From 94e9644642656fcf25261b6109cce7584adf38cf Mon Sep 17 00:00:00 2001
From: Gowtham Rao <rao@ohdsi.org>
Date: Wed, 8 Mar 2023 05:19:59 -0500
Subject: [PATCH 01/11] Support for list of CovariateSettings

https://github.com/OHDSI/Characterization/issues/18
---
 R/HelperFunctions.R | 23 ++++++++++++++---------
 1 file changed, 14 insertions(+), 9 deletions(-)

diff --git a/R/HelperFunctions.R b/R/HelperFunctions.R
index eb98ea6..33a8570 100644
--- a/R/HelperFunctions.R
+++ b/R/HelperFunctions.R
@@ -231,13 +231,18 @@
 
 
 
-.checkCovariateSettings <- function(
-    covariateSettings,
-  errorMessages
-) {
-  checkmate::assertClass(
-    x = covariateSettings,
-    classes = "covariateSettings",
-    add = errorMessages
-  )
+.checkCovariateSettings <- function(covariateSettings,
+                                    errorMessages) {
+  if (class(covariateSettings) == "covariateSettings") {
+    checkmate::assertClass(x = covariateSettings,
+                           classes = "covariateSettings",
+                           add = errorMessages)
+  } else {
+    for (j in (1:length(covariateSetting))) {
+      checkmate::assertClass(x = covariateSettings[[j]],
+                             classes = "covariateSettings",
+                             add = errorMessages)
+    }
+  }
+
 }

From 63e59519973a34f62db7881438193ac2fc289757 Mon Sep 17 00:00:00 2001
From: Gowtham Rao <rao@ohdsi.org>
Date: Wed, 8 Mar 2023 06:31:26 -0500
Subject: [PATCH 02/11] Add tests

---
 R/HelperFunctions.R                      |  2 +-
 tests/testthat/test-aggregateCovariate.R | 31 ++++++++++++++++++++++++
 2 files changed, 32 insertions(+), 1 deletion(-)

diff --git a/R/HelperFunctions.R b/R/HelperFunctions.R
index 33a8570..0901191 100644
--- a/R/HelperFunctions.R
+++ b/R/HelperFunctions.R
@@ -238,7 +238,7 @@
                            classes = "covariateSettings",
                            add = errorMessages)
   } else {
-    for (j in (1:length(covariateSetting))) {
+    for (j in (1:length(covariateSettings))) {
       checkmate::assertClass(x = covariateSettings[[j]],
                              classes = "covariateSettings",
                              add = errorMessages)
diff --git a/tests/testthat/test-aggregateCovariate.R b/tests/testthat/test-aggregateCovariate.R
index 9a2423d..4581ae9 100644
--- a/tests/testthat/test-aggregateCovariate.R
+++ b/tests/testthat/test-aggregateCovariate.R
@@ -30,6 +30,37 @@ test_that("createAggregateCovariateSettings", {
   )
 })
 
+test_that("createAggregateCovariateSettingsList", {
+  targetIds <- sample(x = 100, size = sample(10, 1))
+  outcomeIds <- sample(x = 100, size = sample(10, 1))
+  covariateSettings1 <- FeatureExtraction::createCovariateSettings(
+    useDemographicsGender = T,
+    useDemographicsAge = T,
+    useCharlsonIndex = T
+  )
+  covariateSettings2 <- FeatureExtraction::createCovariateSettings(
+    useConditionOccurrenceAnyTimePrior = TRUE
+  )
+  covariateSetting <- list(covariateSettings1, covariateSettings2)
+
+  res <- createAggregateCovariateSettings(
+    targetIds = targetIds,
+    outcomeIds = outcomeIds,
+    riskWindowStart = 1, startAnchor = "cohort start",
+    riskWindowEnd = 365, endAnchor = "cohort start",
+    covariateSettings = covariateSettings
+  )
+
+  testthat::expect_equal(
+    res$targetIds,
+    targetIds
+  )
+  testthat::expect_equal(
+    res$covariateSettings,
+    covariateSettings
+  )
+})
+
 test_that("computeAggregateCovariateAnalyses", {
   targetIds <- c(1, 2, 4)
   outcomeIds <- c(3)

From c66344db3a94c394d792c5ae16074c8b7973c618 Mon Sep 17 00:00:00 2001
From: Gowtham Rao <rao@ohdsi.org>
Date: Wed, 8 Mar 2023 06:41:13 -0500
Subject: [PATCH 03/11] Update test-aggregateCovariate.R

---
 tests/testthat/test-aggregateCovariate.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/testthat/test-aggregateCovariate.R b/tests/testthat/test-aggregateCovariate.R
index 4581ae9..b7493b8 100644
--- a/tests/testthat/test-aggregateCovariate.R
+++ b/tests/testthat/test-aggregateCovariate.R
@@ -41,7 +41,7 @@ test_that("createAggregateCovariateSettingsList", {
   covariateSettings2 <- FeatureExtraction::createCovariateSettings(
     useConditionOccurrenceAnyTimePrior = TRUE
   )
-  covariateSetting <- list(covariateSettings1, covariateSettings2)
+  covariateSettings <- list(covariateSettings1, covariateSettings2)
 
   res <- createAggregateCovariateSettings(
     targetIds = targetIds,

From 937b1ec6410a7f6457c44d30da9157d7655c235b Mon Sep 17 00:00:00 2001
From: jreps <jreps@its.jnj.com>
Date: Mon, 13 Mar 2023 16:46:25 -0400
Subject: [PATCH 04/11] shiny app in package

- adding shiny app
---
 NAMESPACE                   |   2 +
 R/ViewShiny.R               | 199 ++++++++++++++++++++++++++++++++++++
 inst/shinyConfig.json       |  32 ++++++
 man/viewCharacterization.Rd |  22 ++++
 4 files changed, 255 insertions(+)
 create mode 100644 R/ViewShiny.R
 create mode 100644 inst/shinyConfig.json
 create mode 100644 man/viewCharacterization.Rd

diff --git a/NAMESPACE b/NAMESPACE
index 91a8032..c0204a0 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -26,5 +26,7 @@ export(saveCharacterizationSettings)
 export(saveDechallengeRechallengeAnalyses)
 export(saveRechallengeFailCaseSeriesAnalyses)
 export(saveTimeToEventAnalyses)
+export(viewCharacterization)
 importFrom(dplyr,"%>%")
+importFrom(methods,is)
 importFrom(rlang,.data)
diff --git a/R/ViewShiny.R b/R/ViewShiny.R
new file mode 100644
index 0000000..01676da
--- /dev/null
+++ b/R/ViewShiny.R
@@ -0,0 +1,199 @@
+#' viewCharacterization - Interactively view the characterization results
+#'
+#' @description
+#' This is a shiny app for viewing interactive plots and tables
+#' @details
+#' Input is the output of ...
+#' @param resultLocation   The location of the results
+#' @param cohortDefinitionSet  The cohortDefinitionSet extracted using webAPI
+#' @return
+#' Opens a shiny app for interactively viewing the results
+#'
+#' @export
+viewCharacterization <- function(
+    resultLocation,
+    cohortDefinitionSet = NULL
+    ) {
+
+  server <- file.path(resultLocation, 'sqliteCharacterization', 'sqlite.sqlite')
+
+  connectionDetailsSettings <- list(
+    dbms = 'sqlite',
+    server = server
+  )
+
+  connectionDetails <- do.call(
+    what = DatabaseConnector::createConnectionDetails,
+    args = connectionDetailsSettings
+  )
+
+  con <- DatabaseConnector::connect(connectionDetails)
+  on.exit(DatabaseConnector::disconnect(con))
+
+  tables <- tolower(DatabaseConnector::getTableNames(con, 'main'))
+
+  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::insertTable(
+      connection = con,
+      databaseSchema = 'main',
+      tableName = 'cg_COHORT_DEFINITION',
+      data = data.frame(
+        cohortDefinitionId = cohortIds,
+        cohortName = getCohortNames(cohortIds, cohortDefinitionSet)
+      ),
+      camelCaseToSnakeCase = T
+    )
+  }
+
+  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;')$DATABASE_ID
+      )
+    )
+
+    DatabaseConnector::insertTable(
+      connection = con,
+      databaseSchema = 'main',
+      tableName = 'DATABASE_META_DATA',
+      data = data.frame(
+        databaseId = dbIds,
+        cdmSourceAbbreviation = paste0('database ', dbIds)
+      ),
+      camelCaseToSnakeCase = T
+    )
+  }
+
+  if(!'i_incidence_summary' %in% tables){
+
+    x <- c("refId", "databaseId", "sourceName",
+           "targetCohortDefinitionId", "targetName", "tarId",
+           "tarStartWith", "tarStartOffset", "tarEndWith", "tarEndOffset",
+           "subgroupId", 'subgroupName',
+           'outcomeId','outcomeCohortDefinitionId', 'outcomeName',
+           'clean_window',
+           'ageId', 'ageGroupName',
+           'genderId', 'genderName',
+           'startYear', 'personsAtRiskPe', 'personsAtRisk',
+           'personDaysPe', 'personDays',
+           'personOutcomesPe', 'personOutcomes',
+           'outcomesPe', 'outcomes',
+           'incidenceProportionP100p',
+           'incidenceRateP100py'
+           )
+    df <- data.frame(matrix(ncol = length(x), nrow = 0))
+    colnames(df) <- x
+
+    DatabaseConnector::insertTable(
+      connection = con,
+      databaseSchema = 'main',
+      tableName = 'i_incidence_summary',
+      data = df,
+      camelCaseToSnakeCase = T
+    )
+  }
+
+  databaseSettings <- list(
+    connectionDetailSettings = connectionDetailSettings,
+    schema = 'main',
+    tablePrefix = 'c_',
+    cohortTablePrefix = 'cg_',
+    incidenceTablePrefix = 'i_',
+    databaseTable = 'DATABASE_META_DATA'
+  )
+
+  viewChars(databaseSettings)
+
+}
+
+viewChars <- function(databaseSettings){
+  ensure_installed("ShinyAppBuilder")
+  ensure_installed("ResultModelManager")
+
+  connectionDetails <- do.call(
+    DatabaseConnector::createConnectionDetails,
+    databaseSettings$connectionDetailSettings
+  )
+  connection <- ResultModelManager::ConnectionHandler$new(connectionDetails)
+  databaseSettings$connectionDetailSettings <- NULL
+
+  # set database settings into system variables
+  Sys.setenv("resultDatabaseDetails_characterization" = as.character(ParallelLogger::convertSettingsToJson(databaseSettings)))
+
+  config <- ParallelLogger::loadSettingsFromJson(
+    fileName = system.file(
+      'shinyConfig.json',
+      package = "Characterization"
+    )
+  )
+
+  ShinyAppBuilder::viewShiny(config = config, connection = connection)
+}
+
+
+
+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)
+}
+
+
+# Borrowed from devtools: https://github.com/hadley/devtools/blob/ba7a5a4abd8258c52cb156e7b26bb4bf47a79f0b/R/utils.r#L44
+is_installed <- function (pkg, version = 0) {
+  installed_version <- tryCatch(utils::packageVersion(pkg),
+                                error = function(e) NA)
+  !is.na(installed_version) && installed_version >= version
+}
+
+# Borrowed and adapted from devtools: https://github.com/hadley/devtools/blob/ba7a5a4abd8258c52cb156e7b26bb4bf47a79f0b/R/utils.r#L74
+ensure_installed <- function(pkg) {
+  if (!is_installed(pkg)) {
+    msg <- paste0(sQuote(pkg), " must be installed for this functionality.")
+    if (interactive()) {
+      message(msg, "\nWould you like to install it?")
+      if (utils::menu(c("Yes", "No")) == 1) {
+        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')
+          }
+
+          devtools::install_github(paste0('OHDSI/',pkg))
+        }else{
+          utils::install.packages(pkg)
+        }
+      } else {
+        stop(msg, call. = FALSE)
+      }
+    } else {
+      stop(msg, call. = FALSE)
+    }
+  }
+}
diff --git a/inst/shinyConfig.json b/inst/shinyConfig.json
new file mode 100644
index 0000000..98114b2
--- /dev/null
+++ b/inst/shinyConfig.json
@@ -0,0 +1,32 @@
+{
+  "shinyModules": [
+    {
+      "id": "about",
+      "tabName": "About",
+      "tabText": "About",
+      "shinyModulePackage": "OhdsiShinyModules",
+      "uiFunction": "aboutViewer",
+      "serverFunction": "aboutServer",
+      "databaseConnectionKeyService": null,
+      "databaseConnectionKeyUsername": null,
+      "infoBoxFile": "aboutHelperFile()",
+      "icon": "info",
+      "keyring": true,
+      "order": 1
+    },
+    {
+      "id": "characterization",
+      "tabName": "Characterization",
+      "tabText": "Characterization",
+      "shinyModulePackage": "OhdsiShinyModules",
+      "uiFunction": "descriptionViewer",
+      "serverFunction": "descriptionServer",
+      "databaseConnectionKeyService": "resultDatabaseDetails",
+      "databaseConnectionKeyUsername": "characterization",
+      "infoBoxFile": "descriptionHelperFile()",
+      "icon": "chart-line",
+      "keyring": false,
+      "order": 2
+    }
+  ]
+}
diff --git a/man/viewCharacterization.Rd b/man/viewCharacterization.Rd
new file mode 100644
index 0000000..712066a
--- /dev/null
+++ b/man/viewCharacterization.Rd
@@ -0,0 +1,22 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/ViewShiny.R
+\name{viewCharacterization}
+\alias{viewCharacterization}
+\title{viewCharacterization - Interactively view the characterization results}
+\usage{
+viewCharacterization(resultLocation, cohortDefinitionSet = NULL)
+}
+\arguments{
+\item{resultLocation}{The location of the results}
+
+\item{cohortDefinitionSet}{The cohortDefinitionSet extracted using webAPI}
+}
+\value{
+Opens a shiny app for interactively viewing the results
+}
+\description{
+This is a shiny app for viewing interactive plots and tables
+}
+\details{
+Input is the output of ...
+}

From 79cba46099fe49082a59e434e22dc583150a4bc8 Mon Sep 17 00:00:00 2001
From: jreps <jreps@its.jnj.com>
Date: Mon, 13 Mar 2023 16:48:59 -0400
Subject: [PATCH 05/11] Update DESCRIPTION

adding shiny packages to description
---
 DESCRIPTION | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 6e7ab62..9a3eb9c 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -30,10 +30,14 @@ Suggests:
 	kableExtra,
 	knitr,
 	markdown,
+	ResultModelManager,
+	ShinyAppBuilder,
 	withr
 Remotes:
 	ohdsi/FeatureExtraction,
-	ohdsi/Eunomia
+	ohdsi/Eunomia,
+	ohdsi/ResultModelManager,
+	ohdsi/ShinyAppBuilder
 NeedsCompilation: no
 RoxygenNote: 7.2.3
 Encoding: UTF-8

From 41a438403046f73ceb3737bcf4eceb111329220a Mon Sep 17 00:00:00 2001
From: jreps <jreps@its.jnj.com>
Date: Tue, 14 Mar 2023 08:48:15 -0400
Subject: [PATCH 06/11] Update ViewShiny.R

fixed missing s typo in connectionDetailsSettings
---
 R/ViewShiny.R | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/R/ViewShiny.R b/R/ViewShiny.R
index 01676da..0a3b5b6 100644
--- a/R/ViewShiny.R
+++ b/R/ViewShiny.R
@@ -107,7 +107,7 @@ viewCharacterization <- function(
   }
 
   databaseSettings <- list(
-    connectionDetailSettings = connectionDetailSettings,
+    connectionDetailsSettings = connectionDetailsSettings,
     schema = 'main',
     tablePrefix = 'c_',
     cohortTablePrefix = 'cg_',
@@ -125,10 +125,10 @@ viewChars <- function(databaseSettings){
 
   connectionDetails <- do.call(
     DatabaseConnector::createConnectionDetails,
-    databaseSettings$connectionDetailSettings
+    databaseSettings$connectionDetailsSettings
   )
   connection <- ResultModelManager::ConnectionHandler$new(connectionDetails)
-  databaseSettings$connectionDetailSettings <- NULL
+  databaseSettings$connectionDetailsSettings <- NULL
 
   # set database settings into system variables
   Sys.setenv("resultDatabaseDetails_characterization" = as.character(ParallelLogger::convertSettingsToJson(databaseSettings)))

From 1c081acf5f0107ce1d6b21500abac0e05c3fdb67 Mon Sep 17 00:00:00 2001
From: jreps <jreps@its.jnj.com>
Date: Tue, 14 Mar 2023 08:56:23 -0400
Subject: [PATCH 07/11] fixing R check

fixing R check
---
 DESCRIPTION          | 1 +
 NAMESPACE            | 1 -
 R/Characterization.R | 1 -
 R/HelperFunctions.R  | 6 +++---
 4 files changed, 4 insertions(+), 5 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 9a3eb9c..ef9569c 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -25,6 +25,7 @@ Imports:
 	readr, 
 	rlang
 Suggests:
+  devtools,
 	testthat,
 	Eunomia,
 	kableExtra,
diff --git a/NAMESPACE b/NAMESPACE
index c0204a0..dfa7bce 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -28,5 +28,4 @@ export(saveRechallengeFailCaseSeriesAnalyses)
 export(saveTimeToEventAnalyses)
 export(viewCharacterization)
 importFrom(dplyr,"%>%")
-importFrom(methods,is)
 importFrom(rlang,.data)
diff --git a/R/Characterization.R b/R/Characterization.R
index 20b810e..3885f20 100644
--- a/R/Characterization.R
+++ b/R/Characterization.R
@@ -18,6 +18,5 @@
 "_PACKAGE"
 
 #' @importFrom rlang .data
-#' @importFrom methods is
 #' @importFrom dplyr %>%
 NULL
diff --git a/R/HelperFunctions.R b/R/HelperFunctions.R
index eb98ea6..98b40d5 100644
--- a/R/HelperFunctions.R
+++ b/R/HelperFunctions.R
@@ -29,7 +29,7 @@
   connectionDetails,
   errorMessages
   ) {
-  if (is(connectionDetails, "connectionDetails")) {
+  if (inherits(connectionDetails, "connectionDetails")) {
   checkmate::assertClass(
     x = connectionDetails,
     classes = "connectionDetails",
@@ -99,7 +99,7 @@
     return()
   }
 
-  if(class(settings) == 'timeToEventSettings'){
+  if(inherits(settings,'timeToEventSettings')){
     settings <- list(settings)
   }
 
@@ -133,7 +133,7 @@
     return()
   }
 
-  if(class(settings) == 'aggregateCovariateSettings'){
+  if(inherits(settings,'aggregateCovariateSettings')){
     settings <- list(settings)
   }
 

From a217d88b6be87f14080007437d4fc992944ce485 Mon Sep 17 00:00:00 2001
From: jreps <jreps@its.jnj.com>
Date: Tue, 14 Mar 2023 12:44:39 -0400
Subject: [PATCH 08/11] shiny app test code

- added tests to shiny app
- restructured shiny app code to help code coverage
---
 R/ViewShiny.R                   |  28 ++++--
 tests/testthat/test-viewShiny.R | 149 ++++++++++++++++++++++++++++++++
 2 files changed, 172 insertions(+), 5 deletions(-)
 create mode 100644 tests/testthat/test-viewShiny.R

diff --git a/R/ViewShiny.R b/R/ViewShiny.R
index 0a3b5b6..9215598 100644
--- a/R/ViewShiny.R
+++ b/R/ViewShiny.R
@@ -15,6 +15,18 @@ viewCharacterization <- function(
     cohortDefinitionSet = NULL
     ) {
 
+  databaseSettings <- prepareCharacterizationShiny(
+    resultLocation = resultLocation,
+    cohortDefinitionSet = cohortDefinitionSet
+  )
+
+  viewChars(databaseSettings)
+}
+
+prepareCharacterizationShiny <- function(
+    resultLocation,
+    cohortDefinitionSet
+    ){
   server <- file.path(resultLocation, 'sqliteCharacterization', 'sqlite.sqlite')
 
   connectionDetailsSettings <- list(
@@ -93,7 +105,7 @@ viewCharacterization <- function(
            'outcomesPe', 'outcomes',
            'incidenceProportionP100p',
            'incidenceRateP100py'
-           )
+    )
     df <- data.frame(matrix(ncol = length(x), nrow = 0))
     colnames(df) <- x
 
@@ -115,11 +127,13 @@ viewCharacterization <- function(
     databaseTable = 'DATABASE_META_DATA'
   )
 
-  viewChars(databaseSettings)
-
+  return(databaseSettings)
 }
 
-viewChars <- function(databaseSettings){
+viewChars <- function(
+    databaseSettings,
+    testApp = F
+    ){
   ensure_installed("ShinyAppBuilder")
   ensure_installed("ResultModelManager")
 
@@ -140,7 +154,11 @@ viewChars <- function(databaseSettings){
     )
   )
 
-  ShinyAppBuilder::viewShiny(config = config, connection = connection)
+  if(!testApp){
+    ShinyAppBuilder::viewShiny(config = config, connection = connection)
+  } else{
+    ShinyAppBuilder::createShinyApp(config = config, connection = connection)
+  }
 }
 
 
diff --git a/tests/testthat/test-viewShiny.R b/tests/testthat/test-viewShiny.R
new file mode 100644
index 0000000..93599ad
--- /dev/null
+++ b/tests/testthat/test-viewShiny.R
@@ -0,0 +1,149 @@
+context("ViewShiny")
+
+# create a folder with results for the shiny app
+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)
+})
+
+test_that("ensure_installed", {
+  testthat::expect_equal(ensure_installed('FeatureExtraction'), NULL)
+})
+
+test_that("prepareCharacterizationShiny works", {
+
+  targetIds <- c(1, 2, 4)
+  outcomeIds <- c(3)
+
+  timeToEventSettings1 <- createTimeToEventSettings(
+    targetIds = 1,
+    outcomeIds = c(3, 4)
+  )
+  timeToEventSettings2 <- createTimeToEventSettings(
+    targetIds = 2,
+    outcomeIds = c(3, 4)
+  )
+
+  dechallengeRechallengeSettings <- createDechallengeRechallengeSettings(
+    targetIds = targetIds,
+    outcomeIds = outcomeIds,
+    dechallengeStopInterval = 30,
+    dechallengeEvaluationWindow = 31
+  )
+
+  aggregateCovariateSettings1 <- createAggregateCovariateSettings(
+    targetIds = targetIds,
+    outcomeIds = outcomeIds,
+    riskWindowStart = 1,
+    startAnchor = "cohort start",
+    riskWindowEnd = 365,
+    endAnchor = "cohort start",
+    covariateSettings = FeatureExtraction::createCovariateSettings(
+      useDemographicsGender = T,
+      useDemographicsAge = T,
+      useDemographicsRace = T
+    )
+  )
+
+  aggregateCovariateSettings2 <- createAggregateCovariateSettings(
+    targetIds = targetIds,
+    outcomeIds = outcomeIds,
+    riskWindowStart = 1,
+    startAnchor = "cohort start",
+    riskWindowEnd = 365,
+    endAnchor = "cohort start",
+    covariateSettings = FeatureExtraction::createCovariateSettings(
+      useConditionOccurrenceLongTerm = T
+    )
+  )
+
+  characterizationSettings <- createCharacterizationSettings(
+    timeToEventSettings = list(
+      timeToEventSettings1,
+      timeToEventSettings2
+    ),
+    dechallengeRechallengeSettings = list(
+      dechallengeRechallengeSettings
+    ),
+    aggregateCovariateSettings = list(
+      aggregateCovariateSettings1,
+      aggregateCovariateSettings2
+    )
+  )
+
+  runCharacterizationAnalyses(
+    connectionDetails = connectionDetails,
+    cdmDatabaseSchema = "main",
+    targetDatabaseSchema = "main",
+    targetTable = "cohort",
+    outcomeDatabaseSchema = "main",
+    outcomeTable = "cohort",
+    characterizationSettings = characterizationSettings,
+    saveDirectory = resultLocation,
+    tablePrefix = "c_",
+    databaseId = "1"
+  )
+
+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$databaseTable == 'DATABASE_META_DATA')
+
+connectionDetailsTest <- do.call(
+  what = DatabaseConnector::createConnectionDetails,
+  args = list(
+    dbms = 'sqlite',
+    server = file.path(resultLocation, 'sqliteCharacterization', 'sqlite.sqlite')
+  )
+)
+conTest <- DatabaseConnector::connect(connectionDetailsTest)
+tables <- tolower(
+  DatabaseConnector::getTableNames(
+    connection = conTest,
+    databaseSchema = 'main'
+    )
+)
+
+# make sure the extra tables are added
+testthat::expect_true('cg_cohort_definition' %in% tables)
+testthat::expect_true('database_meta_data' %in% tables)
+testthat::expect_true('i_incidence_summary' %in% tables)
+
+})
+
+test_that("shiny app works", {
+
+  settings <- prepareCharacterizationShiny(
+    resultLocation = resultLocation,
+    cohortDefinitionSet = NULL
+  )
+
+  app <- viewChars(
+    databaseSettings = settings,
+    testApp = T
+  )
+
+shiny::testServer(
+  app = app,
+  args = list(
+  ),
+  expr = {
+
+    testthat::expect_equal(runServer[['About']],0)
+    session$setInputs(menu = 'About')
+    testthat::expect_equal(runServer[['About']],1)
+
+  })
+
+})

From e848a05a0288f6c2c9ad45587c86de1b2a94de1e Mon Sep 17 00:00:00 2001
From: jreps <jreps@its.jnj.com>
Date: Tue, 14 Mar 2023 13:04:48 -0400
Subject: [PATCH 09/11] fixing warnings/notes

- removing class() and adding inherits()
- adding shiny to depends for tests
---
 DESCRIPTION             | 1 +
 R/HelperFunctions.R     | 2 +-
 R/RunCharacterization.R | 6 +++---
 3 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index ef9569c..40270bb 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -33,6 +33,7 @@ Suggests:
 	markdown,
 	ResultModelManager,
 	ShinyAppBuilder,
+	shiny,
 	withr
 Remotes:
 	ohdsi/FeatureExtraction,
diff --git a/R/HelperFunctions.R b/R/HelperFunctions.R
index 98b40d5..a13eb9d 100644
--- a/R/HelperFunctions.R
+++ b/R/HelperFunctions.R
@@ -65,7 +65,7 @@
     return()
   }
 
-  if(class(settings) == 'dechallengeRechallengeSettings'){
+  if(inherits(settings, 'dechallengeRechallengeSettings')){
     settings <- list(settings)
   }
 
diff --git a/R/RunCharacterization.R b/R/RunCharacterization.R
index df98e3c..0a03bb0 100644
--- a/R/RunCharacterization.R
+++ b/R/RunCharacterization.R
@@ -33,13 +33,13 @@ createCharacterizationSettings <- function(
     errorMessages = errorMessages
   )
 
-  if (class(timeToEventSettings) == "timeToEventSettings") {
+  if (inherits(timeToEventSettings, "timeToEventSettings")) {
     timeToEventSettings <- list(timeToEventSettings)
   }
-  if (class(dechallengeRechallengeSettings) == "dechallengeRechallengeSettings") {
+  if (inherits(dechallengeRechallengeSettings, "dechallengeRechallengeSettings")) {
     dechallengeRechallengeSettings <- list(dechallengeRechallengeSettings)
   }
-  if (class(aggregateCovariateSettings) == "aggregateCovariateSettings") {
+  if (inherits(aggregateCovariateSettings, "aggregateCovariateSettings")) {
     aggregateCovariateSettings <- list(aggregateCovariateSettings)
   }
 

From 9d974216c29579170f25766bc0cbc8c1f22a992f Mon Sep 17 00:00:00 2001
From: jreps <jreps@its.jnj.com>
Date: Wed, 15 Mar 2023 11:28:13 -0400
Subject: [PATCH 10/11] issue 22 fix

- adding code to address issue 22
- T is now restricted to first occurrence with a requirement of minPriorObservation days (a new input with default of 0)
- Includes characterization for T with O during and not during TAR plus T with O for the first time during and not during TAR
- added cohort_counts to the database and exported csvs that tell you how many patients are in allT, T, O, firstO, TnO, TnfirstO, TnOc and TnfirstOc
---
 R/AggregateCovariates.R                       |  23 +-
 R/HelperFunctions.R                           |  12 ++
 R/SaveLoad.R                                  |  35 +++-
 .../resultsDataModelSpecification.csv         | 196 +++++++++---------
 .../sql/sql_server/DropAggregateCovariate.sql |  12 ++
 inst/sql/sql_server/ResultTables.sql          |   8 +
 .../createTargetOutcomeCombinations.sql       | 188 ++++++++++++++++-
 man/createAggregateCovariateSettings.Rd       |   3 +
 tests/testthat/test-aggregateCovariate.R      |  16 +-
 9 files changed, 390 insertions(+), 103 deletions(-)

diff --git a/R/AggregateCovariates.R b/R/AggregateCovariates.R
index 0be09dd..02e17ac 100644
--- a/R/AggregateCovariates.R
+++ b/R/AggregateCovariates.R
@@ -18,6 +18,7 @@
 #'
 #' @param targetIds   A list of cohortIds for the target cohorts
 #' @param outcomeIds  A list of cohortIds for the outcome cohorts
+#' @param minPriorObservation The minimum time in the database a patient in the target cohorts must be observed prior to index
 #' @template timeAtRisk
 #' @param covariateSettings   An object created using \code{FeatureExtraction::createCovariateSettings}
 #'
@@ -28,6 +29,7 @@
 createAggregateCovariateSettings <- function(
   targetIds,
   outcomeIds,
+  minPriorObservation = 0,
   riskWindowStart = 1,
   startAnchor = 'cohort start',
   riskWindowEnd = 365,
@@ -57,19 +59,26 @@ createAggregateCovariateSettings <- function(
     endAnchor = endAnchor,
     errorMessages = errorMessages
   )
-  
+
   # check covariateSettings
   .checkCovariateSettings(
     covariateSettings = covariateSettings,
     errorMessages = errorMessages
   )
 
+  # check minPriorObservation
+  .checkMinPriorObservation(
+    minPriorObservation = minPriorObservation,
+    errorMessages = errorMessages
+  )
+
   checkmate::reportAssertions(errorMessages)
 
   # create list
   result <- list(
     targetIds = targetIds,
     outcomeIds = outcomeIds,
+    minPriorObservation = minPriorObservation,
     riskWindowStart = riskWindowStart,
     startAnchor = startAnchor,
     riskWindowEnd = riskWindowEnd ,
@@ -126,6 +135,7 @@ computeAggregateCovariateAnalyses <- function(
   createCohortsOfInterest(
     connection = connection,
     dbms = connectionDetails$dbms,
+    cdmDatabaseSchema = cdmDatabaseSchema,
     aggregateCovariateSettings,
     targetDatabaseSchema,
     targetTable,
@@ -135,16 +145,16 @@ computeAggregateCovariateAnalyses <- function(
   )
 
   ## get counts
-  sql <- 'select cohort_definition_id, count(*) N 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
+    sql = sql,
+    snakeCaseToCamelCase = T,
   )
-  #print(counts) # testing
 
   message("Computing aggregate covariate results")
 
@@ -159,6 +169,8 @@ computeAggregateCovariateAnalyses <- function(
     cdmVersion = cdmVersion,
     aggregated = T
   )
+  # adding counts as a new table
+  result$cohortCounts <- counts
 
   # add databaseId and runId to each table in results
   # could add settings table with this and just have setting id
@@ -234,6 +246,7 @@ computeAggregateCovariateAnalyses <- function(
 
 createCohortsOfInterest <- function(
   connection,
+  cdmDatabaseSchema,
   dbms,
   aggregateCovariateSettings,
   targetDatabaseSchema,
@@ -247,6 +260,7 @@ createCohortsOfInterest <- function(
     sqlFilename = "createTargetOutcomeCombinations.sql",
     packageName = "Characterization",
     dbms = dbms,
+    cdm_database_schema = cdmDatabaseSchema,
     tempEmulationSchema = tempEmulationSchema,
     target_database_schema = targetDatabaseSchema,
     target_table = targetTable,
@@ -254,6 +268,7 @@ createCohortsOfInterest <- function(
     outcome_table = outcomeTable,
     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',
diff --git a/R/HelperFunctions.R b/R/HelperFunctions.R
index a13eb9d..311e6bb 100644
--- a/R/HelperFunctions.R
+++ b/R/HelperFunctions.R
@@ -241,3 +241,15 @@
     add = errorMessages
   )
 }
+
+.checkMinPriorObservation <- function(
+    minPriorObservation,
+  errorMessages
+) {
+  checkmate::assertCount(
+    x = minPriorObservation,
+    null.ok = F,
+    .var.name = 'minPriorObservation',
+    add = errorMessages
+  )
+}
diff --git a/R/SaveLoad.R b/R/SaveLoad.R
index 73b5ca6..1720eee 100644
--- a/R/SaveLoad.R
+++ b/R/SaveLoad.R
@@ -404,6 +404,38 @@ exportAggregateCovariateToCsv <- function(
 
     }
   )
+  # cohort details
+  Andromeda::batchApply(
+    tbl = result$cohortCounts,
+    fun = function(x) {
+
+      append <- file.exists(
+        file.path(
+          saveDirectory,
+          "cohort_counts.csv"
+        )
+      )
+
+      dat <- as.data.frame(
+        x %>%
+          dplyr::collect()
+      )
+
+      colnames(dat) <- SqlRender::camelCaseToSnakeCase(
+        string = colnames(dat)
+      )
+
+      readr::write_csv(
+        x = dat,
+        file = file.path(
+          saveDirectory,
+          "cohort_counts.csv"
+        ),
+        append = append
+      )
+
+    }
+  )
 
   # cohort details
   Andromeda::batchApply(
@@ -577,7 +609,8 @@ exportAggregateCovariateToCsv <- function(
         "analysis_ref.csv",
         "covariate_ref.csv",
         "covariates.csv",
-        "covariates_continuous.csv"
+        "covariates_continuous.csv",
+        "cohort_counts.csv"
       )
     )
   )
diff --git a/inst/settings/resultsDataModelSpecification.csv b/inst/settings/resultsDataModelSpecification.csv
index f960897..29beb0a 100644
--- a/inst/settings/resultsDataModelSpecification.csv
+++ b/inst/settings/resultsDataModelSpecification.csv
@@ -1,94 +1,102 @@
-table_name,column_name,data_type,is_required,primary_key,empty_is_na,min_cell_count,description
-time_to_event,database_id,varchar(100),Y,Y,N,N,The database identifier
-time_to_event,target_cohort_definition_id,bigint,Y,Y,N,N,The cohort definition id for the target cohort
-time_to_event,outcome_cohort_definition_id,bigint,Y,Y,N,N,The cohort definition id for the outcome cohort
-time_to_event,outcome_type,varchar(100),Y,Y,N,N,Is the outvome a first occurrence or repeat
-time_to_event,target_outcome_type,varchar(40),Y,Y,N,N,When does the outcome occur relative to target
-time_to_event,time_to_event,int,Y,N,N,N,The time (in days) from target index to outcome start
-time_to_event,num_events,int,Y,N,N,N,Number of events that occur during the specified time to event
-time_to_event,time_scale,varchar(20),Y,N,N,N,time scale for the number of events
-rechallenge_fail_case_series,database_id,varchar(100),Y,Y,N,N,The database identifier
-rechallenge_fail_case_series,dechallenge_stop_interval,int,Y,N,N,N,The time period that É
-rechallenge_fail_case_series,dechallenge_evaluation_window,int,Y,N,N,N,The time period that É
-rechallenge_fail_case_series,target_cohort_definition_id,bigint,Y,Y,N,N,The cohort definition id for the target cohort
-rechallenge_fail_case_series,outcome_cohort_definition_id,bigint,Y,Y,N,N,The cohort definition id for the outcome cohort
-rechallenge_fail_case_series,person_key,int,Y,Y,N,N,The dense rank for the patient (an identifier that is not the same as the database)
-rechallenge_fail_case_series,subject_id,bigint,Y,N,N,N,The person identifier for the failed case series (optional)
-rechallenge_fail_case_series,dechallenge_exposure_number,int,Y,N,N,N,The number of times a dechallenge has occurred
-rechallenge_fail_case_series,dechallenge_exposure_start_date_offset,int,Y,N,N,N,The offset for the dechallenge start (number of days after index)
-rechallenge_fail_case_series,dechallenge_exposure_end_date_offset,int,Y,N,N,N,The offset for the dechallenge end (number of days after index)
-rechallenge_fail_case_series,dechallenge_outcome_number,int,Y,N,N,N,The number of times an outcome has occurred during the dechallenge
-rechallenge_fail_case_series,dechallenge_outcome_start_date_offset,int,Y,N,N,N,The offset for the outcome start (number of days after index)
-rechallenge_fail_case_series,rechallenge_exposure_number,int,Y,N,N,N,The number of times a rechallenge exposure has occurred
-rechallenge_fail_case_series,rechallenge_exposure_start_date_offset,int,Y,N,N,N,The offset for the rechallenge start (number of days after index)
-rechallenge_fail_case_series,rechallenge_exposure_end_date_offset,int,Y,N,N,N,The offset for the rechallenge end (number of days after index)
-rechallenge_fail_case_series,rechallenge_outcome_number,int,Y,N,N,N,The number of times the outcome has occurred during the rechallenge
-rechallenge_fail_case_series,rechallenge_outcome_start_date_offset,int,Y,N,N,N,The offset for the outcome start (number of days after index)
-dechallenge_rechallenge,database_id,varchar(100),Y,Y,N,N,The database identifier
-dechallenge_rechallenge,dechallenge_stop_interval,int,Y,Y,N,N,The dechallenge stop interval
-dechallenge_rechallenge,dechallenge_evaluation_window,int,Y,Y,N,N,The dechallenge evaluation window
-dechallenge_rechallenge,target_cohort_definition_id,bigint,Y,Y,N,N,The cohort definition id for the target cohort
-dechallenge_rechallenge,outcome_cohort_definition_id,bigint,Y,Y,N,N,The cohort definition id for the outcome cohort
-dechallenge_rechallenge,num_exposure_eras,int,Y,N,N,N,The number of exposure eras
-dechallenge_rechallenge,num_persons_exposed,int,Y,N,N,N,The number of persons exposed
-dechallenge_rechallenge,num_cases,int,Y,N,N,N,The number of cases
-dechallenge_rechallenge,dechallenge_attempt,int,Y,N,N,N,The number of dechallenge attempts
-dechallenge_rechallenge,dechallenge_fail,int,Y,N,N,N,The dechallenge fail count
-dechallenge_rechallenge,dechallenge_success,int,Y,N,N,N,The dechallenge success count
-dechallenge_rechallenge,rechallenge_attempt,int,Y,N,N,N,The rechallenge attempt count
-dechallenge_rechallenge,rechallenge_fail,int,Y,N,N,N,The rechallenge fail count
-dechallenge_rechallenge,rechallenge_success,int,Y,N,N,N,The rechallenge success count
-dechallenge_rechallenge,pct_dechallenge_attempt,float,Y,N,N,N,The percentage of dechallenge attempts
-dechallenge_rechallenge,pct_dechallenge_success,float,Y,N,N,N,The percentage of dechallenge success
-dechallenge_rechallenge,pct_dechallenge_fail,float,Y,N,N,N,The percentage of dechallenge fails
-dechallenge_rechallenge,pct_rechallenge_attempt,float,Y,N,N,N,The percentage of rechallenge attempts
-dechallenge_rechallenge,pct_rechallenge_success,float,Y,N,N,N,The percentage of rechallenge success
-dechallenge_rechallenge,pct_rechallenge_fail,float,Y,N,N,N,The percentage of rechallenge fails
-analysis_ref,database_id,varchar(100),Y,Y,N,N,The database identifier
-analysis_ref,run_id,int,Y,Y,N,N,The run identifier
-analysis_ref,analysis_id,int,Y,Y,N,N,The analysis identifier
-analysis_ref,analysis_name,varchar,Y,N,N,N,The analysis name
-analysis_ref,domain_id,varchar,Y,N,N,N,The domain id
-analysis_ref,start_day,int,Y,N,N,N,The start day
-analysis_ref,end_day,int,Y,N,N,N,The end day
-analysis_ref,is_binary,varchar(1),Y,N,N,N,Is this a binary analysis
-analysis_ref,missing_means_zero,varchar(1),Y,N,N,N,Missing means zero
-covariate_ref,database_id,varchar(100),Y,Y,N,N,The database identifier
-covariate_ref,run_id,int,Y,Y,N,N,The run identifier
-covariate_ref,covariate_id,bigint,Y,Y,N,N,The covariate identifier
-covariate_ref,covariate_name,varchar,Y,N,N,N,The covariate name
-covariate_ref,analysis_id,int,Y,N,N,N,The analysis identifier
-covariate_ref,concept_id,bigint,Y,N,N,N,The concept identifier
-covariates,database_id,varchar(100),Y,Y,N,N,The database identifier
-covariates,run_id,int,Y,Y,N,N,The run identifier
-covariates,cohort_definition_id,int,Y,Y,N,N,The cohort definition id
-covariates,covariate_id,bigint,Y,Y,N,N,The covaraite id
-covariates,sum_value,int,Y,N,N,N,The sum value
-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,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
-covariates_continuous,average_value,float,Y,N,N,N,The average value
-covariates_continuous,standard_deviation,float,Y,N,N,N,The standard devidation
-covariates_continuous,median_value,float,Y,N,N,N,The median value
-covariates_continuous,p_10_value,float,Y,N,N,N,The 10th percentile
-covariates_continuous,p_25_value,float,Y,N,N,N,The 25th percentile
-covariates_continuous,p_75_value,float,Y,N,N,N,The 75th percentile
-covariates_continuous,p_90_value,float,Y,N,N,N,The 90th percentile
-settings,run_id,int,Y,Y,N,N,The run identifier
-settings,database_id,varchar(100),Y,Y,N,N,The database identifier
-settings,covariate_setting_json,varchar,Y,N,N,N,The covariate settings JSON
-settings,risk_window_start,int,Y,N,N,N,The risk window start
-settings,risk_window_end,int,Y,N,N,N,The risk window end
-settings,start_anchor,varchar(15),Y,N,N,N,The start anchor
-settings,end_anchor,varchar(15),Y,N,N,N,The end anchor
-cohort_details,run_id,int,Y,Y,N,N,The run identifier
-cohort_details,database_id,varchar(100),Y,Y,N,N,The database identifier
-cohort_details,cohort_definition_id,int,Y,N,N,N,The study cohort id
-cohort_details,cohort_type,varchar(10),Y,N,N,N,The cohort type
-cohort_details,target_cohort_id,int,Y,N,N,N,The target cohort id
-cohort_details,outcome_cohort_id,int,Y,N,N,N,The outcome cohort id
+table_name,column_name,data_type,is_required,primary_key,empty_is_na,min_cell_count,description
+time_to_event,database_id,varchar(100),Y,Y,N,N,The database identifier
+time_to_event,target_cohort_definition_id,bigint,Y,Y,N,N,The cohort definition id for the target cohort
+time_to_event,outcome_cohort_definition_id,bigint,Y,Y,N,N,The cohort definition id for the outcome cohort
+time_to_event,outcome_type,varchar(100),Y,Y,N,N,Is the outvome a first occurrence or repeat
+time_to_event,target_outcome_type,varchar(40),Y,Y,N,N,When does the outcome occur relative to target
+time_to_event,time_to_event,int,Y,N,N,N,The time (in days) from target index to outcome start
+time_to_event,num_events,int,Y,N,N,N,Number of events that occur during the specified time to event
+time_to_event,time_scale,varchar(20),Y,N,N,N,time scale for the number of events
+rechallenge_fail_case_series,database_id,varchar(100),Y,Y,N,N,The database identifier
+rechallenge_fail_case_series,dechallenge_stop_interval,int,Y,N,N,N,The time period that É
+rechallenge_fail_case_series,dechallenge_evaluation_window,int,Y,N,N,N,The time period that É
+rechallenge_fail_case_series,target_cohort_definition_id,bigint,Y,Y,N,N,The cohort definition id for the target cohort
+rechallenge_fail_case_series,outcome_cohort_definition_id,bigint,Y,Y,N,N,The cohort definition id for the outcome cohort
+rechallenge_fail_case_series,person_key,int,Y,Y,N,N,The dense rank for the patient (an identifier that is not the same as the database)
+rechallenge_fail_case_series,subject_id,bigint,Y,N,N,N,The person identifier for the failed case series (optional)
+rechallenge_fail_case_series,dechallenge_exposure_number,int,Y,N,N,N,The number of times a dechallenge has occurred
+rechallenge_fail_case_series,dechallenge_exposure_start_date_offset,int,Y,N,N,N,The offset for the dechallenge start (number of days after index)
+rechallenge_fail_case_series,dechallenge_exposure_end_date_offset,int,Y,N,N,N,The offset for the dechallenge end (number of days after index)
+rechallenge_fail_case_series,dechallenge_outcome_number,int,Y,N,N,N,The number of times an outcome has occurred during the dechallenge
+rechallenge_fail_case_series,dechallenge_outcome_start_date_offset,int,Y,N,N,N,The offset for the outcome start (number of days after index)
+rechallenge_fail_case_series,rechallenge_exposure_number,int,Y,N,N,N,The number of times a rechallenge exposure has occurred
+rechallenge_fail_case_series,rechallenge_exposure_start_date_offset,int,Y,N,N,N,The offset for the rechallenge start (number of days after index)
+rechallenge_fail_case_series,rechallenge_exposure_end_date_offset,int,Y,N,N,N,The offset for the rechallenge end (number of days after index)
+rechallenge_fail_case_series,rechallenge_outcome_number,int,Y,N,N,N,The number of times the outcome has occurred during the rechallenge
+rechallenge_fail_case_series,rechallenge_outcome_start_date_offset,int,Y,N,N,N,The offset for the outcome start (number of days after index)
+dechallenge_rechallenge,database_id,varchar(100),Y,Y,N,N,The database identifier
+dechallenge_rechallenge,dechallenge_stop_interval,int,Y,Y,N,N,The dechallenge stop interval
+dechallenge_rechallenge,dechallenge_evaluation_window,int,Y,Y,N,N,The dechallenge evaluation window
+dechallenge_rechallenge,target_cohort_definition_id,bigint,Y,Y,N,N,The cohort definition id for the target cohort
+dechallenge_rechallenge,outcome_cohort_definition_id,bigint,Y,Y,N,N,The cohort definition id for the outcome cohort
+dechallenge_rechallenge,num_exposure_eras,int,Y,N,N,N,The number of exposure eras
+dechallenge_rechallenge,num_persons_exposed,int,Y,N,N,N,The number of persons exposed
+dechallenge_rechallenge,num_cases,int,Y,N,N,N,The number of cases
+dechallenge_rechallenge,dechallenge_attempt,int,Y,N,N,N,The number of dechallenge attempts
+dechallenge_rechallenge,dechallenge_fail,int,Y,N,N,N,The dechallenge fail count
+dechallenge_rechallenge,dechallenge_success,int,Y,N,N,N,The dechallenge success count
+dechallenge_rechallenge,rechallenge_attempt,int,Y,N,N,N,The rechallenge attempt count
+dechallenge_rechallenge,rechallenge_fail,int,Y,N,N,N,The rechallenge fail count
+dechallenge_rechallenge,rechallenge_success,int,Y,N,N,N,The rechallenge success count
+dechallenge_rechallenge,pct_dechallenge_attempt,float,Y,N,N,N,The percentage of dechallenge attempts
+dechallenge_rechallenge,pct_dechallenge_success,float,Y,N,N,N,The percentage of dechallenge success
+dechallenge_rechallenge,pct_dechallenge_fail,float,Y,N,N,N,The percentage of dechallenge fails
+dechallenge_rechallenge,pct_rechallenge_attempt,float,Y,N,N,N,The percentage of rechallenge attempts
+dechallenge_rechallenge,pct_rechallenge_success,float,Y,N,N,N,The percentage of rechallenge success
+dechallenge_rechallenge,pct_rechallenge_fail,float,Y,N,N,N,The percentage of rechallenge fails
+analysis_ref,database_id,varchar(100),Y,Y,N,N,The database identifier
+analysis_ref,run_id,int,Y,Y,N,N,The run identifier
+analysis_ref,analysis_id,int,Y,Y,N,N,The analysis identifier
+analysis_ref,analysis_name,varchar,Y,N,N,N,The analysis name
+analysis_ref,domain_id,varchar,Y,N,N,N,The domain id
+analysis_ref,start_day,int,Y,N,N,N,The start day
+analysis_ref,end_day,int,Y,N,N,N,The end day
+analysis_ref,is_binary,varchar(1),Y,N,N,N,Is this a binary analysis
+analysis_ref,missing_means_zero,varchar(1),Y,N,N,N,Missing means zero
+covariate_ref,database_id,varchar(100),Y,Y,N,N,The database identifier
+covariate_ref,run_id,int,Y,Y,N,N,The run identifier
+covariate_ref,covariate_id,bigint,Y,Y,N,N,The covariate identifier
+covariate_ref,covariate_name,varchar,Y,N,N,N,The covariate name
+covariate_ref,analysis_id,int,Y,N,N,N,The analysis identifier
+covariate_ref,concept_id,bigint,Y,N,N,N,The concept identifier
+covariates,database_id,varchar(100),Y,Y,N,N,The database identifier
+covariates,run_id,int,Y,Y,N,N,The run identifier
+covariates,cohort_definition_id,int,Y,Y,N,N,The cohort definition id
+covariates,covariate_id,bigint,Y,Y,N,N,The covaraite id
+covariates,sum_value,int,Y,N,N,N,The sum value
+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,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
+covariates_continuous,average_value,float,Y,N,N,N,The average value
+covariates_continuous,standard_deviation,float,Y,N,N,N,The standard devidation
+covariates_continuous,median_value,float,Y,N,N,N,The median value
+covariates_continuous,p_10_value,float,Y,N,N,N,The 10th percentile
+covariates_continuous,p_25_value,float,Y,N,N,N,The 25th percentile
+covariates_continuous,p_75_value,float,Y,N,N,N,The 75th percentile
+covariates_continuous,p_90_value,float,Y,N,N,N,The 90th percentile
+settings,run_id,int,Y,Y,N,N,The run identifier
+settings,database_id,varchar(100),Y,Y,N,N,The database identifier
+settings,covariate_setting_json,varchar,Y,N,N,N,The covariate settings JSON
+settings,risk_window_start,int,Y,N,N,N,The risk window start
+settings,risk_window_end,int,Y,N,N,N,The risk window end
+settings,start_anchor,varchar(15),Y,N,N,N,The start anchor
+settings,end_anchor,varchar(15),Y,N,N,N,The end anchor
+cohort_details,run_id,int,Y,Y,N,N,The run identifier
+cohort_details,database_id,varchar(100),Y,Y,N,N,The database identifier
+cohort_details,cohort_definition_id,int,Y,N,N,N,The study cohort id
+cohort_details,cohort_type,varchar(10),Y,N,N,N,The cohort type
+cohort_details,target_cohort_id,int,Y,N,N,N,The target cohort id
+cohort_details,outcome_cohort_id,int,Y,N,N,N,The outcome cohort id
+cohort_counts,run_id,int,Y,Y,N,N,The run identifier
+cohort_counts,database_id,varchar(100),Y,Y,N,N,The database identifier
+cohort_counts,cohort_definition_id,int,Y,N,N,N,The study cohort id
+cohort_counts,row_count,int,Y,N,N,N,The number of rows in each cohort
+cohort_counts,person_count,int,Y,N,N,N,The number of distinct people in each cohort
+
+
+
diff --git a/inst/sql/sql_server/DropAggregateCovariate.sql b/inst/sql/sql_server/DropAggregateCovariate.sql
index fb46e83..b319cff 100644
--- a/inst/sql/sql_server/DropAggregateCovariate.sql
+++ b/inst/sql/sql_server/DropAggregateCovariate.sql
@@ -1,20 +1,32 @@
 -- clean up by removing the temp tables
 
+TRUNCATE TABLE #targets_agg_all;
+DROP TABLE #targets_agg_all;
+
 TRUNCATE TABLE #targets_agg;
 DROP TABLE #targets_agg;
 
 TRUNCATE TABLE #outcomes_agg;
 DROP TABLE #outcomes_agg;
 
+TRUNCATE TABLE #outcomes_agg_first;
+DROP TABLE #outcomes_agg_first;
+
 TRUNCATE TABLE #cohort_details;
 DROP TABLE #cohort_details;
 
 TRUNCATE TABLE #target_with_outcome;
 DROP TABLE #target_with_outcome;
 
+TRUNCATE TABLE #target_outcome_f;
+DROP TABLE #target_outcome_f;
+
 TRUNCATE TABLE #target_nooutcome;
 DROP TABLE #target_nooutcome;
 
+TRUNCATE TABLE #target_noout_f;
+DROP TABLE #target_noout_f;
+
 TRUNCATE TABLE #agg_cohorts;
 DROP TABLE #agg_cohorts;
 
diff --git a/inst/sql/sql_server/ResultTables.sql b/inst/sql/sql_server/ResultTables.sql
index 95f47ae..663249e 100644
--- a/inst/sql/sql_server/ResultTables.sql
+++ b/inst/sql/sql_server/ResultTables.sql
@@ -121,3 +121,11 @@ CREATE TABLE @my_schema.@table_prefixcovariates_continuous (
     p_75_value float,
     p_90_value float
 );
+
+CREATE TABLE @my_schema.@table_prefixcohort_counts(
+    run_id int NOT NULL,
+    database_id varchar(100) NOT NULL,
+    cohort_definition_id int NOT NULL,
+    row_count int NOT NULL,
+    person_count int NOT NULL
+);
diff --git a/inst/sql/sql_server/createTargetOutcomeCombinations.sql b/inst/sql/sql_server/createTargetOutcomeCombinations.sql
index c354232..0ba0f12 100644
--- a/inst/sql/sql_server/createTargetOutcomeCombinations.sql
+++ b/inst/sql/sql_server/createTargetOutcomeCombinations.sql
@@ -1,9 +1,26 @@
 --need to know indication/target/outcome tuples
+drop table if exists #targets_agg_all;
+select * into #targets_agg_all
+from @target_database_schema.@target_table
+where cohort_definition_id in
+(@target_ids);
+
+-- first T with > minPrioObs
 drop table if exists #targets_agg;
 select * into #targets_agg
+from
+(select *,
+row_number() over(partition by subject_id, cohort_definition_id, cohort_start_date order by cohort_start_date asc) as rn
 from @target_database_schema.@target_table
 where cohort_definition_id in
-(@target_ids);
+(@target_ids)
+) temp_t
+inner join @cdm_database_schema.observation_period op
+on op.person_id = temp_t.subject_id
+and temp_t.cohort_start_date >= op.observation_period_start_date
+and temp_t.cohort_start_date <= op.observation_period_end_date
+where temp_t.rn = 1
+and datediff(day, op.observation_period_start_date, temp_t.cohort_start_date) >= @min_prior_observation;
 
 drop table if exists #outcomes_agg;
 select * into #outcomes_agg
@@ -11,6 +28,16 @@ from @outcome_database_schema.@outcome_table
 where cohort_definition_id in
 (@outcome_ids);
 
+-- first outcomes
+drop table if exists #outcomes_agg_first;
+select * into #outcomes_agg_first
+from (select *,
+row_number() over(partition by subject_id, cohort_definition_id, cohort_start_date order by cohort_start_date asc) as rn
+from #outcomes_agg
+) as o
+where o.rn = 1
+;
+
 -- create all the cohort details
 drop table if exists #cohort_details;
 
@@ -53,6 +80,39 @@ CROSS JOIN
 
 union
 
+select distinct
+t.cohort_definition_id as target_cohort_id,
+o.cohort_definition_id as outcome_cohort_id,
+'TnfirstO' as cohort_type
+from
+(select distinct cohort_definition_id from #targets_agg) as t
+CROSS JOIN
+(select distinct cohort_definition_id from #outcomes_agg) as o
+
+union
+
+select distinct
+t.cohort_definition_id as target_cohort_id,
+o.cohort_definition_id as outcome_cohort_id,
+'firstOnT' as cohort_type
+from
+(select distinct cohort_definition_id from #targets_agg) as t
+CROSS JOIN
+(select distinct cohort_definition_id from #outcomes_agg) as o
+
+union
+
+select distinct
+t.cohort_definition_id as target_cohort_id,
+o.cohort_definition_id as outcome_cohort_id,
+'TnfirstOc' as cohort_type
+from
+(select distinct cohort_definition_id from #targets_agg) as t
+CROSS JOIN
+(select distinct cohort_definition_id from #outcomes_agg) as o
+
+union
+
 select distinct
 t.cohort_definition_id as target_cohort_id,
 0 as outcome_cohort_id,
@@ -61,12 +121,29 @@ from (select distinct cohort_definition_id from #targets_agg) as t
 
 union
 
+select distinct
+t.cohort_definition_id as target_cohort_id,
+0 as outcome_cohort_id,
+'allT' as cohort_type
+from (select distinct cohort_definition_id from #targets_agg) as t
+
+union
+
 select distinct
 0 as target_cohort_id,
 o.cohort_definition_id as outcome_cohort_id,
 'O' as cohort_type
 from (select distinct cohort_definition_id from #outcomes_agg) as o
 
+union
+
+select distinct
+0 as target_cohort_id,
+o.cohort_definition_id as outcome_cohort_id,
+'firstO' as cohort_type
+from (select distinct cohort_definition_id from #outcomes_agg) as o
+
+
 ) temp;
 
 
@@ -92,6 +169,26 @@ and
 -- outcome starts (ends?) after TAR start
 o.cohort_start_date >= dateadd(day, @tar_start, t.@tar_start_anchor);
 
+-- TnfirstO
+drop table if exists #target_outcome_f;
+select
+t.subject_id,
+t.cohort_start_date,
+t.cohort_end_date,
+o.cohort_start_date as outcome_start_date,
+o.cohort_end_date as outcome_end_date,
+t.cohort_definition_id as target_cohort_id,
+o.cohort_definition_id as outcome_cohort_id
+into #target_outcome_f
+from #targets_agg t inner join #outcomes_agg_first o
+on t.subject_id = o.subject_id
+where
+-- outcome starts before TAR end
+o.cohort_start_date <= dateadd(day, @tar_end, t.@tar_end_anchor)
+and
+-- outcome starts (ends?) after TAR start
+o.cohort_start_date >= dateadd(day, @tar_start, t.@tar_start_anchor);
+
 
 -- 2) get all the people without the outcome in TAR
 drop table if exists #target_nooutcome;
@@ -111,6 +208,23 @@ and t.subject_id = two.subject_id
 and o.cohort_definition_id = two.outcome_cohort_id
 where two.subject_id IS NULL;
 
+drop table if exists #target_noout_f;
+select
+t.subject_id,
+t.cohort_start_date,
+t.cohort_end_date,
+t.cohort_definition_id as target_cohort_id,
+o.cohort_definition_id as outcome_cohort_id
+into #target_noout_f
+from #targets_agg t
+CROSS JOIN
+( select distinct cohort_definition_id from #outcomes_agg) o
+left outer join #target_outcome_f two
+on t.cohort_definition_id = two.target_cohort_id
+and t.subject_id = two.subject_id
+and o.cohort_definition_id = two.outcome_cohort_id
+where two.subject_id IS NULL;
+
 -- Final: select into #agg_cohorts
 
 select * into #agg_cohorts
@@ -132,6 +246,21 @@ and cd.cohort_type = 'TnO'
 
 union
 
+-- T with first O indexed at T
+
+select
+tno.subject_id,
+tno.cohort_start_date,
+tno.cohort_end_date,
+cd.cohort_definition_id
+from #target_outcome_f tno
+INNER JOIN #cohort_details cd
+on cd.target_cohort_id = tno.target_cohort_id
+and cd.outcome_cohort_id = tno.outcome_cohort_id
+and cd.cohort_type = 'TnfirstO'
+
+union
+
 -- T with O indexed at O
 
 select
@@ -143,7 +272,22 @@ from #target_with_outcome tno
 INNER JOIN #cohort_details cd
 on cd.target_cohort_id = tno.target_cohort_id
 and cd.outcome_cohort_id = tno.outcome_cohort_id
-and cd.cohort_type = 'TnOc'
+and cd.cohort_type = 'OnT'
+
+union
+
+-- T with first O indexed at O
+
+select
+tno.subject_id,
+tno.outcome_start_date as cohort_start_date,
+tno.outcome_end_date as cohort_end_date,
+cd.cohort_definition_id
+from #target_outcome_f tno
+INNER JOIN #cohort_details cd
+on cd.target_cohort_id = tno.target_cohort_id
+and cd.outcome_cohort_id = tno.outcome_cohort_id
+and cd.cohort_type = 'firstOnT'
 
 union
 
@@ -162,6 +306,21 @@ and cd.cohort_type = 'TnOc'
 
 union
 
+-- T without first O
+
+select
+tnoc.subject_id,
+tnoc.cohort_start_date,
+tnoc.cohort_end_date,
+cd.cohort_definition_id
+from #target_noout_f tnoc
+INNER JOIN #cohort_details cd
+on cd.target_cohort_id = tnoc.target_cohort_id
+and cd.outcome_cohort_id = tnoc.outcome_cohort_id
+and cd.cohort_type = 'TnfirstOc'
+
+union
+
 -- Ts and Os
 
 select distinct * from (
@@ -178,6 +337,18 @@ and cd.cohort_type = 'T'
 
 union
 
+select
+t.subject_id,
+t.cohort_start_date,
+t.cohort_end_date,
+cd.cohort_definition_id
+from #targets_agg_all as t
+INNER JOIN #cohort_details cd
+on cd.target_cohort_id = t.cohort_definition_id
+and cd.cohort_type = 'allT'
+
+union
+
 select
 o.subject_id,
 o.cohort_start_date,
@@ -187,6 +358,19 @@ from #outcomes_agg as o
 INNER JOIN #cohort_details cd
 on cd.outcome_cohort_id = o.cohort_definition_id
 and cd.cohort_type = 'O'
+
+union
+
+select
+o.subject_id,
+o.cohort_start_date,
+o.cohort_end_date,
+cd.cohort_definition_id
+from #outcomes_agg_first as o
+INNER JOIN #cohort_details cd
+on cd.outcome_cohort_id = o.cohort_definition_id
+and cd.cohort_type = 'firstO'
+
 ) temp_ts
 
 ) temp_ts2;
diff --git a/man/createAggregateCovariateSettings.Rd b/man/createAggregateCovariateSettings.Rd
index 76f7f1c..aed6f80 100644
--- a/man/createAggregateCovariateSettings.Rd
+++ b/man/createAggregateCovariateSettings.Rd
@@ -7,6 +7,7 @@
 createAggregateCovariateSettings(
   targetIds,
   outcomeIds,
+  minPriorObservation = 0,
   riskWindowStart = 1,
   startAnchor = "cohort start",
   riskWindowEnd = 365,
@@ -19,6 +20,8 @@ createAggregateCovariateSettings(
 
 \item{outcomeIds}{A list of cohortIds for the outcome cohorts}
 
+\item{minPriorObservation}{The minimum time in the database a patient in the target cohorts must be observed prior to index}
+
 \item{riskWindowStart}{The start of the risk window (in days) relative to the `startAnchor`.}
 
 \item{startAnchor}{The anchor point for the start of the risk window. Can be `"cohort start"`
diff --git a/tests/testthat/test-aggregateCovariate.R b/tests/testthat/test-aggregateCovariate.R
index 9a2423d..6a35300 100644
--- a/tests/testthat/test-aggregateCovariate.R
+++ b/tests/testthat/test-aggregateCovariate.R
@@ -15,6 +15,7 @@ test_that("createAggregateCovariateSettings", {
   res <- createAggregateCovariateSettings(
     targetIds = targetIds,
     outcomeIds = outcomeIds,
+    minPriorObservation = 10,
     riskWindowStart = 1, startAnchor = "cohort start",
     riskWindowEnd = 365, endAnchor = "cohort start",
     covariateSettings = covariateSettings
@@ -28,6 +29,11 @@ test_that("createAggregateCovariateSettings", {
     res$covariateSettings,
     covariateSettings
   )
+
+  testthat::expect_equal(
+    res$minPriorObservation,
+    10
+  )
 })
 
 test_that("computeAggregateCovariateAnalyses", {
@@ -42,6 +48,7 @@ test_that("computeAggregateCovariateAnalyses", {
   res <- createAggregateCovariateSettings(
     targetIds = targetIds,
     outcomeIds = outcomeIds,
+    minPriorObservation = 30,
     riskWindowStart = 1, startAnchor = "cohort start",
     riskWindowEnd = 5 * 365, endAnchor = "cohort start",
     covariateSettings = covariateSettings
@@ -59,7 +66,7 @@ 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) * 3 + length(res$targetIds) + length(res$outcomeIds))
+  <= length(res$targetIds) * length(res$outcomeIds) * 6 + length(res$targetIds)*2 + length(res$outcomeIds)*2)
   testthat::expect_true(
     sum(names(agc) %in% c(
       "analysisRef",
@@ -71,6 +78,11 @@ test_that("computeAggregateCovariateAnalyses", {
     )) == 6
   )
 
+  testthat::expect_true(
+    nrow(as.data.frame(agc$cohortDetails)) ==
+    nrow(as.data.frame(agc$cohortCounts))
+  )
+
   # check cohortDetails
   testthat::expect_true(
     length(unique(as.data.frame(agc$cohortDetails)$cohortDefinitionId)) ==
@@ -78,7 +90,7 @@ test_that("computeAggregateCovariateAnalyses", {
   )
 
   testthat::expect_true(
-    nrow(as.data.frame(agc$cohortDetails)) == 13 # 4 T/Os, 3 TnO, 3 TnOc, 3 OnT
+    nrow(as.data.frame(agc$cohortDetails)) == 26 # 8 T/Os, 6 TnO, 6 TnOc, 6 OnT
   )
 
   # test saving/loading

From 2042123ae97da248b5cfa06f3c4a62544e4dac58 Mon Sep 17 00:00:00 2001
From: jreps <jreps@its.jnj.com>
Date: Wed, 15 Mar 2023 12:48:09 -0400
Subject: [PATCH 11/11] preparing new release

- updating news
- updating website
- updating description
---
 DESCRIPTION                                   |    4 +-
 NEWS.md                                       |    7 +
 _pkgdown.yml                                  |    6 +-
 docs/404.html                                 |    4 +-
 docs/articles/InstallationGuide.html          |   13 +-
 .../UsingCharacterizationPackage.html         | 2429 ++++++++++++++---
 docs/articles/index.html                      |    4 +-
 docs/authors.html                             |    8 +-
 docs/index.html                               |   25 +-
 docs/news/index.html                          |    9 +-
 docs/pkgdown.yml                              |    4 +-
 docs/pull_request_template.html               |    4 +-
 docs/reference/Characterization-package.html  |    7 +-
 .../computeAggregateCovariateAnalyses.html    |    4 +-
 ...computeDechallengeRechallengeAnalyses.html |    4 +-
 ...puteRechallengeFailCaseSeriesAnalyses.html |    4 +-
 .../reference/computeTimeToEventAnalyses.html |    4 +-
 .../createAggregateCovariateSettings.html     |    9 +-
 .../createCharacterizationSettings.html       |    4 +-
 .../createCharacterizationTables.html         |    4 +-
 .../createDechallengeRechallengeSettings.html |    4 +-
 docs/reference/createSqliteDatabase.html      |    4 +-
 docs/reference/createTimeToEventSettings.html |    4 +-
 .../exportAggregateCovariateToCsv.html        |    4 +-
 docs/reference/exportDatabaseToCsv.html       |    4 +-
 .../exportDechallengeRechallengeToCsv.html    |    4 +-
 .../exportRechallengeFailCaseSeriesToCsv.html |    4 +-
 docs/reference/exportTimeToEventToCsv.html    |    4 +-
 docs/reference/index.html                     |   12 +-
 .../loadAggregateCovariateAnalyses.html       |   10 +-
 .../loadCharacterizationSettings.html         |    8 +-
 .../loadDechallengeRechallengeAnalyses.html   |   10 +-
 ...loadRechallengeFailCaseSeriesAnalyses.html |   10 +-
 docs/reference/loadTimeToEventAnalyses.html   |   10 +-
 .../runCharacterizationAnalyses.html          |    4 +-
 .../saveAggregateCovariateAnalyses.html       |   10 +-
 .../saveCharacterizationSettings.html         |    8 +-
 .../saveDechallengeRechallengeAnalyses.html   |   10 +-
 ...saveRechallengeFailCaseSeriesAnalyses.html |   10 +-
 docs/reference/saveTimeToEventAnalyses.html   |   10 +-
 docs/reference/viewCharacterization.html      |  128 +
 docs/sitemap.xml                              |    3 +
 42 files changed, 2339 insertions(+), 493 deletions(-)
 create mode 100644 docs/reference/viewCharacterization.html

diff --git a/DESCRIPTION b/DESCRIPTION
index 40270bb..59aa8d5 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: Characterization
 Type: Package
 Title: Characterizations of Cohorts
-Version: 0.0.6
-Date: 2023-02-13
+Version: 0.1.0
+Date: 2023-03-13
 Authors@R: c(
 	person("Jenna", "Reps", , "reps@ohdsi.org", role = c("aut", "cre")),
 	person("Patrick", "Ryan", , "ryan@ohdsi.org", role = c("aut"))
diff --git a/NEWS.md b/NEWS.md
index dc98ade..79c5acd 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,10 @@
+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 shiny app
+
+
 Characterization 0.0.1
 ======================
 
diff --git a/_pkgdown.yml b/_pkgdown.yml
index 89c427c..0549e21 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -87,6 +87,10 @@ reference:
       - createSqliteDatabase
       - createCharacterizationTables
       - exportDatabaseToCsv
-
+  - title: "Shiny App"
+    desc: >
+      Functions to interactively exlore the results from runCharacterizationAnalyses().
+    contents:
+      - viewCharacterization
 
 
diff --git a/docs/404.html b/docs/404.html
index 60042e4..20886a8 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="">0.0.4</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.0</span>
       </span>
     </div>
 
@@ -115,7 +115,7 @@ <h1>Page not found (404)</h1>
 
 <div class="pkgdown">
   <p></p>
-<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
       </footer>
diff --git a/docs/articles/InstallationGuide.html b/docs/articles/InstallationGuide.html
index fc35bfb..a2b2c58 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="">0.0.4</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.0</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">2022-12-16</h4>
+            <h4 data-toc-skip class="date">2023-03-15</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>
@@ -107,7 +107,7 @@ <h4 data-toc-skip class="date">2022-12-16</h4>
     
 <!--
 %\VignetteEngine{knitr}
-%\VignetteIndexEntry{Installation guide}
+%\VignetteIndexEntry{Installation_guide}
 -->
 <div class="section level2">
 <h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
@@ -163,7 +163,6 @@ <h3 id="installing-characterization-using-remotes">Installing Characterization u
 <p>To install using <code>remotes</code> run:</p>
 <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"remotes"</span><span class="op">)</span></span>
-<span><span class="fu">remotes</span><span class="fu">::</span><span class="fu"><a href="https://remotes.r-lib.org/reference/install_github.html" class="external-link">install_github</a></span><span class="op">(</span><span class="st">"OHDSI/FeatureExtraction"</span><span class="op">)</span></span>
 <span><span class="fu">remotes</span><span class="fu">::</span><span class="fu"><a href="https://remotes.r-lib.org/reference/install_github.html" class="external-link">install_github</a></span><span class="op">(</span><span class="st">"OHDSI/Characterization"</span><span class="op">)</span></span></code></pre></div>
 <p>When installing make sure to close any other Rstudio sessions that
 are using <code>Characterization</code> or any dependency. Keeping
@@ -199,7 +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 (2022). _Characterization: Characterizations of</span></span>
+<span><span class="co">##   Reps J, Ryan P (2023). _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>
@@ -208,7 +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 = {2022},</span></span>
+<span><span class="co">##     year = {2023},</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>
@@ -231,7 +230,7 @@ <h2 id="acknowledgments">Acknowledgments<a class="anchor" aria-label="anchor" hr
 
 <div class="pkgdown">
   <p></p>
-<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
       </footer>
diff --git a/docs/articles/UsingCharacterizationPackage.html b/docs/articles/UsingCharacterizationPackage.html
index 66e5172..c2be504 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="">0.0.4</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.0</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">2022-12-16</h4>
+            <h4 data-toc-skip class="date">2023-03-15</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>
@@ -108,7 +108,7 @@ <h4 data-toc-skip class="date">2022-12-16</h4>
     
 <!--
 %\VignetteEngine{knitr}
-%\VignetteIndexEntry{Installation guide}
+%\VignetteIndexEntry{Using_Characterization_Package}
 -->
 <div class="section level2">
 <h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
@@ -165,28 +165,28 @@ <h2 id="setup">Setup<a class="anchor" aria-label="anchor" href="#setup"></a>
   |                                                                      |   0%
   |                                                                            
   |======================================================================| 100%</code></pre>
-<pre><code><span><span class="co">## Executing SQL took 0.00556 secs</span></span></code></pre>
+<pre><code><span><span class="co">## Executing SQL took 0.00634 secs</span></span></code></pre>
 <pre><code>## Creating cohort: Diclofenac
 ## 
   |                                                                            
   |                                                                      |   0%
   |                                                                            
   |======================================================================| 100%</code></pre>
-<pre><code><span><span class="co">## Executing SQL took 0.00483 secs</span></span></code></pre>
+<pre><code><span><span class="co">## Executing SQL took 0.00962 secs</span></span></code></pre>
 <pre><code>## Creating cohort: GiBleed
 ## 
   |                                                                            
   |                                                                      |   0%
   |                                                                            
   |======================================================================| 100%</code></pre>
-<pre><code><span><span class="co">## Executing SQL took 0.0104 secs</span></span></code></pre>
+<pre><code><span><span class="co">## Executing SQL took 0.0088 secs</span></span></code></pre>
 <pre><code>## Creating cohort: NSAIDs
 ## 
   |                                                                            
   |                                                                      |   0%
   |                                                                            
   |======================================================================| 100%</code></pre>
-<pre><code><span><span class="co">## Executing SQL took 0.0512 secs</span></span></code></pre>
+<pre><code><span><span class="co">## Executing SQL took 0.0492 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>
@@ -332,16 +332,16 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 1
 </td>
 <td style="text-align:right;">
-100000
+1
 </td>
 <td style="text-align:right;">
 8507001
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 <td style="text-align:right;">
-914
+237
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 <td style="text-align:right;">
-0.4956616
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 <tr>
@@ -352,16 +352,16 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 1
 </td>
 <td style="text-align:right;">
-100000
+1
 </td>
 <td style="text-align:right;">
 8532001
 </td>
 <td style="text-align:right;">
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-0.5043384
+0.5052192
 </td>
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 <tr>
@@ -372,7 +372,7 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 1
 </td>
 <td style="text-align:right;">
-100031
+2
 </td>
 <td style="text-align:right;">
 8507001
@@ -392,7 +392,7 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 1
 </td>
 <td style="text-align:right;">
-100031
+2
 </td>
 <td style="text-align:right;">
 8532001
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 1
 </td>
 <td style="text-align:right;">
-100032
+3
 </td>
 <td style="text-align:right;">
 8507001
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+57
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 <td style="text-align:right;">
-0.4929483
+0.4596774
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 1
 </td>
 <td style="text-align:right;">
-100032
+3
 </td>
 <td style="text-align:right;">
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-0.5070517
+0.5403226
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 1
 </td>
 <td style="text-align:right;">
-100033
+4
 </td>
 <td style="text-align:right;">
 8507001
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 <td style="text-align:right;">
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+0.4947808
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 1
 </td>
 <td style="text-align:right;">
-100033
+4
 </td>
 <td style="text-align:right;">
 8532001
 </td>
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+242
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 <td style="text-align:right;">
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+0.5052192
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 1
 </td>
 <td style="text-align:right;">
-200000
+5
 </td>
 <td style="text-align:right;">
 8507001
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 <td style="text-align:right;">
-0.4788235
+0.4966667
 </td>
 </tr>
 <tr>
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 1
 </td>
 <td style="text-align:right;">
-200000
+5
 </td>
 <td style="text-align:right;">
 8532001
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-0.5211765
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 1
 </td>
 <td style="text-align:right;">
-200031
+6
 </td>
 <td style="text-align:right;">
 8507001
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+395
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-0.4596774
+0.4759036
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 1
 </td>
 <td style="text-align:right;">
-200031
+6
 </td>
 <td style="text-align:right;">
 8532001
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 <td style="text-align:right;">
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+0.5240964
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 1
 </td>
 <td style="text-align:right;">
-200032
+7
 </td>
 <td style="text-align:right;">
 8507001
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+1289
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 1
 </td>
 <td style="text-align:right;">
-200032
+7
 </td>
 <td style="text-align:right;">
 8532001
 </td>
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 </td>
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+0.5098859
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 1
 </td>
 <td style="text-align:right;">
-200033
+8
 </td>
 <td style="text-align:right;">
 8507001
 </td>
 <td style="text-align:right;">
-57
+180
 </td>
 <td style="text-align:right;">
-0.4596774
+0.5070423
 </td>
 </tr>
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 1
 </td>
 <td style="text-align:right;">
-200033
+8
 </td>
 <td style="text-align:right;">
 8532001
 </td>
 <td style="text-align:right;">
-67
+175
 </td>
 <td style="text-align:right;">
-0.5403226
+0.4929577
 </td>
 </tr>
 <tr>
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 1
 </td>
 <td style="text-align:right;">
-300000
+9
 </td>
 <td style="text-align:right;">
 8507001
 </td>
 <td style="text-align:right;">
-237
+57
 </td>
 <td style="text-align:right;">
-0.4947808
+0.4596774
 </td>
 </tr>
 <tr>
@@ -672,16 +672,16 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 1
 </td>
 <td style="text-align:right;">
-300000
+9
 </td>
 <td style="text-align:right;">
 8532001
 </td>
 <td style="text-align:right;">
-242
+67
 </td>
 <td style="text-align:right;">
-0.5052192
+0.5403226
 </td>
 </tr>
 <tr>
@@ -692,16 +692,16 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 1
 </td>
 <td style="text-align:right;">
-400000
+10
 </td>
 <td style="text-align:right;">
 8507001
 </td>
 <td style="text-align:right;">
-1321
+237
 </td>
 <td style="text-align:right;">
-0.4903489
+0.4947808
 </td>
 </tr>
 <tr>
@@ -712,16 +712,16 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 1
 </td>
 <td style="text-align:right;">
-400000
+10
 </td>
 <td style="text-align:right;">
 8532001
 </td>
 <td style="text-align:right;">
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+242
 </td>
 <td style="text-align:right;">
-0.5096511
+0.5052192
 </td>
 </tr>
 <tr>
@@ -732,16 +732,16 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 1
 </td>
 <td style="text-align:right;">
-400031
+11
 </td>
 <td style="text-align:right;">
 8507001
 </td>
 <td style="text-align:right;">
-237
+714
 </td>
 <td style="text-align:right;">
-0.4947808
+0.4941176
 </td>
 </tr>
 <tr>
@@ -752,16 +752,16 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 1
 </td>
 <td style="text-align:right;">
-400031
+11
 </td>
 <td style="text-align:right;">
 8532001
 </td>
 <td style="text-align:right;">
-242
+731
 </td>
 <td style="text-align:right;">
-0.5052192
+0.5058824
 </td>
 </tr>
 <tr>
@@ -772,16 +772,16 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 1
 </td>
 <td style="text-align:right;">
-400032
+12
 </td>
 <td style="text-align:right;">
 8507001
 </td>
 <td style="text-align:right;">
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 </td>
 <td style="text-align:right;">
-0.4893905
+0.4787535
 </td>
 </tr>
 <tr>
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 1
 </td>
 <td style="text-align:right;">
-400032
+12
 </td>
 <td style="text-align:right;">
 8532001
 </td>
 <td style="text-align:right;">
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+368
 </td>
 <td style="text-align:right;">
-0.5106095
+0.5212465
 </td>
 </tr>
 <tr>
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 1
 </td>
 <td style="text-align:right;">
-400033
+13
 </td>
 <td style="text-align:right;">
 8507001
 </td>
 <td style="text-align:right;">
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+1052
 </td>
 <td style="text-align:right;">
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 </td>
 </tr>
 <tr>
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 1
 </td>
 <td style="text-align:right;">
-400033
+13
 </td>
 <td style="text-align:right;">
 8532001
 </td>
 <td style="text-align:right;">
-242
+1099
 </td>
 <td style="text-align:right;">
-0.5052192
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 </td>
 </tr>
-</tbody>
-</table>
-<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>
-<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>
-<table class="table">
-<thead><tr>
-<th style="text-align:left;">
-databaseId
-</th>
-<th style="text-align:right;">
-runId
-</th>
-<th style="text-align:right;">
-cohortDefinitionId
-</th>
-<th style="text-align:right;">
-covariateId
-</th>
-<th style="text-align:right;">
-countValue
-</th>
-<th style="text-align:right;">
-minValue
-</th>
-<th style="text-align:right;">
-maxValue
-</th>
-<th style="text-align:right;">
-averageValue
-</th>
-<th style="text-align:right;">
-standardDeviation
-</th>
-<th style="text-align:right;">
-medianValue
-</th>
-<th style="text-align:right;">
-p10Value
-</th>
-<th style="text-align:right;">
-p25Value
-</th>
-<th style="text-align:right;">
-p75Value
-</th>
-<th style="text-align:right;">
-p90Value
-</th>
-</tr></thead>
-<tbody>
 <tr>
 <td style="text-align:left;">
 Eunomia
@@ -907,40 +852,36 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 1
 </td>
 <td style="text-align:right;">
-200031
-</td>
-<td style="text-align:right;">
-1901
-</td>
-<td style="text-align:right;">
-41
+14
 </td>
 <td style="text-align:right;">
-0
+8507001
 </td>
 <td style="text-align:right;">
-2
+180
 </td>
 <td style="text-align:right;">
-0.4274194
+0.5070423
 </td>
-<td style="text-align:right;">
-0.4606464
+</tr>
+<tr>
+<td style="text-align:left;">
+Eunomia
 </td>
 <td style="text-align:right;">
-0
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+</td>
+</tr>
+</tbody>
+</table>
+<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>
+<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>
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 <tr>
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 <tr>
@@ -1479,31 +3143,31 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
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 <td style="text-align:right;">
-200031
+26
 </td>
 <td style="text-align:right;">
 1002
 </td>
 <td style="text-align:right;">
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 <td style="text-align:right;">
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 <td style="text-align:right;">
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 <td style="text-align:right;">
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 <td style="text-align:right;">
 39
 </td>
 <td style="text-align:right;">
-34
+35
 </td>
 <td style="text-align:right;">
 36
@@ -1523,28 +3187,28 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 1
 </td>
 <td style="text-align:right;">
-200033
+12
 </td>
 <td style="text-align:right;">
 1002
 </td>
 <td style="text-align:right;">
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 </td>
 <td style="text-align:right;">
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 <td style="text-align:right;">
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-38.9758065
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 <td style="text-align:right;">
-3.4226973
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 </td>
 <td style="text-align:right;">
-39
+38
 </td>
 <td style="text-align:right;">
 34
@@ -1556,7 +3220,7 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 41
 </td>
 <td style="text-align:right;">
-44
+43
 </td>
 </tr>
 <tr>
@@ -1567,31 +3231,31 @@ <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 style="text-align:right;">
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 </td>
 <td style="text-align:right;">
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+34
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 <td style="text-align:right;">
 36
@@ -1611,31 +3275,31 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 1
 </td>
 <td style="text-align:right;">
-100033
+6
 </td>
 <td style="text-align:right;">
 1002
 </td>
 <td style="text-align:right;">
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 <td style="text-align:right;">
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 <td style="text-align:right;">
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 <td style="text-align:right;">
 39
 </td>
 <td style="text-align:right;">
-35
+34
 </td>
 <td style="text-align:right;">
 36
@@ -1655,25 +3319,25 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 1
 </td>
 <td style="text-align:right;">
-400031
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 </td>
 <td style="text-align:right;">
 1002
 </td>
 <td style="text-align:right;">
-479
+850
 </td>
 <td style="text-align:right;">
-32
+31
 </td>
 <td style="text-align:right;">
 46
 </td>
 <td style="text-align:right;">
-38.7995825
+38.5658824
 </td>
 <td style="text-align:right;">
-3.3042257
+3.2816028
 </td>
 <td style="text-align:right;">
 39
@@ -1688,7 +3352,7 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 41
 </td>
 <td style="text-align:right;">
-44
+43
 </td>
 </tr>
 <tr>
@@ -1699,31 +3363,31 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 1
 </td>
 <td style="text-align:right;">
-300000
+11
 </td>
 <td style="text-align:right;">
 1002
 </td>
 <td style="text-align:right;">
-479
+1445
 </td>
 <td style="text-align:right;">
-32
+31
 </td>
 <td style="text-align:right;">
 47
 </td>
 <td style="text-align:right;">
-38.9206681
+38.6131488
 </td>
 <td style="text-align:right;">
-3.2884308
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 </td>
 <td style="text-align:right;">
 39
 </td>
 <td style="text-align:right;">
-35
+34
 </td>
 <td style="text-align:right;">
 36
@@ -1732,7 +3396,7 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 41
 </td>
 <td style="text-align:right;">
-44
+43
 </td>
 </tr>
 <tr>
@@ -1743,31 +3407,31 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 1
 </td>
 <td style="text-align:right;">
-400033
+17
 </td>
 <td style="text-align:right;">
 1002
 </td>
 <td style="text-align:right;">
-479
+1445
 </td>
 <td style="text-align:right;">
-32
+31
 </td>
 <td style="text-align:right;">
 47
 </td>
 <td style="text-align:right;">
-38.9206681
+38.6131488
 </td>
 <td style="text-align:right;">
-3.2884308
+3.3329496
 </td>
 <td style="text-align:right;">
 39
 </td>
 <td style="text-align:right;">
-35
+34
 </td>
 <td style="text-align:right;">
 36
@@ -1776,7 +3440,7 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 41
 </td>
 <td style="text-align:right;">
-44
+43
 </td>
 </tr>
 <tr>
@@ -1787,28 +3451,28 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 1
 </td>
 <td style="text-align:right;">
-200032
+5
 </td>
 <td style="text-align:right;">
 1002
 </td>
 <td style="text-align:right;">
-726
+1800
 </td>
 <td style="text-align:right;">
 31
 </td>
 <td style="text-align:right;">
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 </td>
 <td style="text-align:right;">
-38.5137741
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 </td>
 <td style="text-align:right;">
-3.2604976
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 </td>
 <td style="text-align:right;">
-38
+39
 </td>
 <td style="text-align:right;">
 34
@@ -1831,25 +3495,25 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 1
 </td>
 <td style="text-align:right;">
-200000
+20
 </td>
 <td style="text-align:right;">
 1002
 </td>
 <td style="text-align:right;">
-850
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 </td>
 <td style="text-align:right;">
 31
 </td>
 <td style="text-align:right;">
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 </td>
 <td style="text-align:right;">
-38.5658824
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 </td>
 <td style="text-align:right;">
-3.2816028
+3.3192555
 </td>
 <td style="text-align:right;">
 39
@@ -1875,13 +3539,13 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 1
 </td>
 <td style="text-align:right;">
-100032
+13
 </td>
 <td style="text-align:right;">
 1002
 </td>
 <td style="text-align:right;">
-1489
+2151
 </td>
 <td style="text-align:right;">
 31
@@ -1890,10 +3554,10 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 47
 </td>
 <td style="text-align:right;">
-38.6165212
+38.5834496
 </td>
 <td style="text-align:right;">
-3.3301766
+3.3123287
 </td>
 <td style="text-align:right;">
 39
@@ -1919,13 +3583,13 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 1
 </td>
 <td style="text-align:right;">
-100000
+19
 </td>
 <td style="text-align:right;">
 1002
 </td>
 <td style="text-align:right;">
-1844
+2151
 </td>
 <td style="text-align:right;">
 31
@@ -1934,10 +3598,10 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 47
 </td>
 <td style="text-align:right;">
-38.6469631
+38.5834496
 </td>
 <td style="text-align:right;">
-3.3192555
+3.3123287
 </td>
 <td style="text-align:right;">
 39
@@ -1963,13 +3627,13 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 1
 </td>
 <td style="text-align:right;">
-400032
+7
 </td>
 <td style="text-align:right;">
 1002
 </td>
 <td style="text-align:right;">
-2215
+2630
 </td>
 <td style="text-align:right;">
 31
@@ -1978,10 +3642,10 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 47
 </td>
 <td style="text-align:right;">
-38.5828442
+38.6228137
 </td>
 <td style="text-align:right;">
-3.3071156
+3.3112779
 </td>
 <td style="text-align:right;">
 39
@@ -2007,7 +3671,7 @@ <h3 id="aggreagate-covariates">Aggreagate Covariates<a class="anchor" aria-label
 1
 </td>
 <td style="text-align:right;">
-400000
+22
 </td>
 <td style="text-align:right;">
 1002
@@ -2343,8 +4007,8 @@ <h3 id="dechallenge-rechallenge">Dechallenge Rechallenge<a class="anchor" aria-l
   |==========================================================            |  83%
   |                                                                            
   |======================================================================| 100%</code></pre>
-<pre><code><span><span class="co">## Executing SQL took 0.066 secs</span></span>
-<span><span class="co">## Computing dechallenge rechallenge for 3 target ids and 1outcome ids took 0.131 secs</span></span></code></pre>
+<pre><code><span><span class="co">## Executing SQL took 0.00906 secs</span></span>
+<span><span class="co">## Computing dechallenge rechallenge for 3 target ids and 1outcome ids took 0.0708 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>
@@ -2450,8 +4114,8 @@ <h3 id="dechallenge-rechallenge">Dechallenge Rechallenge<a class="anchor" aria-l
   |==========================================================            |  83%
   |                                                                            
   |======================================================================| 100%</code></pre>
-<pre><code><span><span class="co">## Executing SQL took 0.104 secs</span></span>
-<span><span class="co">## Computing dechallenge failed case series for 3 target ids and 1outcome ids took 0.158 secs</span></span></code></pre>
+<pre><code><span><span class="co">## Executing SQL took 0.0936 secs</span></span>
+<span><span class="co">## Computing dechallenge failed case series for 3 target IDs and 1 outcome IDs took 0.135 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>
@@ -2548,6 +4212,7 @@ <h3 id="time-to-event">Time to Event<a class="anchor" aria-label="anchor" href="
 <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 0.00473 secs</span></span>
 <span><span class="co">## Computing time to event results</span></span></code></pre>
 <pre><code>## 
   |                                                                            
@@ -2584,8 +4249,8 @@ <h3 id="time-to-event">Time to Event<a class="anchor" aria-label="anchor" href="
   |==================================================================    |  94%
   |                                                                            
   |======================================================================| 100%</code></pre>
-<pre><code><span><span class="co">## Executing SQL took 0.0434 secs</span></span>
-<span><span class="co">## Computing time-to-event for T-O pairs took 0.158 secs</span></span></code></pre>
+<pre><code><span><span class="co">## Executing SQL took 0.0428 secs</span></span>
+<span><span class="co">## Computing time-to-event for T-O pairs took 0.16 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>
@@ -2989,7 +4654,7 @@ <h3 id="run-multiple">Run Multiple<a class="anchor" aria-label="anchor" href="#r
 <div class="sourceCode" id="cb50"><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'</span><span class="op">)</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>
@@ -3020,7 +4685,7 @@ <h3 id="run-multiple">Run Multiple<a class="anchor" aria-label="anchor" href="#r
 
 <div class="pkgdown">
   <p></p>
-<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
       </footer>
diff --git a/docs/articles/index.html b/docs/articles/index.html
index 819227e..c31bf3e 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="">0.0.4</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.0</span>
       </span>
     </div>
 
@@ -89,7 +89,7 @@ <h3>All vignettes</h3>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
       </footer></div>
diff --git a/docs/authors.html b/docs/authors.html
index c1598ff..d5c9951 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="">0.0.4</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.0</span>
       </span>
     </div>
 
@@ -90,14 +90,14 @@ <h1 id="citation">Citation</h1>
     </div>
 
 
-    <p>Reps J, Ryan P (2022).
+    <p>Reps J, Ryan P (2023).
 <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 = {2022},
+  year = {2023},
   note = {https://ohdsi.github.io/Characterization, https://github.com/OHDSI/Characterization},
 }</pre>
 
@@ -112,7 +112,7 @@ <h1 id="citation">Citation</h1>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
       </footer></div>
diff --git a/docs/index.html b/docs/index.html
index 27cfafc..a809885 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="">0.0.4</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.0</span>
       </span>
     </div>
 
@@ -96,6 +96,8 @@
 <div class="section level1">
 <div class="page-header"><h1 id="characterization">Characterization<a class="anchor" aria-label="anchor" href="#characterization"></a>
 </h1></div>
+<p><a href="https://github.com/OHDSI/Characterization/actions?query=workflow%3AR-CMD-check" class="external-link"><img src="https://github.com/OHDSI/Characterization/workflows/R-CMD-check/badge.svg" alt="Build Status"></a> <a href="https://codecov.io/github/OHDSI/Characterization?branch=main" class="external-link"><img src="https://codecov.io/github/OHDSI/Characterization/coverage.svg?branch=main" alt="codecov.io"></a></p>
+<p>Characterization is part of <a href="https://ohdsi.github.io/Hades/" class="external-link">HADES</a>.</p>
 </div>
 <div class="section level1">
 <h1 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
@@ -224,9 +226,28 @@ <h1 id="user-documentation">User Documentation<a class="anchor" aria-label="anch
 <p>Documentation can be found on the <a href="https://ohdsi.github.io/Characterization" class="external-link">package website</a>.</p>
 </div>
 <div class="section level1">
+<h1 id="support">Support<a class="anchor" aria-label="anchor" href="#support"></a>
+</h1>
+<ul>
+<li>Developer questions/comments/feedback: <a href="http://forums.ohdsi.org/c/developers" class="external-link">OHDSI Forum</a>
+</li>
+<li>We use the <a href="https://github.com/OHDSI/Characterization/issues" class="external-link">GitHub issue tracker</a> for all bugs/issues/enhancements</li>
+</ul>
+</div>
+<div class="section level1">
 <h1 id="contributing">Contributing<a class="anchor" aria-label="anchor" href="#contributing"></a>
 </h1>
 <p>Read <a href="https://ohdsi.github.io/Hades/contribute.html" class="external-link">here</a> how you can contribute to this package.</p>
+</div>
+<div class="section level1">
+<h1 id="license">License<a class="anchor" aria-label="anchor" href="#license"></a>
+</h1>
+<p>Characterization is licensed under Apache License 2.0</p>
+</div>
+<div class="section level1">
+<h1 id="development">Development<a class="anchor" aria-label="anchor" href="#development"></a>
+</h1>
+<p>Characterization is being developed in R Studio.</p>
 </div>
 
   </div>
@@ -277,7 +298,7 @@ <h2 data-toc-skip>Developers</h2>
 
 <div class="pkgdown">
   <p></p>
-<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
       </footer>
diff --git a/docs/news/index.html b/docs/news/index.html
index 192b085..0cdf562 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="">0.0.4</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.0</span>
       </span>
     </div>
 
@@ -72,6 +72,11 @@ <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="0.1.0" 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>
+<li>added shiny app</li>
+</ul></div>
     <div class="section level2">
 <h2 class="page-header" data-toc-text="0.0.1" id="characterization-001">Characterization 0.0.1<a class="anchor" aria-label="anchor" href="#characterization-001"></a></h2>
 <p>Initial version</p>
@@ -90,7 +95,7 @@ <h2 class="page-header" data-toc-text="0.0.1" id="characterization-001">Characte
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
       </footer></div>
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index c92d37c..33dd174 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -1,8 +1,8 @@
 pandoc: 2.19.2
-pkgdown: 2.0.6
+pkgdown: 2.0.7
 pkgdown_sha: ~
 articles:
   InstallationGuide: InstallationGuide.html
   UsingCharacterizationPackage: UsingCharacterizationPackage.html
-last_built: 2022-12-16T22:10Z
+last_built: 2023-03-15T16:42Z
 
diff --git a/docs/pull_request_template.html b/docs/pull_request_template.html
index a2c7f35..8e0be78 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="">0.0.4</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.0</span>
       </span>
     </div>
 
@@ -94,7 +94,7 @@ <h1>NA</h1>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
       </footer></div>
diff --git a/docs/reference/Characterization-package.html b/docs/reference/Characterization-package.html
index a8f7548..0037c39 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="">0.0.4</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.0</span>
       </span>
     </div>
 
@@ -88,7 +88,8 @@ <h2>See also</h2>
     <div id="author">
     <h2>Author</h2>
     <p><strong>Maintainer</strong>: Jenna Reps <a href="mailto:reps@ohdsi.org">reps@ohdsi.org</a></p>
-    </div>
+<p>Authors:</p><ul><li><p>Patrick Ryan <a href="mailto:ryan@ohdsi.org">ryan@ohdsi.org</a></p></li>
+</ul></div>
 
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
@@ -102,7 +103,7 @@ <h2>Author</h2>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
       </footer></div>
diff --git a/docs/reference/computeAggregateCovariateAnalyses.html b/docs/reference/computeAggregateCovariateAnalyses.html
index b2e535b..8ea4096 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="">0.0.4</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.0</span>
       </span>
     </div>
 
@@ -165,7 +165,7 @@ <h2>Value</h2>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
       </footer></div>
diff --git a/docs/reference/computeDechallengeRechallengeAnalyses.html b/docs/reference/computeDechallengeRechallengeAnalyses.html
index d82e5d0..c74d039 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="">0.0.4</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.0</span>
       </span>
     </div>
 
@@ -150,7 +150,7 @@ <h2>Value</h2>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
       </footer></div>
diff --git a/docs/reference/computeRechallengeFailCaseSeriesAnalyses.html b/docs/reference/computeRechallengeFailCaseSeriesAnalyses.html
index 6717c60..60cfc21 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="">0.0.4</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.0</span>
       </span>
     </div>
 
@@ -155,7 +155,7 @@ <h2>Value</h2>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
       </footer></div>
diff --git a/docs/reference/computeTimeToEventAnalyses.html b/docs/reference/computeTimeToEventAnalyses.html
index 88bfbf0..146b10c 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="">0.0.4</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.0</span>
       </span>
     </div>
 
@@ -155,7 +155,7 @@ <h2>Value</h2>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
       </footer></div>
diff --git a/docs/reference/createAggregateCovariateSettings.html b/docs/reference/createAggregateCovariateSettings.html
index da2ee60..a0b0a36 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="">0.0.4</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.0</span>
       </span>
     </div>
 
@@ -81,6 +81,7 @@ <h1>Create aggregate covariate study settings</h1>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">createAggregateCovariateSettings</span><span class="op">(</span></span>
 <span>  <span class="va">targetIds</span>,</span>
 <span>  <span class="va">outcomeIds</span>,</span>
+<span>  minPriorObservation <span class="op">=</span> <span class="fl">0</span>,</span>
 <span>  riskWindowStart <span class="op">=</span> <span class="fl">1</span>,</span>
 <span>  startAnchor <span class="op">=</span> <span class="st">"cohort start"</span>,</span>
 <span>  riskWindowEnd <span class="op">=</span> <span class="fl">365</span>,</span>
@@ -99,6 +100,10 @@ <h2>Arguments</h2>
 <dd><p>A list of cohortIds for the outcome cohorts</p></dd>
 
 
+<dt>minPriorObservation</dt>
+<dd><p>The minimum time in the database a patient in the target cohorts must be observed prior to index</p></dd>
+
+
 <dt>riskWindowStart</dt>
 <dd><p>The start of the risk window (in days) relative to the `startAnchor`.</p></dd>
 
@@ -140,7 +145,7 @@ <h2>Value</h2>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
       </footer></div>
diff --git a/docs/reference/createCharacterizationSettings.html b/docs/reference/createCharacterizationSettings.html
index 1c5101e..5d758d8 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="">0.0.4</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.0</span>
       </span>
     </div>
 
@@ -122,7 +122,7 @@ <h2>Details</h2>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
       </footer></div>
diff --git a/docs/reference/createCharacterizationTables.html b/docs/reference/createCharacterizationTables.html
index e708f68..7eb013f 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="">0.0.4</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.0</span>
       </span>
     </div>
 
@@ -144,7 +144,7 @@ <h2>Details</h2>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
       </footer></div>
diff --git a/docs/reference/createDechallengeRechallengeSettings.html b/docs/reference/createDechallengeRechallengeSettings.html
index f6d1217..8a9fdec 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="">0.0.4</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.0</span>
       </span>
     </div>
 
@@ -123,7 +123,7 @@ <h2>Value</h2>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
       </footer></div>
diff --git a/docs/reference/createSqliteDatabase.html b/docs/reference/createSqliteDatabase.html
index 68017dd..30b14d0 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="">0.0.4</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.0</span>
       </span>
     </div>
 
@@ -110,7 +110,7 @@ <h2>Details</h2>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
       </footer></div>
diff --git a/docs/reference/createTimeToEventSettings.html b/docs/reference/createTimeToEventSettings.html
index 940d4f6..4cb3987 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="">0.0.4</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.0</span>
       </span>
     </div>
 
@@ -110,7 +110,7 @@ <h2>Value</h2>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
       </footer></div>
diff --git a/docs/reference/exportAggregateCovariateToCsv.html b/docs/reference/exportAggregateCovariateToCsv.html
index 326a99f..b8dab95 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="">0.0.4</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.0</span>
       </span>
     </div>
 
@@ -110,7 +110,7 @@ <h2>Value</h2>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
       </footer></div>
diff --git a/docs/reference/exportDatabaseToCsv.html b/docs/reference/exportDatabaseToCsv.html
index f194dab..b6d6dd5 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="">0.0.4</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.0</span>
       </span>
     </div>
 
@@ -144,7 +144,7 @@ <h2>Details</h2>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
       </footer></div>
diff --git a/docs/reference/exportDechallengeRechallengeToCsv.html b/docs/reference/exportDechallengeRechallengeToCsv.html
index 0e4988c..d237188 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="">0.0.4</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.0</span>
       </span>
     </div>
 
@@ -110,7 +110,7 @@ <h2>Value</h2>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
       </footer></div>
diff --git a/docs/reference/exportRechallengeFailCaseSeriesToCsv.html b/docs/reference/exportRechallengeFailCaseSeriesToCsv.html
index d8a6ecd..8fd1a4d 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="">0.0.4</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.0</span>
       </span>
     </div>
 
@@ -110,7 +110,7 @@ <h2>Value</h2>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
       </footer></div>
diff --git a/docs/reference/exportTimeToEventToCsv.html b/docs/reference/exportTimeToEventToCsv.html
index 30b9e67..a7bbca2 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="">0.0.4</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.0</span>
       </span>
     </div>
 
@@ -110,7 +110,7 @@ <h2>Value</h2>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
       </footer></div>
diff --git a/docs/reference/index.html b/docs/reference/index.html
index b59be76..7cc08c8 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="">0.0.4</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.0</span>
       </span>
     </div>
 
@@ -199,6 +199,14 @@ <h2 id="insert-into-database">Insert into Database <a href="#insert-into-databas
           <p><code><a href="exportDatabaseToCsv.html">exportDatabaseToCsv()</a></code> </p>
         </td>
         <td><p>Exports all tables in the result database to csv files</p></td>
+      </tr></tbody><tbody><tr><th colspan="2">
+          <h2 id="shiny-app">Shiny App <a href="#shiny-app" class="anchor" aria-hidden="true"></a></h2>
+          <p class="section-desc"></p><p>Functions to interactively exlore the results from runCharacterizationAnalyses().</p>
+        </th>
+      </tr></tbody><tbody><tr><td>
+          <p><code><a href="viewCharacterization.html">viewCharacterization()</a></code> </p>
+        </td>
+        <td><p>viewCharacterization - Interactively view the characterization results</p></td>
       </tr></tbody></table></div>
 
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
@@ -212,7 +220,7 @@ <h2 id="insert-into-database">Insert into Database <a href="#insert-into-databas
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
       </footer></div>
diff --git a/docs/reference/loadAggregateCovariateAnalyses.html b/docs/reference/loadAggregateCovariateAnalyses.html
index 3db8869..c4eabb2 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="">0.0.4</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.0</span>
       </span>
     </div>
 
@@ -78,13 +78,13 @@ <h1>Load the AggregateCovariate results</h1>
     </div>
 
     <div id="ref-usage">
-    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">loadAggregateCovariateAnalyses</span><span class="op">(</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">loadAggregateCovariateAnalyses</span><span class="op">(</span><span class="va">fileName</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div id="arguments">
     <h2>Arguments</h2>
-    <dl><dt>saveDirectory</dt>
-<dd><p>An directory location to save the results into</p></dd>
+    <dl><dt>fileName</dt>
+<dd><p>The file to save the results into.</p></dd>
 
 </dl></div>
     <div id="value">
@@ -106,7 +106,7 @@ <h2>Value</h2>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
       </footer></div>
diff --git a/docs/reference/loadCharacterizationSettings.html b/docs/reference/loadCharacterizationSettings.html
index b1830e9..988d7c7 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="">0.0.4</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.0</span>
       </span>
     </div>
 
@@ -78,12 +78,12 @@ <h1>Load the characterization settings previously saved as a json file</h1>
     </div>
 
     <div id="ref-usage">
-    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">loadCharacterizationSettings</span><span class="op">(</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">loadCharacterizationSettings</span><span class="op">(</span><span class="va">fileName</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div id="arguments">
     <h2>Arguments</h2>
-    <dl><dt>saveDirectory</dt>
+    <dl><dt>fileName</dt>
 <dd><p>The location of the the json settings</p></dd>
 
 </dl></div>
@@ -110,7 +110,7 @@ <h2>Details</h2>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
       </footer></div>
diff --git a/docs/reference/loadDechallengeRechallengeAnalyses.html b/docs/reference/loadDechallengeRechallengeAnalyses.html
index c2bb526..417352f 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="">0.0.4</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.0</span>
       </span>
     </div>
 
@@ -78,13 +78,13 @@ <h1>Load the DechallengeRechallenge results</h1>
     </div>
 
     <div id="ref-usage">
-    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">loadDechallengeRechallengeAnalyses</span><span class="op">(</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">loadDechallengeRechallengeAnalyses</span><span class="op">(</span><span class="va">fileName</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div id="arguments">
     <h2>Arguments</h2>
-    <dl><dt>saveDirectory</dt>
-<dd><p>An directory location to save the results into</p></dd>
+    <dl><dt>fileName</dt>
+<dd><p>The file to save the results into.</p></dd>
 
 </dl></div>
     <div id="value">
@@ -106,7 +106,7 @@ <h2>Value</h2>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
       </footer></div>
diff --git a/docs/reference/loadRechallengeFailCaseSeriesAnalyses.html b/docs/reference/loadRechallengeFailCaseSeriesAnalyses.html
index 4a7801f..3f6b9a8 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="">0.0.4</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.0</span>
       </span>
     </div>
 
@@ -78,13 +78,13 @@ <h1>Load the RechallengeFailCaseSeries results</h1>
     </div>
 
     <div id="ref-usage">
-    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">loadRechallengeFailCaseSeriesAnalyses</span><span class="op">(</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">loadRechallengeFailCaseSeriesAnalyses</span><span class="op">(</span><span class="va">fileName</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div id="arguments">
     <h2>Arguments</h2>
-    <dl><dt>saveDirectory</dt>
-<dd><p>An directory location to save the results into</p></dd>
+    <dl><dt>fileName</dt>
+<dd><p>The file to save the results into.</p></dd>
 
 </dl></div>
     <div id="value">
@@ -106,7 +106,7 @@ <h2>Value</h2>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
       </footer></div>
diff --git a/docs/reference/loadTimeToEventAnalyses.html b/docs/reference/loadTimeToEventAnalyses.html
index 3563050..af61ae4 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="">0.0.4</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.0</span>
       </span>
     </div>
 
@@ -78,13 +78,13 @@ <h1>Load the TimeToEvent results</h1>
     </div>
 
     <div id="ref-usage">
-    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">loadTimeToEventAnalyses</span><span class="op">(</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">loadTimeToEventAnalyses</span><span class="op">(</span><span class="va">fileName</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div id="arguments">
     <h2>Arguments</h2>
-    <dl><dt>saveDirectory</dt>
-<dd><p>An directory location to save the results into</p></dd>
+    <dl><dt>fileName</dt>
+<dd><p>The file to save the results into.</p></dd>
 
 </dl></div>
     <div id="value">
@@ -106,7 +106,7 @@ <h2>Value</h2>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
       </footer></div>
diff --git a/docs/reference/runCharacterizationAnalyses.html b/docs/reference/runCharacterizationAnalyses.html
index cbd1111..416f975 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="">0.0.4</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.0</span>
       </span>
     </div>
 
@@ -177,7 +177,7 @@ <h2>Details</h2>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
       </footer></div>
diff --git a/docs/reference/saveAggregateCovariateAnalyses.html b/docs/reference/saveAggregateCovariateAnalyses.html
index 4083254..db5c47a 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="">0.0.4</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.0</span>
       </span>
     </div>
 
@@ -78,7 +78,7 @@ <h1>Save the AggregateCovariate results</h1>
     </div>
 
     <div id="ref-usage">
-    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">saveAggregateCovariateAnalyses</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">saveAggregateCovariateAnalyses</span><span class="op">(</span><span class="va">result</span>, <span class="va">fileName</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div id="arguments">
@@ -87,8 +87,8 @@ <h2>Arguments</h2>
 <dd><p>The output of running <code><a href="computeAggregateCovariateAnalyses.html">computeAggregateCovariateAnalyses()</a></code></p></dd>
 
 
-<dt>saveDirectory</dt>
-<dd><p>An directory location to save the results into</p></dd>
+<dt>fileName</dt>
+<dd><p>The file to save the results into.</p></dd>
 
 </dl></div>
     <div id="value">
@@ -110,7 +110,7 @@ <h2>Value</h2>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
       </footer></div>
diff --git a/docs/reference/saveCharacterizationSettings.html b/docs/reference/saveCharacterizationSettings.html
index 452c3df..34ec74e 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="">0.0.4</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.0</span>
       </span>
     </div>
 
@@ -78,7 +78,7 @@ <h1>Save the characterization settings as a json</h1>
     </div>
 
     <div id="ref-usage">
-    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">saveCharacterizationSettings</span><span class="op">(</span><span class="va">settings</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">saveCharacterizationSettings</span><span class="op">(</span><span class="va">settings</span>, <span class="va">fileName</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div id="arguments">
@@ -87,7 +87,7 @@ <h2>Arguments</h2>
 <dd><p>An object of class characterizationSettings created using <code>createCharacterizationSettings</code></p></dd>
 
 
-<dt>saveDirectory</dt>
+<dt>fileName</dt>
 <dd><p>The location to save the json settings</p></dd>
 
 </dl></div>
@@ -114,7 +114,7 @@ <h2>Details</h2>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
       </footer></div>
diff --git a/docs/reference/saveDechallengeRechallengeAnalyses.html b/docs/reference/saveDechallengeRechallengeAnalyses.html
index 1316456..9d465f3 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="">0.0.4</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.0</span>
       </span>
     </div>
 
@@ -78,7 +78,7 @@ <h1>Save the DechallengeRechallenge results</h1>
     </div>
 
     <div id="ref-usage">
-    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">saveDechallengeRechallengeAnalyses</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">saveDechallengeRechallengeAnalyses</span><span class="op">(</span><span class="va">result</span>, <span class="va">fileName</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div id="arguments">
@@ -87,8 +87,8 @@ <h2>Arguments</h2>
 <dd><p>The output of running <code><a href="computeDechallengeRechallengeAnalyses.html">computeDechallengeRechallengeAnalyses()</a></code></p></dd>
 
 
-<dt>saveDirectory</dt>
-<dd><p>An directory location to save the results into</p></dd>
+<dt>fileName</dt>
+<dd><p>The file to save the results into.</p></dd>
 
 </dl></div>
     <div id="value">
@@ -110,7 +110,7 @@ <h2>Value</h2>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
       </footer></div>
diff --git a/docs/reference/saveRechallengeFailCaseSeriesAnalyses.html b/docs/reference/saveRechallengeFailCaseSeriesAnalyses.html
index d56acd8..de8f8b5 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="">0.0.4</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.0</span>
       </span>
     </div>
 
@@ -78,7 +78,7 @@ <h1>Save the RechallengeFailCaseSeries results</h1>
     </div>
 
     <div id="ref-usage">
-    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">saveRechallengeFailCaseSeriesAnalyses</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">saveRechallengeFailCaseSeriesAnalyses</span><span class="op">(</span><span class="va">result</span>, <span class="va">fileName</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div id="arguments">
@@ -87,8 +87,8 @@ <h2>Arguments</h2>
 <dd><p>The output of running <code><a href="computeRechallengeFailCaseSeriesAnalyses.html">computeRechallengeFailCaseSeriesAnalyses()</a></code></p></dd>
 
 
-<dt>saveDirectory</dt>
-<dd><p>An directory location to save the results into</p></dd>
+<dt>fileName</dt>
+<dd><p>The file to save the results into.</p></dd>
 
 </dl></div>
     <div id="value">
@@ -110,7 +110,7 @@ <h2>Value</h2>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
       </footer></div>
diff --git a/docs/reference/saveTimeToEventAnalyses.html b/docs/reference/saveTimeToEventAnalyses.html
index 3d69544..914af23 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="">0.0.4</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.0</span>
       </span>
     </div>
 
@@ -78,7 +78,7 @@ <h1>Save the TimeToEvent results</h1>
     </div>
 
     <div id="ref-usage">
-    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">saveTimeToEventAnalyses</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">saveTimeToEventAnalyses</span><span class="op">(</span><span class="va">result</span>, <span class="va">fileName</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div id="arguments">
@@ -87,8 +87,8 @@ <h2>Arguments</h2>
 <dd><p>The output of running <code><a href="computeTimeToEventAnalyses.html">computeTimeToEventAnalyses()</a></code></p></dd>
 
 
-<dt>saveDirectory</dt>
-<dd><p>An directory location to save the results into</p></dd>
+<dt>fileName</dt>
+<dd><p>The file to save the results into.</p></dd>
 
 </dl></div>
     <div id="value">
@@ -110,7 +110,7 @@ <h2>Value</h2>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
       </footer></div>
diff --git a/docs/reference/viewCharacterization.html b/docs/reference/viewCharacterization.html
new file mode 100644
index 0000000..eb0f2a4
--- /dev/null
+++ b/docs/reference/viewCharacterization.html
@@ -0,0 +1,128 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>viewCharacterization - Interactively view the characterization results — viewCharacterization • Characterization</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="viewCharacterization - Interactively view the characterization results — viewCharacterization"><meta property="og:description" content="This is a shiny app for viewing interactive plots and tables"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]--></head><body data-spy="scroll" data-target="#toc">
+    
+
+    <div class="container template-reference-topic">
+      <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
+  <div class="container">
+    <div class="navbar-header">
+      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+        <span class="sr-only">Toggle navigation</span>
+        <span class="icon-bar"></span>
+        <span class="icon-bar"></span>
+        <span class="icon-bar"></span>
+      </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="">0.1.0</span>
+      </span>
+    </div>
+
+    <div id="navbar" class="navbar-collapse collapse">
+      <ul class="nav navbar-nav"><li>
+  <a href="../index.html">
+    <span class="fa fa-home fa-lg"></span>
+     
+  </a>
+</li>
+<li>
+  <a href="../articles/InstallationGuide.html">Get started</a>
+</li>
+<li>
+  <a href="../reference/index.html">Reference</a>
+</li>
+<li class="dropdown">
+  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
+    Articles
+     
+    <span class="caret"></span>
+  </a>
+  <ul class="dropdown-menu" role="menu"><li>
+      <a href="../articles/InstallationGuide.html">Characterization Installation Guide</a>
+    </li>
+    <li>
+      <a href="../articles/UsingCharacterizationPackage.html">Using Characterization Package</a>
+    </li>
+  </ul></li>
+<li>
+  <a href="../news/index.html">Changelog</a>
+</li>
+      </ul><ul class="nav navbar-nav navbar-right"><li>
+  <a href="https://ohdsi.github.io/Hades" class="external-link"><img src='https://ohdsi.github.io/Hades/images/hadesMini.png' width=80 height=17 style='vertical-align: top;'></a>
+</li>
+<li>
+  <a href="https://github.com/OHDSI/PatientLevelPrediction" class="external-link">
+    <span class="fa fa-github fa-lg"></span>
+     
+  </a>
+</li>
+      </ul></div><!--/.nav-collapse -->
+  </div><!--/.container -->
+</div><!--/.navbar -->
+
+      
+
+      </header><div class="row">
+  <div class="col-md-9 contents">
+    <div class="page-header">
+    <h1>viewCharacterization - Interactively view the characterization results</h1>
+    <small class="dont-index">Source: <a href="https://github.com/OHDSI/Characterization/blob/HEAD/R/ViewShiny.R" class="external-link"><code>R/ViewShiny.R</code></a></small>
+    <div class="hidden name"><code>viewCharacterization.Rd</code></div>
+    </div>
+
+    <div class="ref-description">
+    <p>This is a shiny app for viewing interactive plots and tables</p>
+    </div>
+
+    <div id="ref-usage">
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">viewCharacterization</span><span class="op">(</span><span class="va">resultLocation</span>, cohortDefinitionSet <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span></span></code></pre></div>
+    </div>
+
+    <div id="arguments">
+    <h2>Arguments</h2>
+    <dl><dt>resultLocation</dt>
+<dd><p>The location of the results</p></dd>
+
+
+<dt>cohortDefinitionSet</dt>
+<dd><p>The cohortDefinitionSet extracted using webAPI</p></dd>
+
+</dl></div>
+    <div id="value">
+    <h2>Value</h2>
+    
+
+<p>Opens a shiny app for interactively viewing the results</p>
+    </div>
+    <div id="details">
+    <h2>Details</h2>
+    <p>Input is the output of ...</p>
+    </div>
+
+  </div>
+  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
+    <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2>
+    </nav></div>
+</div>
+
+
+      <footer><div class="copyright">
+  <p></p><p>Developed by Jenna Reps, Patrick Ryan.</p>
+</div>
+
+<div class="pkgdown">
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+</div>
+
+      </footer></div>
+
+  
+
+
+  
+
+  </body></html>
+
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index cd00cad..a679701 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -108,4 +108,7 @@
   <url>
     <loc>/reference/saveTimeToEventAnalyses.html</loc>
   </url>
+  <url>
+    <loc>/reference/viewCharacterization.html</loc>
+  </url>
 </urlset>