cohortDefinitionSet
@@ -25,12 +23,11 @@ viewCharacterization <- function(
 
 prepareCharacterizationShiny <- function(
     resultLocation,
-    cohortDefinitionSet
-    ){
-  server <- file.path(resultLocation, 'sqliteCharacterization', 'sqlite.sqlite')
+    cohortDefinitionSet) {
+  server <- file.path(resultLocation, "sqliteCharacterization", "sqlite.sqlite")
 
   connectionDetailsSettings <- list(
-    dbms = 'sqlite',
+    dbms = "sqlite",
     server = server
   )
 
@@ -42,24 +39,24 @@ prepareCharacterizationShiny <- function(
   con <- DatabaseConnector::connect(connectionDetails)
   on.exit(DatabaseConnector::disconnect(con))
 
-  tables <- tolower(DatabaseConnector::getTableNames(con, 'main'))
+  tables <- tolower(DatabaseConnector::getTableNames(con, "main"))
 
-  if(!'cg_cohort_definition' %in% tables){
+  if (!"cg_cohort_definition" %in% tables) {
     cohortIds <- unique(
       c(
-        DatabaseConnector::querySql(con, 'select distinct TARGET_COHORT_ID from c_cohort_details where TARGET_COHORT_ID != 0;')$TARGET_COHORT_ID,
-        DatabaseConnector::querySql(con, 'select distinct OUTCOME_COHORT_ID from c_cohort_details where OUTCOME_COHORT_ID != 0;')$OUTCOME_COHORT_ID,
-        DatabaseConnector::querySql(con, 'select distinct TARGET_COHORT_DEFINITION_ID from c_time_to_event;')$TARGET_COHORT_DEFINITION_ID,
-        DatabaseConnector::querySql(con, 'select distinct OUTCOME_COHORT_DEFINITION_ID from c_time_to_event;')$OUTCOME_COHORT_DEFINITION_ID,
-        DatabaseConnector::querySql(con, 'select distinct TARGET_COHORT_DEFINITION_ID from c_rechallenge_fail_case_series;')$TARGET_COHORT_DEFINITION_ID,
-        DatabaseConnector::querySql(con, 'select distinct OUTCOME_COHORT_DEFINITION_ID from c_rechallenge_fail_case_series;')$OUTCOME_COHORT_DEFINITION_ID
+        DatabaseConnector::querySql(con, "select distinct TARGET_COHORT_ID from c_cohort_details where TARGET_COHORT_ID != 0;")$TARGET_COHORT_ID,
+        DatabaseConnector::querySql(con, "select distinct OUTCOME_COHORT_ID from c_cohort_details where OUTCOME_COHORT_ID != 0;")$OUTCOME_COHORT_ID,
+        DatabaseConnector::querySql(con, "select distinct TARGET_COHORT_DEFINITION_ID from c_time_to_event;")$TARGET_COHORT_DEFINITION_ID,
+        DatabaseConnector::querySql(con, "select distinct OUTCOME_COHORT_DEFINITION_ID from c_time_to_event;")$OUTCOME_COHORT_DEFINITION_ID,
+        DatabaseConnector::querySql(con, "select distinct TARGET_COHORT_DEFINITION_ID from c_rechallenge_fail_case_series;")$TARGET_COHORT_DEFINITION_ID,
+        DatabaseConnector::querySql(con, "select distinct OUTCOME_COHORT_DEFINITION_ID from c_rechallenge_fail_case_series;")$OUTCOME_COHORT_DEFINITION_ID
       )
     )
 
     DatabaseConnector::insertTable(
       connection = con,
-      databaseSchema = 'main',
-      tableName = 'cg_COHORT_DEFINITION',
+      databaseSchema = "main",
+      tableName = "cg_COHORT_DEFINITION",
       data = data.frame(
         cohortDefinitionId = cohortIds,
         cohortName = getCohortNames(cohortIds, cohortDefinitionSet)
@@ -68,51 +65,51 @@ prepareCharacterizationShiny <- function(
     )
   }
 
-  if(!'database_meta_data' %in% tables){
+  if (!"database_meta_data" %in% tables) {
     dbIds <- unique(
       c(
-        DatabaseConnector::querySql(con, 'select distinct DATABASE_ID from c_analysis_ref;')$DATABASE_ID,
-        DatabaseConnector::querySql(con, 'select distinct DATABASE_ID from c_dechallenge_rechallenge;')$DATABASE_ID,
-        DatabaseConnector::querySql(con, 'select distinct DATABASE_ID from c_time_to_event;')$DATABASE_ID
+        DatabaseConnector::querySql(con, "select distinct DATABASE_ID from c_analysis_ref;")$DATABASE_ID,
+        DatabaseConnector::querySql(con, "select distinct DATABASE_ID from c_dechallenge_rechallenge;")$DATABASE_ID,
+        DatabaseConnector::querySql(con, "select distinct DATABASE_ID from c_time_to_event;")$DATABASE_ID
       )
     )
 
     DatabaseConnector::insertTable(
       connection = con,
-      databaseSchema = 'main',
-      tableName = 'DATABASE_META_DATA',
+      databaseSchema = "main",
+      tableName = "DATABASE_META_DATA",
       data = data.frame(
         databaseId = dbIds,
-        cdmSourceAbbreviation = paste0('database ', dbIds)
+        cdmSourceAbbreviation = paste0("database ", dbIds)
       ),
       camelCaseToSnakeCase = T
     )
   }
 
-  if(!'i_incidence_summary' %in% tables){
-
-    x <- c("refId", "databaseId", "sourceName",
-           "targetCohortDefinitionId", "targetName", "tarId",
-           "tarStartWith", "tarStartOffset", "tarEndWith", "tarEndOffset",
-           "subgroupId", 'subgroupName',
-           'outcomeId','outcomeCohortDefinitionId', 'outcomeName',
-           'clean_window',
-           'ageId', 'ageGroupName',
-           'genderId', 'genderName',
-           'startYear', 'personsAtRiskPe', 'personsAtRisk',
-           'personDaysPe', 'personDays',
-           'personOutcomesPe', 'personOutcomes',
-           'outcomesPe', 'outcomes',
-           'incidenceProportionP100p',
-           'incidenceRateP100py'
+  if (!"i_incidence_summary" %in% tables) {
+    x <- c(
+      "refId", "databaseId", "sourceName",
+      "targetCohortDefinitionId", "targetName", "tarId",
+      "tarStartWith", "tarStartOffset", "tarEndWith", "tarEndOffset",
+      "subgroupId", "subgroupName",
+      "outcomeId", "outcomeCohortDefinitionId", "outcomeName",
+      "clean_window",
+      "ageId", "ageGroupName",
+      "genderId", "genderName",
+      "startYear", "personsAtRiskPe", "personsAtRisk",
+      "personDaysPe", "personDays",
+      "personOutcomesPe", "personOutcomes",
+      "outcomesPe", "outcomes",
+      "incidenceProportionP100p",
+      "incidenceRateP100py"
     )
     df <- data.frame(matrix(ncol = length(x), nrow = 0))
     colnames(df) <- x
 
     DatabaseConnector::insertTable(
       connection = con,
-      databaseSchema = 'main',
-      tableName = 'i_incidence_summary',
+      databaseSchema = "main",
+      tableName = "i_incidence_summary",
       data = df,
       camelCaseToSnakeCase = T
     )
@@ -120,11 +117,11 @@ prepareCharacterizationShiny <- function(
 
   databaseSettings <- list(
     connectionDetailsSettings = connectionDetailsSettings,
-    schema = 'main',
-    tablePrefix = 'c_',
-    cohortTablePrefix = 'cg_',
-    incidenceTablePrefix = 'i_',
-    databaseTable = 'DATABASE_META_DATA'
+    schema = "main",
+    tablePrefix = "c_",
+    cohortTablePrefix = "cg_",
+    incidenceTablePrefix = "i_",
+    databaseTable = "DATABASE_META_DATA"
   )
 
   return(databaseSettings)
@@ -132,8 +129,7 @@ prepareCharacterizationShiny <- function(
 
 viewChars <- function(
     databaseSettings,
-    testApp = F
-    ){
+    testApp = F) {
   ensure_installed("ShinyAppBuilder")
   ensure_installed("ResultModelManager")
 
@@ -145,76 +141,70 @@ viewChars <- function(
   databaseSettings$connectionDetailsSettings <- NULL
 
 
-  if(utils::packageVersion('ShinyAppBuilder') < '1.2.0'){
-    #use old method
+  if (utils::packageVersion("ShinyAppBuilder") < "1.2.0") {
+    # use old method
     # set database settings into system variables
     Sys.setenv("resultDatabaseDetails_characterization" = as.character(ParallelLogger::convertSettingsToJson(databaseSettings)))
 
     config <- ParallelLogger::loadSettingsFromJson(
       fileName = system.file(
-        'shinyConfig.json',
+        "shinyConfig.json",
         package = "Characterization"
       )
     )
 
-    if(!testApp){
+    if (!testApp) {
       ShinyAppBuilder::viewShiny(
         config = config,
         connection = connection
       )
-    } else{
+    } else {
       ShinyAppBuilder::createShinyApp(config = config, connection = connection)
     }
-
-  } else{
+  } else {
     # use new method
 
     config <- ParallelLogger::loadSettingsFromJson(
       fileName = system.file(
-        'shinyConfigUpdate.json',
+        "shinyConfigUpdate.json",
         package = "Characterization"
       )
     )
-    databaseSettings$cTablePrefix = databaseSettings$tablePrefix
-    databaseSettings$cgTablePrefix = databaseSettings$cohortTablePrefix
-    databaseSettings$databaseTable = 'DATABASE_META_DATA'
-    databaseSettings$databaseTablePrefix = ''
-    databaseSettings$iTablePrefix = databaseSettings$incidenceTablePrefix
+    databaseSettings$cTablePrefix <- databaseSettings$tablePrefix
+    databaseSettings$cgTablePrefix <- databaseSettings$cohortTablePrefix
+    databaseSettings$databaseTable <- "DATABASE_META_DATA"
+    databaseSettings$databaseTablePrefix <- ""
+    databaseSettings$iTablePrefix <- databaseSettings$incidenceTablePrefix
     databaseSettings$cgTable <- "cohort_definition"
 
-    if(!testApp){
+    if (!testApp) {
       ShinyAppBuilder::viewShiny(
         config = config,
         connection = connection,
         resultDatabaseSettings = databaseSettings
       )
-    } else{
+    } else {
       ShinyAppBuilder::createShinyApp(
         config = config,
         connection = connection,
         resultDatabaseSettings = databaseSettings
-        )
-
+      )
     }
-
   }
-
-
 }
 
 
 
-getCohortNames <- function(cohortIds, cohortDefinitionSet){
-
-  if(!is.null(cohortDefinitionSet)){
-  cohortNames <- sapply(
-    cohortIds,
-    function(x){
-      cohortDefinitionSet$cohortName[cohortDefinitionSet$cohortId == x]
-    }
-  )
-  } else{
-    cohortNames <- paste0('cohort ', cohortIds)
+getCohortNames <- function(cohortIds, cohortDefinitionSet) {
+  if (!is.null(cohortDefinitionSet)) {
+    cohortNames <- sapply(
+      cohortIds,
+      function(x) {
+        cohortDefinitionSet$cohortName[cohortDefinitionSet$cohortId == x]
+      }
+    )
+  } else {
+    cohortNames <- paste0("cohort ", cohortIds)
   }
 
   return(cohortNames)
@@ -222,9 +212,10 @@ getCohortNames <- function(cohortIds, cohortDefinitionSet){
 
 
 # Borrowed from devtools: https://github.com/hadley/devtools/blob/ba7a5a4abd8258c52cb156e7b26bb4bf47a79f0b/R/utils.r#L44
-is_installed <- function (pkg, version = 0) {
+is_installed <- function(pkg, version = 0) {
   installed_version <- tryCatch(utils::packageVersion(pkg),
-                                error = function(e) NA)
+    error = function(e) NA
+  )
   !is.na(installed_version) && installed_version >= version
 }
 
@@ -235,17 +226,17 @@ ensure_installed <- function(pkg) {
     if (interactive()) {
       message(msg, "\nWould you like to install it?")
       if (utils::menu(c("Yes", "No")) == 1) {
-        if(pkg%in%c("ShinyAppBuilder", "ResultModelManager")){
-
+        if (pkg %in% c("ShinyAppBuilder", "ResultModelManager")) {
           # add code to check for devtools...
-          dvtCheck <- tryCatch(utils::packageVersion('devtools'),
-                               error = function(e) NA)
-          if(is.na(dvtCheck)){
-            utils::install.packages('devtools')
+          dvtCheck <- tryCatch(utils::packageVersion("devtools"),
+            error = function(e) NA
+          )
+          if (is.na(dvtCheck)) {
+            utils::install.packages("devtools")
           }
 
-          devtools::install_github(paste0('OHDSI/',pkg))
-        }else{
+          devtools::install_github(paste0("OHDSI/", pkg))
+        } else {
           utils::install.packages(pkg)
         }
       } else {
diff --git a/docs/404.html b/docs/404.html
index ac0bc8f..a8cd17d 100644
--- a/docs/404.html
+++ b/docs/404.html
@@ -32,7 +32,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">Characterization</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.5</span>
       </span>
     </div>
 
diff --git a/docs/articles/InstallationGuide.html b/docs/articles/InstallationGuide.html
index 1f631f2..9d0754e 100644
--- a/docs/articles/InstallationGuide.html
+++ b/docs/articles/InstallationGuide.html
@@ -33,7 +33,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">Characterization</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.5</span>
       </span>
     </div>
 
@@ -96,7 +96,7 @@
       <h1 data-toc-skip>Characterization Installation Guide</h1>
                         <h4 data-toc-skip class="author">Jenna Reps</h4>
             
-            <h4 data-toc-skip class="date">2023-03-15</h4>
+            <h4 data-toc-skip class="date">2024-04-03</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/OHDSI/Characterization/blob/HEAD/vignettes/InstallationGuide.Rmd" class="external-link"><code>vignettes/InstallationGuide.Rmd</code></a></small>
       <div class="hidden name"><code>InstallationGuide.Rmd</code></div>
@@ -113,7 +113,7 @@ <h4 data-toc-skip class="date">2023-03-15</h4>
 <h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
 </h2>
 <p>This vignette describes how you need to install the Observational
-Health Data Sciencs and Informatics (OHDSI) <a href="http://github.com/OHDSI/Characterization" class="external-link"><code>Characterization</code></a>
+Health Data Sciences and Informatics (OHDSI) <a href="http://github.com/OHDSI/Characterization" class="external-link"><code>Characterization</code></a>
 package under Windows, Mac, and Linux.</p>
 </div>
 <div class="section level2">
@@ -154,7 +154,7 @@ <h2 id="installing-the-package">Installing the Package<a class="anchor" aria-lab
 <code>remotes</code>, which will automatically install the latest
 release and all the latest dependencies.</p>
 <p>If you do not want the official release you could install the
-bleading edge version of the package (latest develop branch).</p>
+bleeding edge version of the package (latest develop branch).</p>
 <p>Note that the latest develop branch could contain bugs, please report
 them to us if you experience problems.</p>
 <div class="section level3">
@@ -177,7 +177,7 @@ <h2 id="installation-issues">Installation issues<a class="anchor" aria-label="an
 <p>The list below provides solutions for some common issues:</p>
 <ol style="list-style-type: decimal">
 <li><p>If you have an error when trying to install a package in R saying
-<strong>‘Dependancy X not available …’</strong> then this can sometimes
+<strong>‘Dependency X not available …’</strong> then this can sometimes
 be fixed by running <code>install.packages('X')</code> and then once
 that completes trying to reinstall the package that had the
 error.</p></li>
@@ -198,7 +198,7 @@ <h2 id="acknowledgments">Acknowledgments<a class="anchor" aria-label="anchor" hr
 <pre><code><span><span class="co">## </span></span>
 <span><span class="co">## To cite package 'Characterization' in publications use:</span></span>
 <span><span class="co">## </span></span>
-<span><span class="co">##   Reps J, Ryan P (2023). _Characterization: Characterizations of</span></span>
+<span><span class="co">##   Reps J, Ryan P (2024). _Characterization: Characterizations of</span></span>
 <span><span class="co">##   Cohorts_. https://ohdsi.github.io/Characterization,</span></span>
 <span><span class="co">##   https://github.com/OHDSI/Characterization.</span></span>
 <span><span class="co">## </span></span>
@@ -207,7 +207,7 @@ <h2 id="acknowledgments">Acknowledgments<a class="anchor" aria-label="anchor" hr
 <span><span class="co">##   @Manual{,</span></span>
 <span><span class="co">##     title = {Characterization: Characterizations of Cohorts},</span></span>
 <span><span class="co">##     author = {Jenna Reps and Patrick Ryan},</span></span>
-<span><span class="co">##     year = {2023},</span></span>
+<span><span class="co">##     year = {2024},</span></span>
 <span><span class="co">##     note = {https://ohdsi.github.io/Characterization, https://github.com/OHDSI/Characterization},</span></span>
 <span><span class="co">##   }</span></span></code></pre>
 </div>
diff --git a/docs/articles/UsingCharacterizationPackage.html b/docs/articles/UsingCharacterizationPackage.html
index 6557e69..0086464 100644
--- a/docs/articles/UsingCharacterizationPackage.html
+++ b/docs/articles/UsingCharacterizationPackage.html
@@ -33,7 +33,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">Characterization</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.5</span>
       </span>
     </div>
 
@@ -97,7 +97,7 @@
       <h1 data-toc-skip>Using Characterization Package</h1>
                         <h4 data-toc-skip class="author">Jenna Reps</h4>
             
-            <h4 data-toc-skip class="date">2023-03-15</h4>
+            <h4 data-toc-skip class="date">2024-04-03</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/OHDSI/Characterization/blob/HEAD/vignettes/UsingCharacterizationPackage.Rmd" class="external-link"><code>vignettes/UsingCharacterizationPackage.Rmd</code></a></small>
       <div class="hidden name"><code>UsingCharacterizationPackage.Rmd</code></div>
@@ -118,7 +118,7 @@ <h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#i
 Characterization package currently contains three different types of
 analyses:</p>
 <ul>
-<li>Aggreagate Covariates: this returns the mean feature value for a set
+<li>Aggregate Covariates: this returns the mean feature value for a set
 of features specified by the user for i) the Target cohort population,
 ii) the Outcome cohort population, iii) the Target population patients
 who had the outcome during some user specified time-at-risk and iv) the
@@ -131,7 +131,7 @@ <h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#i
 the event starts again (a failed rechallenge). In this analysis, the
 Target cohorts are the drug users of interest and the Outcome cohorts
 are the medical events you wish to see whether the drug may cause. The
-user must also specify how close in time a drug msut be stopped after
+user must also specify how close in time a drug must be stopped after
 the outcome to be considered a dechallenge and how close in time an
 Outcome must occur after restarting the drug to be considered a failed
 rechallenge).</li>
@@ -159,34 +159,18 @@ <h2 id="setup">Setup<a class="anchor" aria-label="anchor" href="#setup"></a>
 <code class="sourceCode R"><span><span class="va">connectionDetails</span> <span class="op">&lt;-</span> <span class="fu">Eunomia</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/Eunomia/man/getEunomiaConnectionDetails.html" class="external-link">getEunomiaConnectionDetails</a></span><span class="op">(</span><span class="op">)</span></span>
 <span><span class="fu">Eunomia</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/Eunomia/man/createCohorts.html" class="external-link">createCohorts</a></span><span class="op">(</span>connectionDetails <span class="op">=</span> <span class="va">connectionDetails</span><span class="op">)</span></span></code></pre></div>
 <pre><code><span><span class="co">## Connecting using SQLite driver</span></span></code></pre>
-<pre><code>## Creating cohort: Celecoxib
-## 
-  |                                                                            
-  |                                                                      |   0%
-  |                                                                            
-  |======================================================================| 100%</code></pre>
-<pre><code><span><span class="co">## Executing SQL took 0.00908 secs</span></span></code></pre>
-<pre><code>## Creating cohort: Diclofenac
-## 
-  |                                                                            
-  |                                                                      |   0%
-  |                                                                            
-  |======================================================================| 100%</code></pre>
-<pre><code><span><span class="co">## Executing SQL took 0.00446 secs</span></span></code></pre>
-<pre><code>## Creating cohort: GiBleed
-## 
-  |                                                                            
-  |                                                                      |   0%
-  |                                                                            
-  |======================================================================| 100%</code></pre>
-<pre><code><span><span class="co">## Executing SQL took 0.00896 secs</span></span></code></pre>
-<pre><code>## Creating cohort: NSAIDs
-## 
-  |                                                                            
-  |                                                                      |   0%
-  |                                                                            
-  |======================================================================| 100%</code></pre>
-<pre><code><span><span class="co">## Executing SQL took 0.0542 secs</span></span></code></pre>
+<pre><code><span><span class="co">## Creating cohort: Celecoxib</span></span>
+<span><span class="co">##   |                                                                              |                                                                      |   0%  |                                                                              |======================================================================| 100%</span></span></code></pre>
+<pre><code><span><span class="co">## Executing SQL took 0.0152 secs</span></span></code></pre>
+<pre><code><span><span class="co">## Creating cohort: Diclofenac</span></span>
+<span><span class="co">##   |                                                                              |                                                                      |   0%  |                                                                              |======================================================================| 100%</span></span></code></pre>
+<pre><code><span><span class="co">## Executing SQL took 0.0169 secs</span></span></code></pre>
+<pre><code><span><span class="co">## Creating cohort: GiBleed</span></span>
+<span><span class="co">##   |                                                                              |                                                                      |   0%  |                                                                              |======================================================================| 100%</span></span></code></pre>
+<pre><code><span><span class="co">## Executing SQL took 0.0208 secs</span></span></code></pre>
+<pre><code><span><span class="co">## Creating cohort: NSAIDs</span></span>
+<span><span class="co">##   |                                                                              |                                                                      |   0%  |                                                                              |======================================================================| 100%</span></span></code></pre>
+<pre><code><span><span class="co">## Executing SQL took 0.0579 secs</span></span></code></pre>
 <pre><code><span><span class="co">## Cohorts created in table main.cohort</span></span></code></pre>
 <pre><code><span><span class="co">##   cohortId       name</span></span>
 <span><span class="co">## 1        1  Celecoxib</span></span>
@@ -247,47 +231,47 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 can use cohort ids 1,2 and 4 as the targetIds and cohort id 3 as the
 outcomeIds:</p>
 <div class="sourceCode" id="cb19"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span>  <span class="va">exampleTargetIds</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>,<span class="fl">2</span>,<span class="fl">4</span><span class="op">)</span></span>
-<span>  <span class="va">exampleOutcomeIds</span> <span class="op">&lt;-</span> <span class="fl">3</span></span></code></pre></div>
+<code class="sourceCode R"><span><span class="va">exampleTargetIds</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>, <span class="fl">2</span>, <span class="fl">4</span><span class="op">)</span></span>
+<span><span class="va">exampleOutcomeIds</span> <span class="op">&lt;-</span> <span class="fl">3</span></span></code></pre></div>
 <p>If we want to get information on the sex assigned at birth, age at
 index and Charlson Comorbidity index we can create the settings using
 <code><a href="https://rdrr.io/pkg/FeatureExtraction/man/createCovariateSettings.html" class="external-link">FeatureExtraction::createCovariateSettings</a></code>:</p>
 <div class="sourceCode" id="cb20"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span>  <span class="va">exampleCovariateSettings</span> <span class="op">&lt;-</span> <span class="fu">FeatureExtraction</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/FeatureExtraction/man/createCovariateSettings.html" class="external-link">createCovariateSettings</a></span><span class="op">(</span></span>
-<span>    useDemographicsGender <span class="op">=</span> <span class="cn">T</span>,</span>
-<span>    useDemographicsAge <span class="op">=</span> <span class="cn">T</span>,</span>
-<span>    useCharlsonIndex <span class="op">=</span> <span class="cn">T</span></span>
-<span>    <span class="op">)</span></span></code></pre></div>
+<code class="sourceCode R"><span><span class="va">exampleCovariateSettings</span> <span class="op">&lt;-</span> <span class="fu">FeatureExtraction</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/FeatureExtraction/man/createCovariateSettings.html" class="external-link">createCovariateSettings</a></span><span class="op">(</span></span>
+<span>  useDemographicsGender <span class="op">=</span> <span class="cn">T</span>,</span>
+<span>  useDemographicsAge <span class="op">=</span> <span class="cn">T</span>,</span>
+<span>  useCharlsonIndex <span class="op">=</span> <span class="cn">T</span></span>
+<span><span class="op">)</span></span></code></pre></div>
 <p>If we want to create the aggregate features for all our target
 cohorts, our outcome cohort and each target cohort restricted to those
 with a record of the outcome 1 day after target cohort start date until
 365 days after target cohort end date we can run:</p>
 <div class="sourceCode" id="cb21"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span>  <span class="va">exampleAggregateCovariateSettings</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/createAggregateCovariateSettings.html">createAggregateCovariateSettings</a></span><span class="op">(</span></span>
-<span>    targetIds <span class="op">=</span> <span class="va">exampleTargetIds</span>,</span>
-<span>    outcomeIds <span class="op">=</span> <span class="va">exampleOutcomeIds</span>,</span>
-<span>    riskWindowStart <span class="op">=</span> <span class="fl">1</span>, startAnchor <span class="op">=</span> <span class="st">'cohort start'</span>,</span>
-<span>    riskWindowEnd <span class="op">=</span> <span class="fl">365</span>, endAnchor <span class="op">=</span> <span class="st">'cohort start'</span>,</span>
-<span>    covariateSettings <span class="op">=</span> <span class="va">exampleCovariateSettings</span></span>
-<span>    <span class="op">)</span></span></code></pre></div>
+<code class="sourceCode R"><span><span class="va">exampleAggregateCovariateSettings</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/createAggregateCovariateSettings.html">createAggregateCovariateSettings</a></span><span class="op">(</span></span>
+<span>  targetIds <span class="op">=</span> <span class="va">exampleTargetIds</span>,</span>
+<span>  outcomeIds <span class="op">=</span> <span class="va">exampleOutcomeIds</span>,</span>
+<span>  riskWindowStart <span class="op">=</span> <span class="fl">1</span>, startAnchor <span class="op">=</span> <span class="st">"cohort start"</span>,</span>
+<span>  riskWindowEnd <span class="op">=</span> <span class="fl">365</span>, endAnchor <span class="op">=</span> <span class="st">"cohort start"</span>,</span>
+<span>  covariateSettings <span class="op">=</span> <span class="va">exampleCovariateSettings</span></span>
+<span><span class="op">)</span></span></code></pre></div>
 <p>Next we need to use the
 <code>exampleAggregateCovariateSettings</code> as the settings to
 <code>computeAggregateCovariateAnalyses</code>, we need to use the
 Eunomia connectionDetails and in Eunomia the OMOP CDM data and cohort
 table are in the ‘main’ schema. The cohort table name is ‘cohort’. The
-following code will apply the aggregative covariates analysis using the
+following code will apply the aggregated covariates analysis using the
 previously specified settings on the simulated Eunomia data:</p>
 <div class="sourceCode" id="cb22"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">agc</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/computeAggregateCovariateAnalyses.html">computeAggregateCovariateAnalyses</a></span><span class="op">(</span></span>
-<span>    connectionDetails <span class="op">=</span> <span class="va">connectionDetails</span>,</span>
-<span>    cdmDatabaseSchema <span class="op">=</span> <span class="st">'main'</span>,</span>
-<span>    cdmVersion <span class="op">=</span> <span class="fl">5</span>,</span>
-<span>    targetDatabaseSchema <span class="op">=</span> <span class="st">'main'</span>,</span>
-<span>    targetTable <span class="op">=</span> <span class="st">'cohort'</span>,</span>
-<span>    aggregateCovariateSettings <span class="op">=</span> <span class="va">exampleAggregateCovariateSettings</span>,</span>
-<span>    databaseId <span class="op">=</span> <span class="st">'Eunomia'</span>, </span>
-<span>    runId <span class="op">=</span> <span class="fl">1</span></span>
-<span>    <span class="op">)</span></span></code></pre></div>
+<span>  connectionDetails <span class="op">=</span> <span class="va">connectionDetails</span>,</span>
+<span>  cdmDatabaseSchema <span class="op">=</span> <span class="st">"main"</span>,</span>
+<span>  cdmVersion <span class="op">=</span> <span class="fl">5</span>,</span>
+<span>  targetDatabaseSchema <span class="op">=</span> <span class="st">"main"</span>,</span>
+<span>  targetTable <span class="op">=</span> <span class="st">"cohort"</span>,</span>
+<span>  aggregateCovariateSettings <span class="op">=</span> <span class="va">exampleAggregateCovariateSettings</span>,</span>
+<span>  databaseId <span class="op">=</span> <span class="st">"Eunomia"</span>,</span>
+<span>  runId <span class="op">=</span> <span class="fl">1</span></span>
+<span><span class="op">)</span></span></code></pre></div>
 <p>If you would like to save the results you can use the function
 <code>saveAggregateCovariateAnalyses</code> and this can then be loaded
 using <code>loadAggregateCovariateAnalyses</code>.</p>
@@ -297,11 +281,9 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 <li>covariates:</li>
 </ul>
 <div class="sourceCode" id="cb23"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="va">agc</span><span class="op">$</span><span class="va">covariates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> </span>
+<code class="sourceCode R"><span><span class="va">agc</span><span class="op">$</span><span class="va">covariates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
 <span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/compute.html" class="external-link">collect</a></span><span class="op">(</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
-<span>  <span class="fu">kableExtra</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/kableExtra/man/kbl.html" class="external-link">kbl</a></span><span class="op">(</span><span class="op">)</span> </span></code></pre></div>
-<pre><code><span><span class="co">## Warning in !is.null(rmarkdown::metadata$output) &amp;&amp; rmarkdown::metadata$output</span></span>
-<span><span class="co">## %in% : 'length(x) = 3 &gt; 1' in coercion to 'logical(1)'</span></span></code></pre>
+<span>  <span class="fu">kableExtra</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/kableExtra/man/kbl.html" class="external-link">kbl</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
 <table class="table">
 <thead><tr>
 <th style="text-align:left;">
@@ -738,126 +720,6 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 8507001
 </td>
 <td style="text-align:right;">
-714
-</td>
-<td style="text-align:right;">
-0.4941176
-</td>
-</tr>
-<tr>
-<td style="text-align:left;">
-Eunomia
-</td>
-<td style="text-align:right;">
-1
-</td>
-<td style="text-align:right;">
-11
-</td>
-<td style="text-align:right;">
-8532001
-</td>
-<td style="text-align:right;">
-731
-</td>
-<td style="text-align:right;">
-0.5058824
-</td>
-</tr>
-<tr>
-<td style="text-align:left;">
-Eunomia
-</td>
-<td style="text-align:right;">
-1
-</td>
-<td style="text-align:right;">
-12
-</td>
-<td style="text-align:right;">
-8507001
-</td>
-<td style="text-align:right;">
-338
-</td>
-<td style="text-align:right;">
-0.4787535
-</td>
-</tr>
-<tr>
-<td style="text-align:left;">
-Eunomia
-</td>
-<td style="text-align:right;">
-1
-</td>
-<td style="text-align:right;">
-12
-</td>
-<td style="text-align:right;">
-8532001
-</td>
-<td style="text-align:right;">
-368
-</td>
-<td style="text-align:right;">
-0.5212465
-</td>
-</tr>
-<tr>
-<td style="text-align:left;">
-Eunomia
-</td>
-<td style="text-align:right;">
-1
-</td>
-<td style="text-align:right;">
-13
-</td>
-<td style="text-align:right;">
-8507001
-</td>
-<td style="text-align:right;">
-1052
-</td>
-<td style="text-align:right;">
-0.4890748
-</td>
-</tr>
-<tr>
-<td style="text-align:left;">
-Eunomia
-</td>
-<td style="text-align:right;">
-1
-</td>
-<td style="text-align:right;">
-13
-</td>
-<td style="text-align:right;">
-8532001
-</td>
-<td style="text-align:right;">
-1099
-</td>
-<td style="text-align:right;">
-0.5109252
-</td>
-</tr>
-<tr>
-<td style="text-align:left;">
-Eunomia
-</td>
-<td style="text-align:right;">
-1
-</td>
-<td style="text-align:right;">
-14
-</td>
-<td style="text-align:right;">
-8507001
-</td>
-<td style="text-align:right;">
 180
 </td>
 <td style="text-align:right;">
@@ -872,7 +734,7 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 1
 </td>
 <td style="text-align:right;">
-14
+11
 </td>
 <td style="text-align:right;">
 8532001
@@ -892,7 +754,7 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 1
 </td>
 <td style="text-align:right;">
-15
+12
 </td>
 <td style="text-align:right;">
 8507001
@@ -912,7 +774,7 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 1
 </td>
 <td style="text-align:right;">
-15
+12
 </td>
 <td style="text-align:right;">
 8532001
@@ -932,7 +794,7 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 1
 </td>
 <td style="text-align:right;">
-16
+13
 </td>
 <td style="text-align:right;">
 8507001
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 1
 </td>
 <td style="text-align:right;">
-16
+13
 </td>
 <td style="text-align:right;">
 8532001
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-<td style="text-align:right;">
-20
+14
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 <td style="text-align:right;">
 8507001
@@ -1112,7 +854,7 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 1
 </td>
 <td style="text-align:right;">
-20
+14
 </td>
 <td style="text-align:right;">
 8532001
@@ -1132,7 +874,7 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 1
 </td>
 <td style="text-align:right;">
-21
+15
 </td>
 <td style="text-align:right;">
 8507001
@@ -1152,7 +894,7 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 1
 </td>
 <td style="text-align:right;">
-21
+15
 </td>
 <td style="text-align:right;">
 8532001
@@ -1172,7 +914,7 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 1
 </td>
 <td style="text-align:right;">
-22
+16
 </td>
 <td style="text-align:right;">
 8507001
@@ -1192,7 +934,7 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 1
 </td>
 <td style="text-align:right;">
-22
+16
 </td>
 <td style="text-align:right;">
 8532001
@@ -1212,7 +954,7 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 1
 </td>
 <td style="text-align:right;">
-23
+17
 </td>
 <td style="text-align:right;">
 8507001
@@ -1232,7 +974,7 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 1
 </td>
 <td style="text-align:right;">
-23
+17
 </td>
 <td style="text-align:right;">
 8532001
@@ -1252,7 +994,7 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 1
 </td>
 <td style="text-align:right;">
-24
+18
 </td>
 <td style="text-align:right;">
 8507001
@@ -1272,7 +1014,7 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 1
 </td>
 <td style="text-align:right;">
-24
+18
 </td>
 <td style="text-align:right;">
 8532001
@@ -1292,7 +1034,7 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 1
 </td>
 <td style="text-align:right;">
-25
+19
 </td>
 <td style="text-align:right;">
 8507001
@@ -1312,7 +1054,7 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 1
 </td>
 <td style="text-align:right;">
-25
+19
 </td>
 <td style="text-align:right;">
 8532001
@@ -1332,7 +1074,7 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 1
 </td>
 <td style="text-align:right;">
-26
+20
 </td>
 <td style="text-align:right;">
 8507001
@@ -1352,7 +1094,7 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 1
 </td>
 <td style="text-align:right;">
-26
+20
 </td>
 <td style="text-align:right;">
 8532001
@@ -1369,10 +1111,10 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 <ul>
 <li>covariatesContinuous:</li>
 </ul>
-<div class="sourceCode" id="cb25"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="va">agc</span><span class="op">$</span><span class="va">covariatesContinuous</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> </span>
+<div class="sourceCode" id="cb24"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="va">agc</span><span class="op">$</span><span class="va">covariatesContinuous</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
 <span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/compute.html" class="external-link">collect</a></span><span class="op">(</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
-<span>  <span class="fu">kableExtra</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/kableExtra/man/kbl.html" class="external-link">kbl</a></span><span class="op">(</span><span class="op">)</span> </span></code></pre></div>
+<span>  <span class="fu">kableExtra</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/kableExtra/man/kbl.html" class="external-link">kbl</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
 <table class="table">
 <thead><tr>
 <th style="text-align:left;">
@@ -1515,7 +1257,7 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 1
 </td>
 <td style="text-align:right;">
-15
+12
 </td>
 <td style="text-align:right;">
 1901
@@ -1559,7 +1301,7 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 1
 </td>
 <td style="text-align:right;">
-25
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 </td>
 <td style="text-align:right;">
 1901
@@ -1603,110 +1345,22 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 1
 </td>
 <td style="text-align:right;">
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+8
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 <td style="text-align:right;">
 1901
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 0.4233403
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 1
 </td>
 <td style="text-align:right;">
-14
+11
 </td>
 <td style="text-align:right;">
 1901
@@ -1823,7 +1477,7 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 1
 </td>
 <td style="text-align:right;">
-24
+18
 </td>
 <td style="text-align:right;">
 1901
@@ -1911,7 +1565,7 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 1
 </td>
 <td style="text-align:right;">
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+15
 </td>
 <td style="text-align:right;">
 1901
@@ -1999,7 +1653,7 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 1
 </td>
 <td style="text-align:right;">
-16
+13
 </td>
 <td style="text-align:right;">
 1901
@@ -2131,7 +1785,7 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 1
 </td>
 <td style="text-align:right;">
-23
+17
 </td>
 <td style="text-align:right;">
 1901
@@ -2175,7 +1829,7 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 1
 </td>
 <td style="text-align:right;">
-26
+20
 </td>
 <td style="text-align:right;">
 1901
@@ -2219,57 +1873,13 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 1
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 <td style="text-align:right;">
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 </td>
 <td style="text-align:right;">
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+935
 </td>
 <td style="text-align:right;">
 0
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 2
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 <td style="text-align:right;">
 1
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 <td style="text-align:right;">
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 <td style="text-align:right;">
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 1
 </td>
 <td style="text-align:right;">
-5
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 </td>
 <td style="text-align:right;">
 1901
 </td>
 <td style="text-align:right;">
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 </td>
 <td style="text-align:right;">
 0
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 2
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 </td>
 <td style="text-align:right;">
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 <td style="text-align:right;">
 1
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 1
 </td>
 <td style="text-align:right;">
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 </td>
 <td style="text-align:right;">
 1901
 </td>
 <td style="text-align:right;">
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-3.2746121
+0.3777510
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 <td style="text-align:right;">
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+0
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 <td style="text-align:right;">
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+0
 </td>
 <td style="text-align:right;">
-36
+0
 </td>
 <td style="text-align:right;">
-41
+1
 </td>
 <td style="text-align:right;">
-43
+1
 </td>
 </tr>
 <tr>
@@ -2791,40 +2005,40 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 1
 </td>
 <td style="text-align:right;">
-14
+16
 </td>
 <td style="text-align:right;">
-1002
+1901
 </td>
 <td style="text-align:right;">
-355
+1262
 </td>
 <td style="text-align:right;">
-32
+0
 </td>
 <td style="text-align:right;">
-46
+3
 </td>
 <td style="text-align:right;">
-38.7746479
+0.5478842
 </td>
 <td style="text-align:right;">
-3.2746121
+0.3775118
 </td>
 <td style="text-align:right;">
-39
+0
 </td>
 <td style="text-align:right;">
-35
+0
 </td>
 <td style="text-align:right;">
-36
+0
 </td>
 <td style="text-align:right;">
-41
+1
 </td>
 <td style="text-align:right;">
-43
+1
 </td>
 </tr>
 <tr>
@@ -2835,13 +2049,13 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 1
 </td>
 <td style="text-align:right;">
-2
+9
 </td>
 <td style="text-align:right;">
 1002
 </td>
 <td style="text-align:right;">
-355
+124
 </td>
 <td style="text-align:right;">
 32
@@ -2850,16 +2064,16 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 46
 </td>
 <td style="text-align:right;">
-38.9014085
+38.8709677
 </td>
 <td style="text-align:right;">
-3.2449654
+3.4000663
 </td>
 <td style="text-align:right;">
 39
 </td>
 <td style="text-align:right;">
-35
+34
 </td>
 <td style="text-align:right;">
 36
@@ -2868,7 +2082,7 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 41
 </td>
 <td style="text-align:right;">
-43
+44
 </td>
 </tr>
 <tr>
@@ -2879,13 +2093,13 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 1
 </td>
 <td style="text-align:right;">
-24
+12
 </td>
 <td style="text-align:right;">
 1002
 </td>
 <td style="text-align:right;">
-355
+124
 </td>
 <td style="text-align:right;">
 32
@@ -2894,16 +2108,16 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 46
 </td>
 <td style="text-align:right;">
-38.9014085
+38.8709677
 </td>
 <td style="text-align:right;">
-3.2449654
+3.4000663
 </td>
 <td style="text-align:right;">
 39
 </td>
 <td style="text-align:right;">
-35
+34
 </td>
 <td style="text-align:right;">
 36
@@ -2912,7 +2126,7 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 41
 </td>
 <td style="text-align:right;">
-43
+44
 </td>
 </tr>
 <tr>
@@ -2923,25 +2137,25 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 1
 </td>
 <td style="text-align:right;">
-10
+3
 </td>
 <td style="text-align:right;">
 1002
 </td>
 <td style="text-align:right;">
-479
+124
 </td>
 <td style="text-align:right;">
 32
 </td>
 <td style="text-align:right;">
-46
+47
 </td>
 <td style="text-align:right;">
-38.7995825
+38.9758065
 </td>
 <td style="text-align:right;">
-3.3042257
+3.4226973
 </td>
 <td style="text-align:right;">
 39
@@ -2967,25 +2181,25 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 1
 </td>
 <td style="text-align:right;">
-16
+19
 </td>
 <td style="text-align:right;">
 1002
 </td>
 <td style="text-align:right;">
-479
+124
 </td>
 <td style="text-align:right;">
 32
 </td>
 <td style="text-align:right;">
-46
+47
 </td>
 <td style="text-align:right;">
-38.7995825
+38.9758065
 </td>
 <td style="text-align:right;">
-3.3042257
+3.4226973
 </td>
 <td style="text-align:right;">
 39
@@ -3011,25 +2225,25 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 1
 </td>
 <td style="text-align:right;">
-1
+8
 </td>
 <td style="text-align:right;">
 1002
 </td>
 <td style="text-align:right;">
-479
+355
 </td>
 <td style="text-align:right;">
 32
 </td>
 <td style="text-align:right;">
-47
+46
 </td>
 <td style="text-align:right;">
-38.9206681
+38.7746479
 </td>
 <td style="text-align:right;">
-3.2884308
+3.2746121
 </td>
 <td style="text-align:right;">
 39
@@ -3044,7 +2258,7 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 41
 </td>
 <td style="text-align:right;">
-44
+43
 </td>
 </tr>
 <tr>
@@ -3055,25 +2269,25 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 1
 </td>
 <td style="text-align:right;">
-4
+11
 </td>
 <td style="text-align:right;">
 1002
 </td>
 <td style="text-align:right;">
-479
+355
 </td>
 <td style="text-align:right;">
 32
 </td>
 <td style="text-align:right;">
-47
+46
 </td>
 <td style="text-align:right;">
-38.9206681
+38.7746479
 </td>
 <td style="text-align:right;">
-3.2884308
+3.2746121
 </td>
 <td style="text-align:right;">
 39
@@ -3088,7 +2302,7 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 41
 </td>
 <td style="text-align:right;">
-44
+43
 </td>
 </tr>
 <tr>
@@ -3099,25 +2313,25 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 1
 </td>
 <td style="text-align:right;">
-23
+2
 </td>
 <td style="text-align:right;">
 1002
 </td>
 <td style="text-align:right;">
-479
+355
 </td>
 <td style="text-align:right;">
 32
 </td>
 <td style="text-align:right;">
-47
+46
 </td>
 <td style="text-align:right;">
-38.9206681
+38.9014085
 </td>
 <td style="text-align:right;">
-3.2884308
+3.2449654
 </td>
 <td style="text-align:right;">
 39
@@ -3132,7 +2346,7 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 41
 </td>
 <td style="text-align:right;">
-44
+43
 </td>
 </tr>
 <tr>
@@ -3143,25 +2357,25 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 1
 </td>
 <td style="text-align:right;">
-26
+18
 </td>
 <td style="text-align:right;">
 1002
 </td>
 <td style="text-align:right;">
-479
+355
 </td>
 <td style="text-align:right;">
 32
 </td>
 <td style="text-align:right;">
-47
+46
 </td>
 <td style="text-align:right;">
-38.9206681
+38.9014085
 </td>
 <td style="text-align:right;">
-3.2884308
+3.2449654
 </td>
 <td style="text-align:right;">
 39
@@ -3176,7 +2390,7 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 41
 </td>
 <td style="text-align:right;">
-44
+43
 </td>
 </tr>
 <tr>
@@ -3187,28 +2401,28 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 1
 </td>
 <td style="text-align:right;">
-12
+10
 </td>
 <td style="text-align:right;">
 1002
 </td>
 <td style="text-align:right;">
-706
+479
 </td>
 <td style="text-align:right;">
-31
+32
 </td>
 <td style="text-align:right;">
 46
 </td>
 <td style="text-align:right;">
-38.5226629
+38.7995825
 </td>
 <td style="text-align:right;">
-3.2712236
+3.3042257
 </td>
 <td style="text-align:right;">
-38
+39
 </td>
 <td style="text-align:right;">
 34
@@ -3220,7 +2434,7 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 41
 </td>
 <td style="text-align:right;">
-43
+44
 </td>
 </tr>
 <tr>
@@ -3231,28 +2445,28 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 1
 </td>
 <td style="text-align:right;">
-18
+13
 </td>
 <td style="text-align:right;">
 1002
 </td>
 <td style="text-align:right;">
-706
+479
 </td>
 <td style="text-align:right;">
-31
+32
 </td>
 <td style="text-align:right;">
 46
 </td>
 <td style="text-align:right;">
-38.5226629
+38.7995825
 </td>
 <td style="text-align:right;">
-3.2712236
+3.3042257
 </td>
 <td style="text-align:right;">
-38
+39
 </td>
 <td style="text-align:right;">
 34
@@ -3264,7 +2478,7 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 41
 </td>
 <td style="text-align:right;">
-43
+44
 </td>
 </tr>
 <tr>
@@ -3275,31 +2489,31 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 1
 </td>
 <td style="text-align:right;">
-6
+1
 </td>
 <td style="text-align:right;">
 1002
 </td>
 <td style="text-align:right;">
-830
+479
 </td>
 <td style="text-align:right;">
-31
+32
 </td>
 <td style="text-align:right;">
-46
+47
 </td>
 <td style="text-align:right;">
-38.5746988
+38.9206681
 </td>
 <td style="text-align:right;">
-3.2910429
+3.2884308
 </td>
 <td style="text-align:right;">
 39
 </td>
 <td style="text-align:right;">
-34
+35
 </td>
 <td style="text-align:right;">
 36
@@ -3308,7 +2522,7 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 41
 </td>
 <td style="text-align:right;">
-43
+44
 </td>
 </tr>
 <tr>
@@ -3319,31 +2533,31 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 1
 </td>
 <td style="text-align:right;">
-21
+4
 </td>
 <td style="text-align:right;">
 1002
 </td>
 <td style="text-align:right;">
-850
+479
 </td>
 <td style="text-align:right;">
-31
+32
 </td>
 <td style="text-align:right;">
-46
+47
 </td>
 <td style="text-align:right;">
-38.5658824
+38.9206681
 </td>
 <td style="text-align:right;">
-3.2816028
+3.2884308
 </td>
 <td style="text-align:right;">
 39
 </td>
 <td style="text-align:right;">
-34
+35
 </td>
 <td style="text-align:right;">
 36
@@ -3352,7 +2566,7 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 41
 </td>
 <td style="text-align:right;">
-43
+44
 </td>
 </tr>
 <tr>
@@ -3363,31 +2577,31 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 1
 </td>
 <td style="text-align:right;">
-11
+17
 </td>
 <td style="text-align:right;">
 1002
 </td>
 <td style="text-align:right;">
-1445
+479
 </td>
 <td style="text-align:right;">
-31
+32
 </td>
 <td style="text-align:right;">
 47
 </td>
 <td style="text-align:right;">
-38.6131488
+38.9206681
 </td>
 <td style="text-align:right;">
-3.3329496
+3.2884308
 </td>
 <td style="text-align:right;">
 39
 </td>
 <td style="text-align:right;">
-34
+35
 </td>
 <td style="text-align:right;">
 36
@@ -3396,7 +2610,7 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 41
 </td>
 <td style="text-align:right;">
-43
+44
 </td>
 </tr>
 <tr>
@@ -3407,31 +2621,31 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 1
 </td>
 <td style="text-align:right;">
-17
+20
 </td>
 <td style="text-align:right;">
 1002
 </td>
 <td style="text-align:right;">
-1445
+479
 </td>
 <td style="text-align:right;">
-31
+32
 </td>
 <td style="text-align:right;">
 47
 </td>
 <td style="text-align:right;">
-38.6131488
+38.9206681
 </td>
 <td style="text-align:right;">
-3.3329496
+3.2884308
 </td>
 <td style="text-align:right;">
 39
 </td>
 <td style="text-align:right;">
-34
+35
 </td>
 <td style="text-align:right;">
 36
@@ -3440,7 +2654,7 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 41
 </td>
 <td style="text-align:right;">
-43
+44
 </td>
 </tr>
 <tr>
@@ -3451,25 +2665,25 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 1
 </td>
 <td style="text-align:right;">
-5
+6
 </td>
 <td style="text-align:right;">
 1002
 </td>
 <td style="text-align:right;">
-1800
+830
 </td>
 <td style="text-align:right;">
 31
 </td>
 <td style="text-align:right;">
-47
+46
 </td>
 <td style="text-align:right;">
-38.6450000
+38.5746988
 </td>
 <td style="text-align:right;">
-3.3212435
+3.2910429
 </td>
 <td style="text-align:right;">
 39
@@ -3495,25 +2709,25 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 1
 </td>
 <td style="text-align:right;">
-20
+15
 </td>
 <td style="text-align:right;">
 1002
 </td>
 <td style="text-align:right;">
-1844
+850
 </td>
 <td style="text-align:right;">
 31
 </td>
 <td style="text-align:right;">
-47
+46
 </td>
 <td style="text-align:right;">
-38.6469631
+38.5658824
 </td>
 <td style="text-align:right;">
-3.3192555
+3.2816028
 </td>
 <td style="text-align:right;">
 39
@@ -3539,13 +2753,13 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 1
 </td>
 <td style="text-align:right;">
-13
+5
 </td>
 <td style="text-align:right;">
 1002
 </td>
 <td style="text-align:right;">
-2151
+1800
 </td>
 <td style="text-align:right;">
 31
@@ -3554,10 +2768,10 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 47
 </td>
 <td style="text-align:right;">
-38.5834496
+38.6450000
 </td>
 <td style="text-align:right;">
-3.3123287
+3.3212435
 </td>
 <td style="text-align:right;">
 39
@@ -3583,13 +2797,13 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 1
 </td>
 <td style="text-align:right;">
-19
+14
 </td>
 <td style="text-align:right;">
 1002
 </td>
 <td style="text-align:right;">
-2151
+1844
 </td>
 <td style="text-align:right;">
 31
@@ -3598,10 +2812,10 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 47
 </td>
 <td style="text-align:right;">
-38.5834496
+38.6469631
 </td>
 <td style="text-align:right;">
-3.3123287
+3.3192555
 </td>
 <td style="text-align:right;">
 39
@@ -3671,7 +2885,7 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 1
 </td>
 <td style="text-align:right;">
-22
+16
 </td>
 <td style="text-align:right;">
 1002
@@ -3712,10 +2926,10 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 <ul>
 <li>covariateRef:</li>
 </ul>
-<div class="sourceCode" id="cb26"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="va">agc</span><span class="op">$</span><span class="va">covariateRef</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> </span>
+<div class="sourceCode" id="cb25"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="va">agc</span><span class="op">$</span><span class="va">covariateRef</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
 <span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/compute.html" class="external-link">collect</a></span><span class="op">(</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
-<span>  <span class="fu">kableExtra</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/kableExtra/man/kbl.html" class="external-link">kbl</a></span><span class="op">(</span><span class="op">)</span> </span></code></pre></div>
+<span>  <span class="fu">kableExtra</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/kableExtra/man/kbl.html" class="external-link">kbl</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
 <table class="table">
 <thead><tr>
 <th style="text-align:left;">
@@ -3823,10 +3037,10 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 <ul>
 <li>analysisRef:</li>
 </ul>
-<div class="sourceCode" id="cb27"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="va">agc</span><span class="op">$</span><span class="va">analysisRef</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> </span>
+<div class="sourceCode" id="cb26"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="va">agc</span><span class="op">$</span><span class="va">analysisRef</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
 <span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/compute.html" class="external-link">collect</a></span><span class="op">(</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
-<span>  <span class="fu">kableExtra</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/kableExtra/man/kbl.html" class="external-link">kbl</a></span><span class="op">(</span><span class="op">)</span> </span></code></pre></div>
+<span>  <span class="fu">kableExtra</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/kableExtra/man/kbl.html" class="external-link">kbl</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
 <table class="table">
 <thead><tr>
 <th style="text-align:left;">
@@ -3965,60 +3179,46 @@ <h3 id="dechallenge-rechallenge">Dechallenge Rechallenge<a class="anchor" aria-l
 <p>Using the Eunomia data were we previous generated four cohorts, we
 can use cohort ids 1,2 and 4 as the targetIds and cohort id 3 as the
 outcomeIds:</p>
-<div class="sourceCode" id="cb28"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span>  <span class="va">exampleTargetIds</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>,<span class="fl">2</span>,<span class="fl">4</span><span class="op">)</span></span>
-<span>  <span class="va">exampleOutcomeIds</span> <span class="op">&lt;-</span> <span class="fl">3</span></span></code></pre></div>
+<div class="sourceCode" id="cb27"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="va">exampleTargetIds</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>, <span class="fl">2</span>, <span class="fl">4</span><span class="op">)</span></span>
+<span><span class="va">exampleOutcomeIds</span> <span class="op">&lt;-</span> <span class="fl">3</span></span></code></pre></div>
 <p>If we want to create the dechallenge rechallenge for all our target
 cohorts and our outcome cohort with a 30 day dechallengeStopInterval and
 31 day dechallengeEvaluationWindow:</p>
-<div class="sourceCode" id="cb29"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span>  <span class="va">exampleDechallengeRechallengeSettings</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/createDechallengeRechallengeSettings.html">createDechallengeRechallengeSettings</a></span><span class="op">(</span></span>
-<span>    targetIds <span class="op">=</span> <span class="va">exampleTargetIds</span>,</span>
-<span>    outcomeIds <span class="op">=</span> <span class="va">exampleOutcomeIds</span>,</span>
-<span>    dechallengeStopInterval <span class="op">=</span> <span class="fl">30</span>,</span>
-<span>    dechallengeEvaluationWindow <span class="op">=</span> <span class="fl">31</span></span>
-<span>    <span class="op">)</span></span></code></pre></div>
+<div class="sourceCode" id="cb28"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="va">exampleDechallengeRechallengeSettings</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/createDechallengeRechallengeSettings.html">createDechallengeRechallengeSettings</a></span><span class="op">(</span></span>
+<span>  targetIds <span class="op">=</span> <span class="va">exampleTargetIds</span>,</span>
+<span>  outcomeIds <span class="op">=</span> <span class="va">exampleOutcomeIds</span>,</span>
+<span>  dechallengeStopInterval <span class="op">=</span> <span class="fl">30</span>,</span>
+<span>  dechallengeEvaluationWindow <span class="op">=</span> <span class="fl">31</span></span>
+<span><span class="op">)</span></span></code></pre></div>
 <p>We can then run the analysis on the Eunomia data using
 <code>computeDechallengeRechallengeAnalyses</code> and the settings
 previously specified:</p>
-<div class="sourceCode" id="cb30"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb29"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">dc</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/computeDechallengeRechallengeAnalyses.html">computeDechallengeRechallengeAnalyses</a></span><span class="op">(</span></span>
-<span>    connectionDetails <span class="op">=</span> <span class="va">connectionDetails</span>,</span>
-<span>    targetDatabaseSchema <span class="op">=</span> <span class="st">'main'</span>,</span>
-<span>    targetTable <span class="op">=</span> <span class="st">'cohort'</span>,</span>
-<span>    dechallengeRechallengeSettings <span class="op">=</span> <span class="va">exampleDechallengeRechallengeSettings</span>,</span>
-<span>    databaseId <span class="op">=</span> <span class="st">'Eunomia'</span></span>
-<span>    <span class="op">)</span></span></code></pre></div>
+<span>  connectionDetails <span class="op">=</span> <span class="va">connectionDetails</span>,</span>
+<span>  targetDatabaseSchema <span class="op">=</span> <span class="st">"main"</span>,</span>
+<span>  targetTable <span class="op">=</span> <span class="st">"cohort"</span>,</span>
+<span>  dechallengeRechallengeSettings <span class="op">=</span> <span class="va">exampleDechallengeRechallengeSettings</span>,</span>
+<span>  databaseId <span class="op">=</span> <span class="st">"Eunomia"</span></span>
+<span><span class="op">)</span></span></code></pre></div>
 <pre><code><span><span class="co">## Inputs checked</span></span></code></pre>
 <pre><code><span><span class="co">## Connecting using SQLite driver</span></span>
 <span><span class="co">## Computing dechallenge rechallenge results</span></span></code></pre>
-<pre><code>## 
-  |                                                                            
-  |                                                                      |   0%
-  |                                                                            
-  |============                                                          |  17%
-  |                                                                            
-  |=======================                                               |  33%
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-  |===================================                                   |  50%
-  |                                                                            
-  |===============================================                       |  67%
-  |                                                                            
-  |==========================================================            |  83%
-  |                                                                            
-  |======================================================================| 100%</code></pre>
-<pre><code><span><span class="co">## Executing SQL took 0.00792 secs</span></span>
-<span><span class="co">## Computing dechallenge rechallenge for 3 target ids and 1outcome ids took 0.0625 secs</span></span></code></pre>
+<pre><code><span><span class="co">##   |                                                                              |                                                                      |   0%  |                                                                              |============                                                          |  17%  |                                                                              |=======================                                               |  33%  |                                                                              |===================================                                   |  50%  |                                                                              |===============================================                       |  67%  |                                                                              |==========================================================            |  83%  |                                                                              |======================================================================| 100%</span></span></code></pre>
+<pre><code><span><span class="co">## Executing SQL took 0.00758 secs</span></span>
+<span><span class="co">## Computing dechallenge rechallenge for 3 target ids and 1outcome ids took 0.165 secs</span></span></code></pre>
 <p>If you would like to save the results you can use the function
 <code>saveDechallengeRechallengeAnalyses</code> and this can then be
 loaded using <code>loadDechallengeRechallengeAnalyses</code>.</p>
 <p>The results are Andromeda objects that can we viewed using
 <code>dplyr</code>. There is just one table named
 dechallengeRechallenge:</p>
-<div class="sourceCode" id="cb35"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="va">dc</span><span class="op">$</span><span class="va">dechallengeRechallenge</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> </span>
+<div class="sourceCode" id="cb34"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="va">dc</span><span class="op">$</span><span class="va">dechallengeRechallenge</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
 <span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/compute.html" class="external-link">collect</a></span><span class="op">(</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
-<span>  <span class="fu">kableExtra</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/kableExtra/man/kbl.html" class="external-link">kbl</a></span><span class="op">(</span><span class="op">)</span> </span></code></pre></div>
+<span>  <span class="fu">kableExtra</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/kableExtra/man/kbl.html" class="external-link">kbl</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
 <table class="table">
 <thead><tr>
 <th style="text-align:right;">
@@ -4086,43 +3286,29 @@ <h3 id="dechallenge-rechallenge">Dechallenge Rechallenge<a class="anchor" aria-l
 </table>
 <p>Next it is possible to computer and extract the failed rechallenge
 cases</p>
-<div class="sourceCode" id="cb36"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb35"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">failed</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/computeRechallengeFailCaseSeriesAnalyses.html">computeRechallengeFailCaseSeriesAnalyses</a></span><span class="op">(</span></span>
 <span>  connectionDetails <span class="op">=</span> <span class="va">connectionDetails</span>,</span>
-<span>  targetDatabaseSchema <span class="op">=</span> <span class="st">'main'</span>,</span>
-<span>  targetTable <span class="op">=</span> <span class="st">'cohort'</span>,</span>
+<span>  targetDatabaseSchema <span class="op">=</span> <span class="st">"main"</span>,</span>
+<span>  targetTable <span class="op">=</span> <span class="st">"cohort"</span>,</span>
 <span>  dechallengeRechallengeSettings <span class="op">=</span> <span class="va">exampleDechallengeRechallengeSettings</span>,</span>
-<span>  outcomeDatabaseSchema <span class="op">=</span> <span class="st">'main'</span>,</span>
-<span>  outcomeTable <span class="op">=</span> <span class="st">'cohort'</span>,</span>
-<span>  databaseId <span class="op">=</span> <span class="st">'Eunomia'</span></span>
+<span>  outcomeDatabaseSchema <span class="op">=</span> <span class="st">"main"</span>,</span>
+<span>  outcomeTable <span class="op">=</span> <span class="st">"cohort"</span>,</span>
+<span>  databaseId <span class="op">=</span> <span class="st">"Eunomia"</span></span>
 <span><span class="op">)</span></span></code></pre></div>
 <pre><code><span><span class="co">## Inputs checked</span></span></code></pre>
 <pre><code><span><span class="co">## Connecting using SQLite driver</span></span>
 <span><span class="co">## Computing dechallenge rechallenge results</span></span></code></pre>
-<pre><code>## 
-  |                                                                            
-  |                                                                      |   0%
-  |                                                                            
-  |============                                                          |  17%
-  |                                                                            
-  |=======================                                               |  33%
-  |                                                                            
-  |===================================                                   |  50%
-  |                                                                            
-  |===============================================                       |  67%
-  |                                                                            
-  |==========================================================            |  83%
-  |                                                                            
-  |======================================================================| 100%</code></pre>
-<pre><code><span><span class="co">## Executing SQL took 0.0925 secs</span></span>
-<span><span class="co">## Computing dechallenge failed case series for 3 target IDs and 1 outcome IDs took 0.133 secs</span></span></code></pre>
+<pre><code><span><span class="co">##   |                                                                              |                                                                      |   0%  |                                                                              |============                                                          |  17%  |                                                                              |=======================                                               |  33%  |                                                                              |===================================                                   |  50%  |                                                                              |===============================================                       |  67%  |                                                                              |==========================================================            |  83%  |                                                                              |======================================================================| 100%</span></span></code></pre>
+<pre><code><span><span class="co">## Executing SQL took 0.0748 secs</span></span>
+<span><span class="co">## Computing dechallenge failed case series for 3 target IDs and 1 outcome IDs took 0.219 secs</span></span></code></pre>
 <p>The results are Andromeda objects that can we viewed using
 <code>dplyr</code>. There is just one table named
 rechallengeFailCaseSeries:</p>
-<div class="sourceCode" id="cb41"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="va">failed</span><span class="op">$</span><span class="va">rechallengeFailCaseSeries</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> </span>
+<div class="sourceCode" id="cb40"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="va">failed</span><span class="op">$</span><span class="va">rechallengeFailCaseSeries</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
 <span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/compute.html" class="external-link">collect</a></span><span class="op">(</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
-<span>  <span class="fu">kableExtra</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/kableExtra/man/kbl.html" class="external-link">kbl</a></span><span class="op">(</span><span class="op">)</span> </span></code></pre></div>
+<span>  <span class="fu">kableExtra</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/kableExtra/man/kbl.html" class="external-link">kbl</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
 <table class="table">
 <thead><tr>
 <th style="text-align:right;">
@@ -4192,75 +3378,41 @@ <h3 id="time-to-event">Time to Event<a class="anchor" aria-label="anchor" href="
 <li>one or more outcomeIds (these must be pre-generated in a cohort
 table)</li>
 </ul>
-<div class="sourceCode" id="cb42"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span>  <span class="va">exampleTimeToEventSettings</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/createTimeToEventSettings.html">createTimeToEventSettings</a></span><span class="op">(</span></span>
-<span>    targetIds <span class="op">=</span> <span class="va">exampleTargetIds</span>,</span>
-<span>    outcomeIds <span class="op">=</span> <span class="va">exampleOutcomeIds</span></span>
-<span>    <span class="op">)</span></span></code></pre></div>
+<div class="sourceCode" id="cb41"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="va">exampleTimeToEventSettings</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/createTimeToEventSettings.html">createTimeToEventSettings</a></span><span class="op">(</span></span>
+<span>  targetIds <span class="op">=</span> <span class="va">exampleTargetIds</span>,</span>
+<span>  outcomeIds <span class="op">=</span> <span class="va">exampleOutcomeIds</span></span>
+<span><span class="op">)</span></span></code></pre></div>
 <p>We can then run the analysis on the Eunomia data using
 <code>computeTimeToEventAnalyses</code> and the settings previously
 specified:</p>
-<div class="sourceCode" id="cb43"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb42"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">tte</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/computeTimeToEventAnalyses.html">computeTimeToEventAnalyses</a></span><span class="op">(</span></span>
-<span>    connectionDetails <span class="op">=</span> <span class="va">connectionDetails</span>,</span>
-<span>    cdmDatabaseSchema <span class="op">=</span> <span class="st">'main'</span>,</span>
-<span>    targetDatabaseSchema <span class="op">=</span> <span class="st">'main'</span>,</span>
-<span>    targetTable <span class="op">=</span> <span class="st">'cohort'</span>, </span>
-<span>    timeToEventSettings <span class="op">=</span>  <span class="va">exampleTimeToEventSettings</span>,</span>
-<span>    databaseId <span class="op">=</span> <span class="st">'Eunomia'</span></span>
-<span>    <span class="op">)</span></span></code></pre></div>
+<span>  connectionDetails <span class="op">=</span> <span class="va">connectionDetails</span>,</span>
+<span>  cdmDatabaseSchema <span class="op">=</span> <span class="st">"main"</span>,</span>
+<span>  targetDatabaseSchema <span class="op">=</span> <span class="st">"main"</span>,</span>
+<span>  targetTable <span class="op">=</span> <span class="st">"cohort"</span>,</span>
+<span>  timeToEventSettings <span class="op">=</span> <span class="va">exampleTimeToEventSettings</span>,</span>
+<span>  databaseId <span class="op">=</span> <span class="st">"Eunomia"</span></span>
+<span><span class="op">)</span></span></code></pre></div>
 <pre><code><span><span class="co">## Connecting using SQLite driver</span></span>
 <span><span class="co">## Uploading #cohort_settings</span></span>
 <span><span class="co">## </span></span>
-<span><span class="co">## Inserting data took 0.0043 secs</span></span>
+<span><span class="co">## Inserting data took 0.00654 secs</span></span>
 <span><span class="co">## Computing time to event results</span></span></code></pre>
-<pre><code>## 
-  |                                                                            
-  |                                                                      |   0%
-  |                                                                            
-  |====                                                                  |   6%
-  |                                                                            
-  |=========                                                             |  12%
-  |                                                                            
-  |=============                                                         |  19%
-  |                                                                            
-  |==================                                                    |  25%
-  |                                                                            
-  |======================                                                |  31%
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-  |==========================                                            |  38%
-  |                                                                            
-  |===============================                                       |  44%
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-  |===================================                                   |  50%
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-  |=======================================                               |  56%
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-  |                                                                            
-  |==================================================================    |  94%
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-  |======================================================================| 100%</code></pre>
-<pre><code><span><span class="co">## Executing SQL took 0.0418 secs</span></span>
-<span><span class="co">## Computing time-to-event for T-O pairs took 0.145 secs</span></span></code></pre>
+<pre><code><span><span class="co">##   |                                                                              |                                                                      |   0%  |                                                                              |===                                                                   |   4%  |                                                                              |======                                                                |   8%  |                                                                              |=========                                                             |  12%  |                                                                              |============                                                          |  17%  |                                                                              |===============                                                       |  21%  |                                                                              |==================                                                    |  25%  |                                                                              |====================                                                  |  29%  |                                                                              |=======================                                               |  33%  |                                                                              |==========================                                            |  38%  |                                                                              |=============================                                         |  42%  |                                                                              |================================                                      |  46%  |                                                                              |===================================                                   |  50%  |                                                                              |======================================                                |  54%  |                                                                              |=========================================                             |  58%  |                                                                              |============================================                          |  62%  |                                                                              |===============================================                       |  67%  |                                                                              |==================================================                    |  71%  |                                                                              |====================================================                  |  75%  |                                                                              |=======================================================               |  79%  |                                                                              |==========================================================            |  83%  |                                                                              |=============================================================         |  88%  |                                                                              |================================================================      |  92%  |                                                                              |===================================================================   |  96%  |                                                                              |======================================================================| 100%</span></span></code></pre>
+<pre><code><span><span class="co">## Executing SQL took 0.0462 secs</span></span>
+<span><span class="co">## Computing time-to-event for T-O pairs took 0.268 secs</span></span></code></pre>
 <p>If you would like to save the results you can use the function
 <code>saveTimeToEventAnalyses</code> and this can then be loaded using
 <code>loadTimeToEventAnalyses</code>.</p>
 <p>The results are Andromeda objects that can we viewed using
 <code>dplyr</code>. There is just one table named timeToEvent:</p>
-<div class="sourceCode" id="cb47"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="va">tte</span><span class="op">$</span><span class="va">timeToEvent</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> </span>
+<div class="sourceCode" id="cb46"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="va">tte</span><span class="op">$</span><span class="va">timeToEvent</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
 <span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/compute.html" class="external-link">collect</a></span><span class="op">(</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
 <span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/top_n.html" class="external-link">top_n</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
-<span>  <span class="fu">kableExtra</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/kableExtra/man/kbl.html" class="external-link">kbl</a></span><span class="op">(</span><span class="op">)</span> </span></code></pre></div>
+<span>  <span class="fu">kableExtra</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/kableExtra/man/kbl.html" class="external-link">kbl</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
 <pre><code><span><span class="co">## Selecting by timeScale</span></span></code></pre>
 <table class="table">
 <thead><tr>
@@ -4613,56 +3765,56 @@ <h3 id="run-multiple">Run Multiple<a class="anchor" aria-label="anchor" href="#r
 input a list of each of the settings (or NULL if you do not want to run
 one type of analysis). To run all the analyses previously shown in one
 function:</p>
-<div class="sourceCode" id="cb49"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span>  <span class="va">characterizationSettings</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/createCharacterizationSettings.html">createCharacterizationSettings</a></span><span class="op">(</span></span>
-<span>    timeToEventSettings <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span></span>
-<span>      <span class="va">exampleTimeToEventSettings</span></span>
-<span>      <span class="op">)</span>,</span>
-<span>    dechallengeRechallengeSettings <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span></span>
-<span>      <span class="va">exampleDechallengeRechallengeSettings</span></span>
-<span>    <span class="op">)</span>,</span>
-<span>    aggregateCovariateSettings <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span></span>
-<span>      <span class="va">exampleAggregateCovariateSettings</span></span>
-<span>      <span class="op">)</span></span>
+<div class="sourceCode" id="cb48"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="va">characterizationSettings</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/createCharacterizationSettings.html">createCharacterizationSettings</a></span><span class="op">(</span></span>
+<span>  timeToEventSettings <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span></span>
+<span>    <span class="va">exampleTimeToEventSettings</span></span>
+<span>  <span class="op">)</span>,</span>
+<span>  dechallengeRechallengeSettings <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span></span>
+<span>    <span class="va">exampleDechallengeRechallengeSettings</span></span>
+<span>  <span class="op">)</span>,</span>
+<span>  aggregateCovariateSettings <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span></span>
+<span>    <span class="va">exampleAggregateCovariateSettings</span></span>
 <span>  <span class="op">)</span></span>
+<span><span class="op">)</span></span>
 <span></span>
 <span><span class="co"># save the settings using</span></span>
 <span><span class="fu"><a href="../reference/saveCharacterizationSettings.html">saveCharacterizationSettings</a></span><span class="op">(</span></span>
-<span>  settings <span class="op">=</span> <span class="va">characterizationSettings</span>, </span>
-<span>  saveDirectory <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/file.path.html" class="external-link">file.path</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/tempfile.html" class="external-link">tempdir</a></span><span class="op">(</span><span class="op">)</span>, <span class="st">'saveSettings'</span><span class="op">)</span></span>
-<span>    <span class="op">)</span></span>
+<span>  settings <span class="op">=</span> <span class="va">characterizationSettings</span>,</span>
+<span>  saveDirectory <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/file.path.html" class="external-link">file.path</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/tempfile.html" class="external-link">tempdir</a></span><span class="op">(</span><span class="op">)</span>, <span class="st">"saveSettings"</span><span class="op">)</span></span>
+<span><span class="op">)</span></span>
 <span></span>
 <span><span class="co"># the settings can be loaded</span></span>
 <span><span class="va">characterizationSettings</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/loadCharacterizationSettings.html">loadCharacterizationSettings</a></span><span class="op">(</span></span>
-<span>  saveDirectory <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/file.path.html" class="external-link">file.path</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/tempfile.html" class="external-link">tempdir</a></span><span class="op">(</span><span class="op">)</span>, <span class="st">'saveSettings'</span><span class="op">)</span></span>
-<span>    <span class="op">)</span></span>
+<span>  saveDirectory <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/file.path.html" class="external-link">file.path</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/tempfile.html" class="external-link">tempdir</a></span><span class="op">(</span><span class="op">)</span>, <span class="st">"saveSettings"</span><span class="op">)</span></span>
+<span><span class="op">)</span></span>
 <span></span>
 <span><span class="fu"><a href="../reference/runCharacterizationAnalyses.html">runCharacterizationAnalyses</a></span><span class="op">(</span></span>
 <span>  connectionDetails <span class="op">=</span> <span class="va">connectionDetails</span>,</span>
-<span>  cdmDatabaseSchema <span class="op">=</span> <span class="st">'main'</span>,</span>
-<span>  targetDatabaseSchema <span class="op">=</span> <span class="st">'main'</span>,</span>
-<span>  targetTable <span class="op">=</span> <span class="st">'cohort'</span>,</span>
-<span>  outcomeDatabaseSchema <span class="op">=</span> <span class="st">'main'</span>,</span>
-<span>  outcomeTable <span class="op">=</span> <span class="st">'cohort'</span>,</span>
+<span>  cdmDatabaseSchema <span class="op">=</span> <span class="st">"main"</span>,</span>
+<span>  targetDatabaseSchema <span class="op">=</span> <span class="st">"main"</span>,</span>
+<span>  targetTable <span class="op">=</span> <span class="st">"cohort"</span>,</span>
+<span>  outcomeDatabaseSchema <span class="op">=</span> <span class="st">"main"</span>,</span>
+<span>  outcomeTable <span class="op">=</span> <span class="st">"cohort"</span>,</span>
 <span>  characterizationSettings <span class="op">=</span> <span class="va">characterizationSettings</span>,</span>
-<span>  saveDirectory <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/file.path.html" class="external-link">file.path</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/tempfile.html" class="external-link">tempdir</a></span><span class="op">(</span><span class="op">)</span>, <span class="st">'example'</span><span class="op">)</span>,</span>
-<span>  tablePrefix <span class="op">=</span> <span class="st">'c_'</span>,</span>
-<span>  databaseId <span class="op">=</span> <span class="st">'1'</span></span>
+<span>  saveDirectory <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/file.path.html" class="external-link">file.path</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/tempfile.html" class="external-link">tempdir</a></span><span class="op">(</span><span class="op">)</span>, <span class="st">"example"</span><span class="op">)</span>,</span>
+<span>  tablePrefix <span class="op">=</span> <span class="st">"c_"</span>,</span>
+<span>  databaseId <span class="op">=</span> <span class="st">"1"</span></span>
 <span><span class="op">)</span></span></code></pre></div>
 <p>This will create an SQLITE database with all the analyses saved into
 the saveDirectory. You can export the results as csv files using:</p>
-<div class="sourceCode" id="cb50"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb49"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">connectionDetailsT</span> <span class="op">&lt;-</span> <span class="fu">DatabaseConnector</span><span class="fu">::</span><span class="fu"><a href="https://ohdsi.github.io/DatabaseConnector/reference/createConnectionDetails.html" class="external-link">createConnectionDetails</a></span><span class="op">(</span></span>
-<span>  dbms <span class="op">=</span> <span class="st">'sqlite'</span>,</span>
-<span>  server <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/file.path.html" class="external-link">file.path</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/tempfile.html" class="external-link">tempdir</a></span><span class="op">(</span><span class="op">)</span>,<span class="st">'example'</span>,<span class="st">'sqliteCharacterization'</span>, <span class="st">'sqlite.sqlite'</span><span class="op">)</span></span>
+<span>  dbms <span class="op">=</span> <span class="st">"sqlite"</span>,</span>
+<span>  server <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/file.path.html" class="external-link">file.path</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/tempfile.html" class="external-link">tempdir</a></span><span class="op">(</span><span class="op">)</span>, <span class="st">"example"</span>, <span class="st">"sqliteCharacterization"</span>, <span class="st">"sqlite.sqlite"</span><span class="op">)</span></span>
 <span><span class="op">)</span></span>
 <span></span>
 <span><span class="fu"><a href="../reference/exportDatabaseToCsv.html">exportDatabaseToCsv</a></span><span class="op">(</span></span>
 <span>  connectionDetails <span class="op">=</span> <span class="va">connectionDetailsT</span>,</span>
-<span>  resultSchema <span class="op">=</span> <span class="st">'main'</span>,</span>
-<span>  targetDialect <span class="op">=</span> <span class="st">'sqlite'</span>,</span>
-<span>  tablePrefix <span class="op">=</span> <span class="st">'c_'</span>,</span>
-<span>  saveDirectory <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/file.path.html" class="external-link">file.path</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/tempfile.html" class="external-link">tempdir</a></span><span class="op">(</span><span class="op">)</span>,<span class="st">'csv'</span><span class="op">)</span></span>
+<span>  resultSchema <span class="op">=</span> <span class="st">"main"</span>,</span>
+<span>  targetDialect <span class="op">=</span> <span class="st">"sqlite"</span>,</span>
+<span>  tablePrefix <span class="op">=</span> <span class="st">"c_"</span>,</span>
+<span>  saveDirectory <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/file.path.html" class="external-link">file.path</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/tempfile.html" class="external-link">tempdir</a></span><span class="op">(</span><span class="op">)</span>, <span class="st">"csv"</span><span class="op">)</span></span>
 <span><span class="op">)</span></span></code></pre></div>
 </div>
 </div>
diff --git a/docs/articles/index.html b/docs/articles/index.html
index e50dfae..4e375e9 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">Characterization</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.5</span>
       </span>
     </div>
 
diff --git a/docs/authors.html b/docs/authors.html
index 9dfa84f..930b70d 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">Characterization</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.5</span>
       </span>
     </div>
 
@@ -90,14 +90,14 @@ <h1 id="citation">Citation</h1>
     </div>
 
 
-    <p>Reps J, Ryan P (2023).
+    <p>Reps J, Ryan P (2024).
 <em>Characterization: Characterizations of Cohorts</em>.
 https://ohdsi.github.io/Characterization, https://github.com/OHDSI/Characterization. 
 </p>
     <pre>@Manual{,
   title = {Characterization: Characterizations of Cohorts},
   author = {Jenna Reps and Patrick Ryan},
-  year = {2023},
+  year = {2024},
   note = {https://ohdsi.github.io/Characterization, https://github.com/OHDSI/Characterization},
 }</pre>
 
diff --git a/docs/index.html b/docs/index.html
index 1f63a1c..13d8406 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -33,7 +33,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">Characterization</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.5</span>
       </span>
     </div>
 
diff --git a/docs/news/index.html b/docs/news/index.html
index 2dddd1d..b82f989 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">Characterization</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.5</span>
       </span>
     </div>
 
@@ -72,13 +72,29 @@ <h1 data-toc-skip>Changelog <small></small></h1>
       <small>Source: <a href="https://github.com/OHDSI/Characterization/blob/HEAD/NEWS.md" class="external-link"><code>NEWS.md</code></a></small>
     </div>
 
+    <div class="section level2">
+<h2 class="page-header" data-toc-text="0.1.5" id="characterization-015">Characterization 0.1.5<a class="anchor" aria-label="anchor" href="#characterization-015"></a></h2>
+<p>Changed export to csv approach to use batch export from SQLite (<a href="https://github.com/OHDSI/Characterization/issues/41" class="external-link">#41</a>)</p>
+</div>
+    <div class="section level2">
+<h2 class="page-header" data-toc-text="0.1.4" id="characterization-014">Characterization 0.1.4<a class="anchor" aria-label="anchor" href="#characterization-014"></a></h2>
+<p>Added extra error logging</p>
+</div>
+    <div class="section level2">
+<h2 class="page-header" data-toc-text="0.1.3" id="characterization-013">Characterization 0.1.3<a class="anchor" aria-label="anchor" href="#characterization-013"></a></h2>
+<p>Optimized aggregate features to remove T and not Os (as these can be calculated using T and T and Os) - requires latest shiny app though Optimized database extraction to csv</p>
+</div>
+    <div class="section level2">
+<h2 class="page-header" data-toc-text="0.1.2" id="characterization-012">Characterization 0.1.2<a class="anchor" aria-label="anchor" href="#characterization-012"></a></h2>
+<p>Fixing bug where first outcome was still all outcomes Updating shiny app to work with old and new ShinyAppBuilder</p>
+</div>
     <div class="section level2">
 <h2 class="page-header" data-toc-text="0.1.1" id="characterization-011">Characterization 0.1.1<a class="anchor" aria-label="anchor" href="#characterization-011"></a></h2>
 <p>Fixing bug where cohort_counts were not being saved in the database</p>
 </div>
     <div class="section level2">
 <h2 class="page-header" data-toc-text="0.1.0" id="characterization-010">Characterization 0.1.0<a class="anchor" aria-label="anchor" href="#characterization-010"></a></h2>
-<ul><li>added support to enable target cohorts with multiple cohort entries for the aggregate covariate analysis by restructing to first cohort entry and ensuring the subject has a user specified minPriorObservation days observation in the database at first entry and also perform analysis on first outcomes and any outcome that is recorded during TAR.</li>
+<ul><li>added support to enable target cohorts with multiple cohort entries for the aggregate covariate analysis by restricting to first cohort entry and ensuring the subject has a user specified minPriorObservation days observation in the database at first entry and also perform analysis on first outcomes and any outcome that is recorded during TAR.</li>
 <li>added shiny app</li>
 </ul></div>
     <div class="section level2">
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 036bdeb..c233713 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -1,8 +1,8 @@
-pandoc: 2.19.2
+pandoc: 3.1.1
 pkgdown: 2.0.7
 pkgdown_sha: ~
 articles:
   InstallationGuide: InstallationGuide.html
   UsingCharacterizationPackage: UsingCharacterizationPackage.html
-last_built: 2023-03-16T00:54Z
+last_built: 2024-04-03T18:44Z
 
diff --git a/docs/pull_request_template.html b/docs/pull_request_template.html
index 9233960..3935c1f 100644
--- a/docs/pull_request_template.html
+++ b/docs/pull_request_template.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">Characterization</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.5</span>
       </span>
     </div>
 
diff --git a/docs/reference/Characterization-package.html b/docs/reference/Characterization-package.html
index 1d1611e..3666700 100644
--- a/docs/reference/Characterization-package.html
+++ b/docs/reference/Characterization-package.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">Characterization</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.5</span>
       </span>
     </div>
 
diff --git a/docs/reference/computeAggregateCovariateAnalyses.html b/docs/reference/computeAggregateCovariateAnalyses.html
index 085e4f9..dec7ad9 100644
--- a/docs/reference/computeAggregateCovariateAnalyses.html
+++ b/docs/reference/computeAggregateCovariateAnalyses.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">Characterization</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.5</span>
       </span>
     </div>
 
diff --git a/docs/reference/computeDechallengeRechallengeAnalyses.html b/docs/reference/computeDechallengeRechallengeAnalyses.html
index 311f42c..052b108 100644
--- a/docs/reference/computeDechallengeRechallengeAnalyses.html
+++ b/docs/reference/computeDechallengeRechallengeAnalyses.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">Characterization</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.5</span>
       </span>
     </div>
 
diff --git a/docs/reference/computeRechallengeFailCaseSeriesAnalyses.html b/docs/reference/computeRechallengeFailCaseSeriesAnalyses.html
index 35496ff..201027e 100644
--- a/docs/reference/computeRechallengeFailCaseSeriesAnalyses.html
+++ b/docs/reference/computeRechallengeFailCaseSeriesAnalyses.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">Characterization</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.5</span>
       </span>
     </div>
 
diff --git a/docs/reference/computeTimeToEventAnalyses.html b/docs/reference/computeTimeToEventAnalyses.html
index ff0d09d..f34a698 100644
--- a/docs/reference/computeTimeToEventAnalyses.html
+++ b/docs/reference/computeTimeToEventAnalyses.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">Characterization</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.5</span>
       </span>
     </div>
 
diff --git a/docs/reference/createAggregateCovariateSettings.html b/docs/reference/createAggregateCovariateSettings.html
index 3765fc4..dd26870 100644
--- a/docs/reference/createAggregateCovariateSettings.html
+++ b/docs/reference/createAggregateCovariateSettings.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">Characterization</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.5</span>
       </span>
     </div>
 
diff --git a/docs/reference/createCharacterizationSettings.html b/docs/reference/createCharacterizationSettings.html
index 755fbf0..f02ea35 100644
--- a/docs/reference/createCharacterizationSettings.html
+++ b/docs/reference/createCharacterizationSettings.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">Characterization</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.5</span>
       </span>
     </div>
 
diff --git a/docs/reference/createCharacterizationTables.html b/docs/reference/createCharacterizationTables.html
index e3bef67..409a2cc 100644
--- a/docs/reference/createCharacterizationTables.html
+++ b/docs/reference/createCharacterizationTables.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">Characterization</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.5</span>
       </span>
     </div>
 
diff --git a/docs/reference/createDechallengeRechallengeSettings.html b/docs/reference/createDechallengeRechallengeSettings.html
index ea36615..4361238 100644
--- a/docs/reference/createDechallengeRechallengeSettings.html
+++ b/docs/reference/createDechallengeRechallengeSettings.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">Characterization</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.5</span>
       </span>
     </div>
 
diff --git a/docs/reference/createSqliteDatabase.html b/docs/reference/createSqliteDatabase.html
index 70750dc..f553e0c 100644
--- a/docs/reference/createSqliteDatabase.html
+++ b/docs/reference/createSqliteDatabase.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">Characterization</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.5</span>
       </span>
     </div>
 
diff --git a/docs/reference/createTimeToEventSettings.html b/docs/reference/createTimeToEventSettings.html
index d1a87c1..c44d96d 100644
--- a/docs/reference/createTimeToEventSettings.html
+++ b/docs/reference/createTimeToEventSettings.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">Characterization</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.5</span>
       </span>
     </div>
 
diff --git a/docs/reference/exportAggregateCovariateToCsv.html b/docs/reference/exportAggregateCovariateToCsv.html
index 1e1d94e..7b834e1 100644
--- a/docs/reference/exportAggregateCovariateToCsv.html
+++ b/docs/reference/exportAggregateCovariateToCsv.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">Characterization</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.5</span>
       </span>
     </div>
 
@@ -78,7 +78,7 @@ <h1>export the AggregateCovariate results as csv</h1>
     </div>
 
     <div id="ref-usage">
-    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">exportAggregateCovariateToCsv</span><span class="op">(</span><span class="va">result</span>, <span class="va">saveDirectory</span><span class="op">)</span></span></code></pre></div>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">exportAggregateCovariateToCsv</span><span class="op">(</span><span class="va">result</span>, <span class="va">saveDirectory</span>, minCellCount <span class="op">=</span> <span class="fl">0</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div id="arguments">
@@ -90,6 +90,10 @@ <h2>Arguments</h2>
 <dt>saveDirectory</dt>
 <dd><p>An directory location to save the results into</p></dd>
 
+
+<dt>minCellCount</dt>
+<dd><p>The minimum value that will be displayed in count columns</p></dd>
+
 </dl></div>
     <div id="value">
     <h2>Value</h2>
diff --git a/docs/reference/exportDatabaseToCsv.html b/docs/reference/exportDatabaseToCsv.html
index e1b473d..421d14a 100644
--- a/docs/reference/exportDatabaseToCsv.html
+++ b/docs/reference/exportDatabaseToCsv.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">Characterization</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.5</span>
       </span>
     </div>
 
@@ -81,11 +81,12 @@ <h1>Exports all tables in the result database to csv files</h1>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">exportDatabaseToCsv</span><span class="op">(</span></span>
 <span>  <span class="va">connectionDetails</span>,</span>
 <span>  <span class="va">resultSchema</span>,</span>
-<span>  <span class="va">targetDialect</span>,</span>
+<span>  targetDialect <span class="op">=</span> <span class="cn">NULL</span>,</span>
 <span>  tablePrefix <span class="op">=</span> <span class="st">"c_"</span>,</span>
 <span>  filePrefix <span class="op">=</span> <span class="cn">NULL</span>,</span>
-<span>  tempEmulationSchema <span class="op">=</span> <span class="cn">NULL</span>,</span>
-<span>  <span class="va">saveDirectory</span></span>
+<span>  tempEmulationSchema <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"sqlRenderTempEmulationSchema"</span><span class="op">)</span>,</span>
+<span>  <span class="va">saveDirectory</span>,</span>
+<span>  minMeanCovariateValue <span class="op">=</span> <span class="fl">0.001</span></span>
 <span><span class="op">)</span></span></code></pre></div>
     </div>
 
@@ -102,7 +103,7 @@ <h2>Arguments</h2>
 
 
 <dt>targetDialect</dt>
-<dd><p>The database management system being used</p></dd>
+<dd><p>DEPRECATED: derived from <code>connectionDetails</code>.</p></dd>
 
 
 <dt>tablePrefix</dt>
@@ -120,6 +121,12 @@ <h2>Arguments</h2>
 <dt>saveDirectory</dt>
 <dd><p>The directory to save the csv results</p></dd>
 
+
+<dt>minMeanCovariateValue</dt>
+<dd><p>The minimum mean covariate value (i.e. the minimum proportion for
+binary covariates) for a covariate to be included in covariate table.
+Other covariates are removed to save space.</p></dd>
+
 </dl></div>
     <div id="value">
     <h2>Value</h2>
diff --git a/docs/reference/exportDechallengeRechallengeToCsv.html b/docs/reference/exportDechallengeRechallengeToCsv.html
index 7411746..98f69f4 100644
--- a/docs/reference/exportDechallengeRechallengeToCsv.html
+++ b/docs/reference/exportDechallengeRechallengeToCsv.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">Characterization</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.5</span>
       </span>
     </div>
 
@@ -78,7 +78,7 @@ <h1>export the DechallengeRechallenge results as csv</h1>
     </div>
 
     <div id="ref-usage">
-    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">exportDechallengeRechallengeToCsv</span><span class="op">(</span><span class="va">result</span>, <span class="va">saveDirectory</span><span class="op">)</span></span></code></pre></div>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">exportDechallengeRechallengeToCsv</span><span class="op">(</span><span class="va">result</span>, <span class="va">saveDirectory</span>, minCellCount <span class="op">=</span> <span class="fl">0</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div id="arguments">
@@ -90,6 +90,10 @@ <h2>Arguments</h2>
 <dt>saveDirectory</dt>
 <dd><p>An directory location to save the results into</p></dd>
 
+
+<dt>minCellCount</dt>
+<dd><p>The minimum value that will be displayed in count columns</p></dd>
+
 </dl></div>
     <div id="value">
     <h2>Value</h2>
diff --git a/docs/reference/exportRechallengeFailCaseSeriesToCsv.html b/docs/reference/exportRechallengeFailCaseSeriesToCsv.html
index ea6cd1c..1409775 100644
--- a/docs/reference/exportRechallengeFailCaseSeriesToCsv.html
+++ b/docs/reference/exportRechallengeFailCaseSeriesToCsv.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">Characterization</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.5</span>
       </span>
     </div>
 
diff --git a/docs/reference/exportTimeToEventToCsv.html b/docs/reference/exportTimeToEventToCsv.html
index fcd50ba..258e9e6 100644
--- a/docs/reference/exportTimeToEventToCsv.html
+++ b/docs/reference/exportTimeToEventToCsv.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">Characterization</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.5</span>
       </span>
     </div>
 
@@ -78,7 +78,7 @@ <h1>export the TimeToEvent results as csv</h1>
     </div>
 
     <div id="ref-usage">
-    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">exportTimeToEventToCsv</span><span class="op">(</span><span class="va">result</span>, <span class="va">saveDirectory</span><span class="op">)</span></span></code></pre></div>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">exportTimeToEventToCsv</span><span class="op">(</span><span class="va">result</span>, <span class="va">saveDirectory</span>, minCellCount <span class="op">=</span> <span class="fl">0</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div id="arguments">
@@ -90,6 +90,10 @@ <h2>Arguments</h2>
 <dt>saveDirectory</dt>
 <dd><p>An directory location to save the results into</p></dd>
 
+
+<dt>minCellCount</dt>
+<dd><p>The minimum value that will be displayed in count columns</p></dd>
+
 </dl></div>
     <div id="value">
     <h2>Value</h2>
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 9c974ba..86949d3 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">Characterization</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.5</span>
       </span>
     </div>
 
diff --git a/docs/reference/loadAggregateCovariateAnalyses.html b/docs/reference/loadAggregateCovariateAnalyses.html
index 2bd1d85..60a1e79 100644
--- a/docs/reference/loadAggregateCovariateAnalyses.html
+++ b/docs/reference/loadAggregateCovariateAnalyses.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">Characterization</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.5</span>
       </span>
     </div>
 
diff --git a/docs/reference/loadCharacterizationSettings.html b/docs/reference/loadCharacterizationSettings.html
index 272c8bb..c2a649b 100644
--- a/docs/reference/loadCharacterizationSettings.html
+++ b/docs/reference/loadCharacterizationSettings.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">Characterization</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.5</span>
       </span>
     </div>
 
diff --git a/docs/reference/loadDechallengeRechallengeAnalyses.html b/docs/reference/loadDechallengeRechallengeAnalyses.html
index 404959a..90b9001 100644
--- a/docs/reference/loadDechallengeRechallengeAnalyses.html
+++ b/docs/reference/loadDechallengeRechallengeAnalyses.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">Characterization</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.5</span>
       </span>
     </div>
 
diff --git a/docs/reference/loadRechallengeFailCaseSeriesAnalyses.html b/docs/reference/loadRechallengeFailCaseSeriesAnalyses.html
index cab7d7a..6eb84c6 100644
--- a/docs/reference/loadRechallengeFailCaseSeriesAnalyses.html
+++ b/docs/reference/loadRechallengeFailCaseSeriesAnalyses.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">Characterization</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.5</span>
       </span>
     </div>
 
diff --git a/docs/reference/loadTimeToEventAnalyses.html b/docs/reference/loadTimeToEventAnalyses.html
index f6fbc2f..9524be7 100644
--- a/docs/reference/loadTimeToEventAnalyses.html
+++ b/docs/reference/loadTimeToEventAnalyses.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">Characterization</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.5</span>
       </span>
     </div>
 
diff --git a/docs/reference/runCharacterizationAnalyses.html b/docs/reference/runCharacterizationAnalyses.html
index b5a253c..f2afb6e 100644
--- a/docs/reference/runCharacterizationAnalyses.html
+++ b/docs/reference/runCharacterizationAnalyses.html
@@ -18,7 +18,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">Characterization</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.5</span>
       </span>
     </div>
 
@@ -92,7 +92,8 @@ <h1>execute a large-scale characterization study</h1>
 <span>  <span class="va">saveDirectory</span>,</span>
 <span>  tablePrefix <span class="op">=</span> <span class="st">"c_"</span>,</span>
 <span>  databaseId <span class="op">=</span> <span class="st">"1"</span>,</span>
-<span>  showSubjectId <span class="op">=</span> <span class="cn">F</span></span>
+<span>  showSubjectId <span class="op">=</span> <span class="cn">F</span>,</span>
+<span>  minCellCount <span class="op">=</span> <span class="fl">0</span></span>
 <span><span class="op">)</span></span></code></pre></div>
     </div>
 
@@ -145,12 +146,16 @@ <h2>Arguments</h2>
 
 
 <dt>databaseId</dt>
-<dd><p>The unqiue identifier for the cdm database</p></dd>
+<dd><p>The unique identifier for the cdm database</p></dd>
 
 
 <dt>showSubjectId</dt>
 <dd><p>Whether to include subjectId of failed rechallenge case series or hide</p></dd>
 
+
+<dt>minCellCount</dt>
+<dd><p>The minimum count value that is calculated</p></dd>
+
 </dl></div>
     <div id="value">
     <h2>Value</h2>
diff --git a/docs/reference/saveAggregateCovariateAnalyses.html b/docs/reference/saveAggregateCovariateAnalyses.html
index 55099f9..32da3b4 100644
--- a/docs/reference/saveAggregateCovariateAnalyses.html
+++ b/docs/reference/saveAggregateCovariateAnalyses.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">Characterization</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.5</span>
       </span>
     </div>
 
diff --git a/docs/reference/saveCharacterizationSettings.html b/docs/reference/saveCharacterizationSettings.html
index da41528..77f30d8 100644
--- a/docs/reference/saveCharacterizationSettings.html
+++ b/docs/reference/saveCharacterizationSettings.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">Characterization</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.5</span>
       </span>
     </div>
 
@@ -95,7 +95,7 @@ <h2>Arguments</h2>
     <h2>Value</h2>
     
 
-<p>Returns the location of the drectory containing the json settings</p>
+<p>Returns the location of the directory containing the json settings</p>
     </div>
     <div id="details">
     <h2>Details</h2>
diff --git a/docs/reference/saveDechallengeRechallengeAnalyses.html b/docs/reference/saveDechallengeRechallengeAnalyses.html
index db2a78a..b141793 100644
--- a/docs/reference/saveDechallengeRechallengeAnalyses.html
+++ b/docs/reference/saveDechallengeRechallengeAnalyses.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">Characterization</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.5</span>
       </span>
     </div>
 
diff --git a/docs/reference/saveRechallengeFailCaseSeriesAnalyses.html b/docs/reference/saveRechallengeFailCaseSeriesAnalyses.html
index 948b610..5c4a6c1 100644
--- a/docs/reference/saveRechallengeFailCaseSeriesAnalyses.html
+++ b/docs/reference/saveRechallengeFailCaseSeriesAnalyses.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">Characterization</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.5</span>
       </span>
     </div>
 
diff --git a/docs/reference/saveTimeToEventAnalyses.html b/docs/reference/saveTimeToEventAnalyses.html
index 9d1c0c8..58c8e4b 100644
--- a/docs/reference/saveTimeToEventAnalyses.html
+++ b/docs/reference/saveTimeToEventAnalyses.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">Characterization</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.5</span>
       </span>
     </div>
 
diff --git a/docs/reference/viewCharacterization.html b/docs/reference/viewCharacterization.html
index 65184e8..dafe528 100644
--- a/docs/reference/viewCharacterization.html
+++ b/docs/reference/viewCharacterization.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">Characterization</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.5</span>
       </span>
     </div>
 
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index a679701..140421f 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -4,13 +4,13 @@
     <loc>/404.html</loc>
   </url>
   <url>
-    <loc>/articles/InstallationGuide.html</loc>
+    <loc>/articles/index.html</loc>
   </url>
   <url>
-    <loc>/articles/UsingCharacterizationPackage.html</loc>
+    <loc>/articles/InstallationGuide.html</loc>
   </url>
   <url>
-    <loc>/articles/index.html</loc>
+    <loc>/articles/UsingCharacterizationPackage.html</loc>
   </url>
   <url>
     <loc>/authors.html</loc>
diff --git a/extras/Characterization.pdf b/extras/Characterization.pdf
index 66746a4..9051939 100644
Binary files a/extras/Characterization.pdf and b/extras/Characterization.pdf differ
diff --git a/extras/PackageMaintenance.R b/extras/PackageMaintenance.R
index d5fe8b8..2118769 100644
--- a/extras/PackageMaintenance.R
+++ b/extras/PackageMaintenance.R
@@ -1,4 +1,4 @@
-# Copyright 2022 Observational Health Data Sciences and Informatics
+# Copyright 2024 Observational Health Data Sciences and Informatics
 #
 # This file is part of Characterization
 #
diff --git a/inst/doc/InstallationGuide.pdf b/inst/doc/InstallationGuide.pdf
new file mode 100644
index 0000000..1250cac
Binary files /dev/null and b/inst/doc/InstallationGuide.pdf differ
diff --git a/inst/doc/UsingCharacterizationPackage.pdf b/inst/doc/UsingCharacterizationPackage.pdf
new file mode 100644
index 0000000..553d7f0
Binary files /dev/null and b/inst/doc/UsingCharacterizationPackage.pdf differ
diff --git a/inst/settings/resultsDataModelSpecification.csv b/inst/settings/resultsDataModelSpecification.csv
index 29beb0a..4578e80 100644
--- a/inst/settings/resultsDataModelSpecification.csv
+++ b/inst/settings/resultsDataModelSpecification.csv
@@ -68,7 +68,7 @@ covariates,average_value,float,Y,N,N,N,The average value
 covariates_continuous,database_id,varchar(100),Y,Y,N,N,The database identifier
 covariates_continuous,run_id,int,Y,Y,N,N,The run identifier
 covariates_continuous,cohort_definition_id,bigint,Y,Y,N,N,The cohort definition id
-covariates_continuous,covariate_id,int,Y,Y,N,N,The covariate identifier
+covariates_continuous,covariate_id,bigint,Y,Y,N,N,The covariate identifier
 covariates_continuous,count_value,int,Y,N,N,N,The count value
 covariates_continuous,min_value,float,Y,N,N,N,The min value
 covariates_continuous,max_value,float,Y,N,N,N,The max value
diff --git a/man/exportDatabaseToCsv.Rd b/man/exportDatabaseToCsv.Rd
index e39f860..df9de08 100644
--- a/man/exportDatabaseToCsv.Rd
+++ b/man/exportDatabaseToCsv.Rd
@@ -10,7 +10,7 @@ exportDatabaseToCsv(
   targetDialect = NULL,
   tablePrefix = "c_",
   filePrefix = NULL,
-  tempEmulationSchema = NULL,
+  tempEmulationSchema = getOption("sqlRenderTempEmulationSchema"),
   saveDirectory,
   minMeanCovariateValue = 0.001
 )
diff --git a/man/runCharacterizationAnalyses.Rd b/man/runCharacterizationAnalyses.Rd
index 8ef7b71..501a38e 100644
--- a/man/runCharacterizationAnalyses.Rd
+++ b/man/runCharacterizationAnalyses.Rd
@@ -47,7 +47,7 @@ can be created}
 
 \item{tablePrefix}{A string to append the tables in the results}
 
-\item{databaseId}{The unqiue identifier for the cdm database}
+\item{databaseId}{The unique identifier for the cdm database}
 
 \item{showSubjectId}{Whether to include subjectId of failed rechallenge case series or hide}
 
diff --git a/man/saveCharacterizationSettings.Rd b/man/saveCharacterizationSettings.Rd
index 3c0e314..b08962a 100644
--- a/man/saveCharacterizationSettings.Rd
+++ b/man/saveCharacterizationSettings.Rd
@@ -12,7 +12,7 @@ saveCharacterizationSettings(settings, fileName)
 \item{fileName}{The location to save the json settings}
 }
 \value{
-Returns the location of the drectory containing the json settings
+Returns the location of the directory containing the json settings
 }
 \description{
 This function converts the settings into a json object and saves it
diff --git a/tests/testthat/test-Database.R b/tests/testthat/test-Database.R
index 20b3c6d..d223946 100644
--- a/tests/testthat/test-Database.R
+++ b/tests/testthat/test-Database.R
@@ -1,63 +1,62 @@
 context("Database")
 
 test_that("removeMinCell", {
-data <- data.frame(name = rep('dfd', 10), val = 1:10)
-newData <- removeMinCell(
-  data = data, minCellCount = 5, minCellCountColumns = list()
-)
-testthat::expect_equal(newData, data)
+  data <- data.frame(name = rep("dfd", 10), val = 1:10)
+  newData <- removeMinCell(
+    data = data, minCellCount = 5, minCellCountColumns = list()
+  )
+  testthat::expect_equal(newData, data)
 
-newData <- removeMinCell(
-  data = data, minCellCount = 5, minCellCountColumns = list('val')
-)
-testthat::expect_equal(newData$val[5:10], data$val[5:10])
-testthat::expect_equal(newData$val[1:4], rep(-1,4))
+  newData <- removeMinCell(
+    data = data, minCellCount = 5, minCellCountColumns = list("val")
+  )
+  testthat::expect_equal(newData$val[5:10], data$val[5:10])
+  testthat::expect_equal(newData$val[1:4], rep(-1, 4))
 
-newData <- removeMinCell(
-  data = data, minCellCount = 50, minCellCountColumns = list('val')
-)
-testthat::expect_equal(newData$val, rep(-1,10))
+  newData <- removeMinCell(
+    data = data, minCellCount = 50, minCellCountColumns = list("val")
+  )
+  testthat::expect_equal(newData$val, rep(-1, 10))
 
-data <- data.frame(
-  name = rep('dfd', 10),
-  val = 1:10,
-  val2 = c(1,10,1,10,1,10,1,10,1,10)
-)
-newData <- removeMinCell(
-  data = data, minCellCount = 5, minCellCountColumns = list('val')
-)
-testthat::expect_equal(newData$val[1:4], rep(-1,4))
-testthat::expect_equal(newData$val2, data$val2,)
+  data <- data.frame(
+    name = rep("dfd", 10),
+    val = 1:10,
+    val2 = c(1, 10, 1, 10, 1, 10, 1, 10, 1, 10)
+  )
+  newData <- removeMinCell(
+    data = data, minCellCount = 5, minCellCountColumns = list("val")
+  )
+  testthat::expect_equal(newData$val[1:4], rep(-1, 4))
+  testthat::expect_equal(newData$val2, data$val2, )
 
-newData <- removeMinCell(
-  data = data, minCellCount = 5, minCellCountColumns = list(c('val','val2'))
-)
-testthat::expect_equal(
-  sum(
-    (newData$val > 0 & newData$val < 5) | (newData$val2 > 0 & newData$val2 < 5)
-  ),
-  0
-)
-
-data <- data.frame(
-  name = rep('dfd', 10),
-  val = 1:10,
-  val2 = c(1,10,1,10,1,10,1,10,1,10),
-  val3 = c(10,10,10,10,10,1,1,10,10,10)
-)
-newData <- removeMinCell(
-  data = data,
-  minCellCount = 5,
-  minCellCountColumns =
-    list(c('val','val2'), 'val3')
-)
-testthat::expect_equal(
-  sum(
-    (newData$val > 0 & newData$val < 5) |
-      (newData$val2 > 0 & newData$val2 < 5) |
-      (newData$val3 > 0 & newData$val3 < 5)
-  ),
-  0
-)
+  newData <- removeMinCell(
+    data = data, minCellCount = 5, minCellCountColumns = list(c("val", "val2"))
+  )
+  testthat::expect_equal(
+    sum(
+      (newData$val > 0 & newData$val < 5) | (newData$val2 > 0 & newData$val2 < 5)
+    ),
+    0
+  )
 
+  data <- data.frame(
+    name = rep("dfd", 10),
+    val = 1:10,
+    val2 = c(1, 10, 1, 10, 1, 10, 1, 10, 1, 10),
+    val3 = c(10, 10, 10, 10, 10, 1, 1, 10, 10, 10)
+  )
+  newData <- removeMinCell(
+    data = data,
+    minCellCount = 5,
+    minCellCountColumns =
+      list(c("val", "val2"), "val3")
+  )
+  testthat::expect_equal(
+    sum(
+      (newData$val > 0 & newData$val < 5) |
+        (newData$val2 > 0 & newData$val2 < 5) |
+        (newData$val3 > 0 & newData$val3 < 5)
+    ),
+    0
+  )
 })
diff --git a/tests/testthat/test-aggregateCovariate.R b/tests/testthat/test-aggregateCovariate.R
index 9f1e9d0..ca261ea 100644
--- a/tests/testthat/test-aggregateCovariate.R
+++ b/tests/testthat/test-aggregateCovariate.R
@@ -97,7 +97,7 @@ test_that("computeAggregateCovariateAnalyses", {
 
   testthat::expect_true(inherits(agc, "CovariateData"))
   testthat::expect_true(length(unique(as.data.frame(agc$covariates)$cohortDefinitionId))
-  <= length(res$targetIds) * length(res$outcomeIds) * 4 + length(res$targetIds)*2 + length(res$outcomeIds)*2)
+  <= length(res$targetIds) * length(res$outcomeIds) * 4 + length(res$targetIds) * 2 + length(res$outcomeIds) * 2)
   testthat::expect_true(
     sum(names(agc) %in% c(
       "analysisRef",
@@ -111,7 +111,7 @@ test_that("computeAggregateCovariateAnalyses", {
 
   testthat::expect_true(
     nrow(as.data.frame(agc$cohortDetails)) ==
-    nrow(as.data.frame(agc$cohortCounts))
+      nrow(as.data.frame(agc$cohortCounts))
   )
 
   # check cohortDetails
diff --git a/tests/testthat/test-runCharacterization.R b/tests/testthat/test-runCharacterization.R
index 5f3dbc9..9c86693 100644
--- a/tests/testthat/test-runCharacterization.R
+++ b/tests/testthat/test-runCharacterization.R
@@ -172,5 +172,4 @@ test_that("runCharacterizationAnalyses", {
   testthat::expect_true(
     file.exists(file.path(tempFolder, "csv", "time_to_event.csv"))
   )
-
 })
diff --git a/tests/testthat/test-timeToEvent.R b/tests/testthat/test-timeToEvent.R
index b65d52c..20e1c76 100644
--- a/tests/testthat/test-timeToEvent.R
+++ b/tests/testthat/test-timeToEvent.R
@@ -99,7 +99,7 @@ test_that("computeTimeToEventSettings", {
 
   tte2 <- loadTimeToEventAnalyses(tempFile)
 
-  testthat::expect_equal(dplyr::collect(tte$timeToEvent ), dplyr::collect(tte2$timeToEvent))
+  testthat::expect_equal(dplyr::collect(tte$timeToEvent), dplyr::collect(tte2$timeToEvent))
 
   # test csv export
   tempFolder <- tempfile("exportToCsv")
@@ -110,7 +110,7 @@ test_that("computeTimeToEventSettings", {
     saveDirectory = tempFolder
   )
 
-  testthat::expect_true(file.exists(file.path(tempFolder,"time_to_event.csv")))
+  testthat::expect_true(file.exists(file.path(tempFolder, "time_to_event.csv")))
 
   # check it saved correctly and uses snake case
   res <- readr::read_csv(
diff --git a/tests/testthat/test-viewShiny.R b/tests/testthat/test-viewShiny.R
index 93599ad..60948d0 100644
--- a/tests/testthat/test-viewShiny.R
+++ b/tests/testthat/test-viewShiny.R
@@ -1,22 +1,21 @@
 context("ViewShiny")
 
 # create a folder with results for the shiny app
-resultLocation <- file.path(tempdir(), 'shinyResults')
-if(!dir.exists(resultLocation)){
+resultLocation <- file.path(tempdir(), "shinyResults")
+if (!dir.exists(resultLocation)) {
   dir.create(resultLocation, recursive = T)
 }
 
 test_that("is_installed", {
-  testthat::expect_equal(is_installed('FeatureExtraction'), T)
-  testthat::expect_equal(is_installed('MadeUp4u834t3f'), F)
+  testthat::expect_equal(is_installed("FeatureExtraction"), T)
+  testthat::expect_equal(is_installed("MadeUp4u834t3f"), F)
 })
 
 test_that("ensure_installed", {
-  testthat::expect_equal(ensure_installed('FeatureExtraction'), NULL)
+  testthat::expect_equal(ensure_installed("FeatureExtraction"), NULL)
 })
 
 test_that("prepareCharacterizationShiny works", {
-
   targetIds <- c(1, 2, 4)
   outcomeIds <- c(3)
 
@@ -89,41 +88,39 @@ test_that("prepareCharacterizationShiny works", {
     databaseId = "1"
   )
 
-settings <- prepareCharacterizationShiny(
+  settings <- prepareCharacterizationShiny(
     resultLocation = resultLocation,
     cohortDefinitionSet = NULL
-)
-
-testthat::expect_true(settings$schema == 'main')
-testthat::expect_true(settings$tablePrefix == 'c_')
-testthat::expect_true(settings$cohortTablePrefix == 'cg_')
-testthat::expect_true(settings$incidenceTablePrefix == 'i_')
-testthat::expect_true(settings$databaseTable == 'DATABASE_META_DATA')
-
-connectionDetailsTest <- do.call(
-  what = DatabaseConnector::createConnectionDetails,
-  args = list(
-    dbms = 'sqlite',
-    server = file.path(resultLocation, 'sqliteCharacterization', 'sqlite.sqlite')
   )
-)
-conTest <- DatabaseConnector::connect(connectionDetailsTest)
-tables <- tolower(
-  DatabaseConnector::getTableNames(
-    connection = conTest,
-    databaseSchema = 'main'
-    )
-)
 
-# make sure the extra tables are added
-testthat::expect_true('cg_cohort_definition' %in% tables)
-testthat::expect_true('database_meta_data' %in% tables)
-testthat::expect_true('i_incidence_summary' %in% tables)
+  testthat::expect_true(settings$schema == "main")
+  testthat::expect_true(settings$tablePrefix == "c_")
+  testthat::expect_true(settings$cohortTablePrefix == "cg_")
+  testthat::expect_true(settings$incidenceTablePrefix == "i_")
+  testthat::expect_true(settings$databaseTable == "DATABASE_META_DATA")
+
+  connectionDetailsTest <- do.call(
+    what = DatabaseConnector::createConnectionDetails,
+    args = list(
+      dbms = "sqlite",
+      server = file.path(resultLocation, "sqliteCharacterization", "sqlite.sqlite")
+    )
+  )
+  conTest <- DatabaseConnector::connect(connectionDetailsTest)
+  tables <- tolower(
+    DatabaseConnector::getTableNames(
+      connection = conTest,
+      databaseSchema = "main"
+    )
+  )
 
+  # make sure the extra tables are added
+  testthat::expect_true("cg_cohort_definition" %in% tables)
+  testthat::expect_true("database_meta_data" %in% tables)
+  testthat::expect_true("i_incidence_summary" %in% tables)
 })
 
 test_that("shiny app works", {
-
   settings <- prepareCharacterizationShiny(
     resultLocation = resultLocation,
     cohortDefinitionSet = NULL
@@ -134,16 +131,13 @@ test_that("shiny app works", {
     testApp = T
   )
 
-shiny::testServer(
-  app = app,
-  args = list(
-  ),
-  expr = {
-
-    testthat::expect_equal(runServer[['About']],0)
-    session$setInputs(menu = 'About')
-    testthat::expect_equal(runServer[['About']],1)
-
-  })
-
+  shiny::testServer(
+    app = app,
+    args = list(),
+    expr = {
+      testthat::expect_equal(runServer[["About"]], 0)
+      session$setInputs(menu = "About")
+      testthat::expect_equal(runServer[["About"]], 1)
+    }
+  )
 })
diff --git a/vignettes/InstallationGuide.Rmd b/vignettes/InstallationGuide.Rmd
index 9552cfe..dd1bd41 100644
--- a/vignettes/InstallationGuide.Rmd
+++ b/vignettes/InstallationGuide.Rmd
@@ -29,7 +29,7 @@ output:
 -->
 
 # Introduction
-This vignette describes how you need to install the Observational Health Data Sciencs and Informatics (OHDSI) [`Characterization`](http://github.com/OHDSI/Characterization) package under Windows, Mac, and Linux.
+This vignette describes how you need to install the Observational Health Data Sciences and Informatics (OHDSI) [`Characterization`](http://github.com/OHDSI/Characterization) package under Windows, Mac, and Linux.
 
 # Software Prerequisites
 
@@ -53,7 +53,7 @@ Under Mac and Linux the OHDSI Characterization package requires installing:
 # Installing the Package
 The preferred way to install the package is by using `remotes`, which will automatically install the latest release and all the latest dependencies.
 
-If you do not want the official release you could install the bleading edge version of the package (latest develop branch).
+If you do not want the official release you could install the bleeding edge version of the package (latest develop branch).
 
 Note that the latest develop branch could contain bugs, please report them to us if you experience problems.
 
@@ -73,7 +73,7 @@ http://github.com/OHDSI/Characterization/issues
 
 The list below provides solutions for some common issues:
 
-1. If you have an error when trying to install a package in R saying **'Dependancy X not available ...'** then this can sometimes be fixed by running `install.packages('X')` and then once that completes trying to reinstall the package that had the error.
+1. If you have an error when trying to install a package in R saying **'Dependency X not available ...'** then this can sometimes be fixed by running `install.packages('X')` and then once that completes trying to reinstall the package that had the error.
 
 2. I have found that using the github `remotes`` to install packages can be impacted if you have **multiple R sessions** open as one session with a library open can cause the library to be locked and this can prevent an install of a package that depends on that library.
 
diff --git a/vignettes/UsingCharacterizationPackage.Rmd b/vignettes/UsingCharacterizationPackage.Rmd
index d2ebdb3..db15f7e 100644
--- a/vignettes/UsingCharacterizationPackage.Rmd
+++ b/vignettes/UsingCharacterizationPackage.Rmd
@@ -31,8 +31,8 @@ output:
 # Introduction
 This vignette describes how you can use the Characterization package for various descriptive studies using OMOP CDM data. The Characterization package currently contains three different types of analyses:
 
-- Aggreagate Covariates: this returns the mean feature value for a set of features specified by the user for i) the Target cohort population, ii) the Outcome cohort population, iii) the Target population patients who had the outcome during some user specified time-at-risk and iv) the Target population patients who did not have the outcome during some user specified time-at-risk.
-- DechallengeRechallenge: this is mainly aimed at investigating whether a drug and event are causally related by seeing whether the drug is stopped close in time to the event occurrence (dechallenge) and then whether the drug is restarted (a rechallenge occurs) and if so, whether the event starts again (a failed rechallenge). In this analysis, the Target cohorts are the drug users of interest and the Outcome cohorts are the medical events you wish to see whether the drug may cause.  The user must also specify how close in time a drug msut be stopped after the outcome to be considered a dechallenge and how close in time an Outcome must occur after restarting the drug to be considered a failed rechallenge).
+- Aggregate Covariates: this returns the mean feature value for a set of features specified by the user for i) the Target cohort population, ii) the Outcome cohort population, iii) the Target population patients who had the outcome during some user specified time-at-risk and iv) the Target population patients who did not have the outcome during some user specified time-at-risk.
+- DechallengeRechallenge: this is mainly aimed at investigating whether a drug and event are causally related by seeing whether the drug is stopped close in time to the event occurrence (dechallenge) and then whether the drug is restarted (a rechallenge occurs) and if so, whether the event starts again (a failed rechallenge). In this analysis, the Target cohorts are the drug users of interest and the Outcome cohorts are the medical events you wish to see whether the drug may cause.  The user must also specify how close in time a drug must be stopped after the outcome to be considered a dechallenge and how close in time an Outcome must occur after restarting the drug to be considered a failed rechallenge).
 - Time-to-event: this returns descriptive results showing the timing between the target cohort and outcome.  This can help identify whether the outcome often precedes the target cohort or whether it generally comes after.
 
 # Setup
@@ -40,8 +40,8 @@ This vignette describes how you can use the Characterization package for various
 In this vignette we will show working examples using the `Eunomia` R package that contains simulated data.  Run the following code to install the `Eunomia` R package:
 
 ```{r tidy=TRUE,eval=FALSE}
-install.packages('remotes')
-remotes::install_github('ohdsi/Eunomia')
+install.packages("remotes")
+remotes::install_github("ohdsi/Eunomia")
 ```
 
 Eunomia can be used to create a temporary SQLITE database with the simulated data.  The function `getEunomiaConnectionDetails` creates a SQLITE connection to a temporary location. The function `createCohorts` then populates the temporary SQLITE database with the simulated data ready to be used.
@@ -53,8 +53,8 @@ Eunomia::createCohorts(connectionDetails = connectionDetails)
 
 We also need to have the Characterization package installed and loaded
 ```{r tidy=TRUE,eval=FALSE}
-remotes::install_github('ohdsi/FeatureExtraction')
-remotes::install_github('ohdsi/Characterization')
+remotes::install_github("ohdsi/FeatureExtraction")
+remotes::install_github("ohdsi/Characterization")
 ```
 
 ```{r tidy=TRUE,eval=TRUE}
@@ -79,45 +79,45 @@ To run an 'Aggregate Covariate' analysis you need to create a setting object usi
 Using the Eunomia data were we previous generated four cohorts, we can use cohort ids 1,2 and 4 as the targetIds and cohort id 3 as the outcomeIds:  
 
 ```{r eval=TRUE}
-  exampleTargetIds <- c(1,2,4)
-  exampleOutcomeIds <- 3
+exampleTargetIds <- c(1, 2, 4)
+exampleOutcomeIds <- 3
 ```
 
 If we want to get information on the sex assigned at birth, age at index and Charlson Comorbidity index we can create the settings using `FeatureExtraction::createCovariateSettings`:
 
 ```{r eval=TRUE}
-  exampleCovariateSettings <- FeatureExtraction::createCovariateSettings(
-    useDemographicsGender = T,
-    useDemographicsAge = T,
-    useCharlsonIndex = T
-    )
+exampleCovariateSettings <- FeatureExtraction::createCovariateSettings(
+  useDemographicsGender = T,
+  useDemographicsAge = T,
+  useCharlsonIndex = T
+)
 ```
 
 If we want to create the aggregate features for all our target cohorts, our outcome cohort and each target cohort restricted to those with a record of the outcome 1 day after target cohort start date until 365 days after target cohort end date we can run:
 
 ```{r eval=TRUE}
-  exampleAggregateCovariateSettings <- createAggregateCovariateSettings(
-    targetIds = exampleTargetIds,
-    outcomeIds = exampleOutcomeIds,
-    riskWindowStart = 1, startAnchor = 'cohort start',
-    riskWindowEnd = 365, endAnchor = 'cohort start',
-    covariateSettings = exampleCovariateSettings
-    )
+exampleAggregateCovariateSettings <- createAggregateCovariateSettings(
+  targetIds = exampleTargetIds,
+  outcomeIds = exampleOutcomeIds,
+  riskWindowStart = 1, startAnchor = "cohort start",
+  riskWindowEnd = 365, endAnchor = "cohort start",
+  covariateSettings = exampleCovariateSettings
+)
 ```
 
-Next we need to use the `exampleAggregateCovariateSettings` as the settings to `computeAggregateCovariateAnalyses`, we need to use the Eunomia connectionDetails and in Eunomia the OMOP CDM data and cohort table are in the 'main' schema.  The cohort table name is 'cohort'.  The following code will apply the aggregative covariates analysis using the previously specified settings on the simulated Eunomia data:
+Next we need to use the `exampleAggregateCovariateSettings` as the settings to `computeAggregateCovariateAnalyses`, we need to use the Eunomia connectionDetails and in Eunomia the OMOP CDM data and cohort table are in the 'main' schema.  The cohort table name is 'cohort'.  The following code will apply the aggregated covariates analysis using the previously specified settings on the simulated Eunomia data:
 
 ```{r eval=TRUE,results='hide',error=FALSE,warning=FALSE,message=FALSE}
 agc <- computeAggregateCovariateAnalyses(
-    connectionDetails = connectionDetails,
-    cdmDatabaseSchema = 'main',
-    cdmVersion = 5,
-    targetDatabaseSchema = 'main',
-    targetTable = 'cohort',
-    aggregateCovariateSettings = exampleAggregateCovariateSettings,
-    databaseId = 'Eunomia', 
-    runId = 1
-    )
+  connectionDetails = connectionDetails,
+  cdmDatabaseSchema = "main",
+  cdmVersion = 5,
+  targetDatabaseSchema = "main",
+  targetTable = "cohort",
+  aggregateCovariateSettings = exampleAggregateCovariateSettings,
+  databaseId = "Eunomia",
+  runId = 1
+)
 ```
 
 If you would like to save the results you can use the function `saveAggregateCovariateAnalyses` and this can then be loaded using `loadAggregateCovariateAnalyses`.
@@ -126,30 +126,30 @@ The results are Andromeda objects that can we viewed using `dplyr`.  There are f
  
 - covariates:
 ```{r eval=TRUE}
-agc$covariates %>% 
+agc$covariates %>%
   collect() %>%
-  kableExtra::kbl() 
+  kableExtra::kbl()
 ```
 
 - covariatesContinuous:
 ```{r eval=TRUE}
-agc$covariatesContinuous %>% 
+agc$covariatesContinuous %>%
   collect() %>%
-  kableExtra::kbl() 
+  kableExtra::kbl()
 ```
 
 - covariateRef:
 ```{r eval=TRUE}
-agc$covariateRef %>% 
+agc$covariateRef %>%
   collect() %>%
-  kableExtra::kbl() 
+  kableExtra::kbl()
 ```
 
 - analysisRef:
 ```{r eval=TRUE}
-agc$analysisRef %>% 
+agc$analysisRef %>%
   collect() %>%
-  kableExtra::kbl() 
+  kableExtra::kbl()
 ```
 
 ## Dechallenge Rechallenge
@@ -164,31 +164,31 @@ To run a 'Dechallenge Rechallenge' analysis you need to create a setting object
 Using the Eunomia data were we previous generated four cohorts, we can use cohort ids 1,2 and 4 as the targetIds and cohort id 3 as the outcomeIds:  
 
 ```{r eval=TRUE}
-  exampleTargetIds <- c(1,2,4)
-  exampleOutcomeIds <- 3
+exampleTargetIds <- c(1, 2, 4)
+exampleOutcomeIds <- 3
 ```
 
 If we want to create the dechallenge rechallenge for all our target cohorts and our outcome cohort with a 30 day dechallengeStopInterval and 31 day dechallengeEvaluationWindow:
 
 ```{r eval=TRUE}
-  exampleDechallengeRechallengeSettings <- createDechallengeRechallengeSettings(
-    targetIds = exampleTargetIds,
-    outcomeIds = exampleOutcomeIds,
-    dechallengeStopInterval = 30,
-    dechallengeEvaluationWindow = 31
-    )
+exampleDechallengeRechallengeSettings <- createDechallengeRechallengeSettings(
+  targetIds = exampleTargetIds,
+  outcomeIds = exampleOutcomeIds,
+  dechallengeStopInterval = 30,
+  dechallengeEvaluationWindow = 31
+)
 ```
 
 We can then run  the analysis on the Eunomia data using `computeDechallengeRechallengeAnalyses` and the settings previously specified:
 
 ```{r eval=TRUE}
 dc <- computeDechallengeRechallengeAnalyses(
-    connectionDetails = connectionDetails,
-    targetDatabaseSchema = 'main',
-    targetTable = 'cohort',
-    dechallengeRechallengeSettings = exampleDechallengeRechallengeSettings,
-    databaseId = 'Eunomia'
-    )
+  connectionDetails = connectionDetails,
+  targetDatabaseSchema = "main",
+  targetTable = "cohort",
+  dechallengeRechallengeSettings = exampleDechallengeRechallengeSettings,
+  databaseId = "Eunomia"
+)
 ```
 
 If you would like to save the results you can use the function `saveDechallengeRechallengeAnalyses` and this can then be loaded using `loadDechallengeRechallengeAnalyses`.
@@ -196,9 +196,9 @@ If you would like to save the results you can use the function `saveDechallengeR
 The results are Andromeda objects that can we viewed using `dplyr`.  There is just one table named dechallengeRechallenge:
  
 ```{r eval=TRUE}
-dc$dechallengeRechallenge %>% 
+dc$dechallengeRechallenge %>%
   collect() %>%
-  kableExtra::kbl() 
+  kableExtra::kbl()
 ```
 
 Next it is possible to computer and extract the failed rechallenge cases
@@ -206,21 +206,21 @@ Next it is possible to computer and extract the failed rechallenge cases
 ```{r eval=TRUE}
 failed <- computeRechallengeFailCaseSeriesAnalyses(
   connectionDetails = connectionDetails,
-  targetDatabaseSchema = 'main',
-  targetTable = 'cohort',
+  targetDatabaseSchema = "main",
+  targetTable = "cohort",
   dechallengeRechallengeSettings = exampleDechallengeRechallengeSettings,
-  outcomeDatabaseSchema = 'main',
-  outcomeTable = 'cohort',
-  databaseId = 'Eunomia'
+  outcomeDatabaseSchema = "main",
+  outcomeTable = "cohort",
+  databaseId = "Eunomia"
 )
 ```
 
 The results are Andromeda objects that can we viewed using `dplyr`.  There is just one table named rechallengeFailCaseSeries:
  
 ```{r eval=TRUE}
-failed$rechallengeFailCaseSeries %>% 
+failed$rechallengeFailCaseSeries %>%
   collect() %>%
-  kableExtra::kbl() 
+  kableExtra::kbl()
 ```
 
 ## Time to Event
@@ -231,23 +231,23 @@ To run a 'Time-to-event' analysis you need to create a setting object using `cre
 - one or more outcomeIds (these must be pre-generated in a cohort table)
 
 ```{r eval=TRUE}
-  exampleTimeToEventSettings <- createTimeToEventSettings(
-    targetIds = exampleTargetIds,
-    outcomeIds = exampleOutcomeIds
-    )
+exampleTimeToEventSettings <- createTimeToEventSettings(
+  targetIds = exampleTargetIds,
+  outcomeIds = exampleOutcomeIds
+)
 ```
 
 We can then run  the analysis on the Eunomia data using `computeTimeToEventAnalyses` and the settings previously specified:
 
 ```{r eval=TRUE}
 tte <- computeTimeToEventAnalyses(
-    connectionDetails = connectionDetails,
-    cdmDatabaseSchema = 'main',
-    targetDatabaseSchema = 'main',
-    targetTable = 'cohort', 
-    timeToEventSettings =  exampleTimeToEventSettings,
-    databaseId = 'Eunomia'
-    )
+  connectionDetails = connectionDetails,
+  cdmDatabaseSchema = "main",
+  targetDatabaseSchema = "main",
+  targetTable = "cohort",
+  timeToEventSettings = exampleTimeToEventSettings,
+  databaseId = "Eunomia"
+)
 ```
 
 If you would like to save the results you can use the function `saveTimeToEventAnalyses` and this can then be loaded using `loadTimeToEventAnalyses`.
@@ -255,10 +255,10 @@ If you would like to save the results you can use the function `saveTimeToEventA
 The results are Andromeda objects that can we viewed using `dplyr`.  There is just one table named timeToEvent:
  
 ```{r eval=TRUE}
-tte$timeToEvent %>% 
+tte$timeToEvent %>%
   collect() %>%
   top_n(10) %>%
-  kableExtra::kbl() 
+  kableExtra::kbl()
 ```
 
 
@@ -267,57 +267,56 @@ tte$timeToEvent %>%
 If you want to run multiple analyses (of the three previously shown) you can use `createCharacterizationSettings`.  You need to input a list of each of the settings (or NULL if you do not want to run one type of analysis).  To run all the analyses previously shown in one function:
 
 ```{r eval=FALSE,results='hide',error=FALSE,warning=FALSE,message=FALSE}
-  characterizationSettings <- createCharacterizationSettings(
-    timeToEventSettings = list(
-      exampleTimeToEventSettings
-      ),
-    dechallengeRechallengeSettings = list(
-      exampleDechallengeRechallengeSettings
-    ),
-    aggregateCovariateSettings = list(
-      exampleAggregateCovariateSettings
-      )
+characterizationSettings <- createCharacterizationSettings(
+  timeToEventSettings = list(
+    exampleTimeToEventSettings
+  ),
+  dechallengeRechallengeSettings = list(
+    exampleDechallengeRechallengeSettings
+  ),
+  aggregateCovariateSettings = list(
+    exampleAggregateCovariateSettings
   )
+)
 
 # save the settings using
 saveCharacterizationSettings(
-  settings = characterizationSettings, 
-  saveDirectory = file.path(tempdir(), 'saveSettings')
-    )
+  settings = characterizationSettings,
+  saveDirectory = file.path(tempdir(), "saveSettings")
+)
 
 # the settings can be loaded
 characterizationSettings <- loadCharacterizationSettings(
-  saveDirectory = file.path(tempdir(), 'saveSettings')
-    )
+  saveDirectory = file.path(tempdir(), "saveSettings")
+)
 
 runCharacterizationAnalyses(
   connectionDetails = connectionDetails,
-  cdmDatabaseSchema = 'main',
-  targetDatabaseSchema = 'main',
-  targetTable = 'cohort',
-  outcomeDatabaseSchema = 'main',
-  outcomeTable = 'cohort',
+  cdmDatabaseSchema = "main",
+  targetDatabaseSchema = "main",
+  targetTable = "cohort",
+  outcomeDatabaseSchema = "main",
+  outcomeTable = "cohort",
   characterizationSettings = characterizationSettings,
-  saveDirectory = file.path(tempdir(), 'example'),
-  tablePrefix = 'c_',
-  databaseId = '1'
+  saveDirectory = file.path(tempdir(), "example"),
+  tablePrefix = "c_",
+  databaseId = "1"
 )
-
 ```
 
 This will create an SQLITE database with all the analyses saved into the saveDirectory.  You can export the results as csv files using:
 
 ```{r eval=FALSE}
 connectionDetailsT <- DatabaseConnector::createConnectionDetails(
-  dbms = 'sqlite',
-  server = file.path(tempdir(),'example','sqliteCharacterization', 'sqlite.sqlite')
+  dbms = "sqlite",
+  server = file.path(tempdir(), "example", "sqliteCharacterization", "sqlite.sqlite")
 )
 
 exportDatabaseToCsv(
   connectionDetails = connectionDetailsT,
-  resultSchema = 'main',
-  targetDialect = 'sqlite',
-  tablePrefix = 'c_',
-  saveDirectory = file.path(tempdir(),'csv')
+  resultSchema = "main",
+  targetDialect = "sqlite",
+  tablePrefix = "c_",
+  saveDirectory = file.path(tempdir(), "csv")
 )
 ```