diff --git a/.github/workflows/R_CMD_check_Hades.yml b/.github/workflows/R_CMD_check_Hades.yml
index 266cc52a7..52f905c20 100644
--- a/.github/workflows/R_CMD_check_Hades.yml
+++ b/.github/workflows/R_CMD_check_Hades.yml
@@ -3,10 +3,11 @@
 on:
   push:
     branches:
-      - '**'
+      - develop
+      - main
   pull_request:
     branches:
-      - '**'
+      - main
 
 name: R-CMD-check
 
diff --git a/.github/workflows/R_CMD_check_Hades_minor.yml b/.github/workflows/R_CMD_check_Hades_minor.yml
new file mode 100644
index 000000000..ab750dc70
--- /dev/null
+++ b/.github/workflows/R_CMD_check_Hades_minor.yml
@@ -0,0 +1,128 @@
+#Designed to be a fast github actions check - longer running actions to only run on releases
+on:
+  pull_request:
+    branches:
+      - '**'
+      - '!main'
+
+name: R-CMD-check-minor
+
+jobs:
+  R-CMD-check-minor:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      max-parallel: 1
+      fail-fast: false
+      matrix:
+        config:
+          - {os: windows-latest, r: 'release'}  # Does not appear to have Java 32-bit, hence the --no-multiarch
+          - {os: macOS-latest, r: 'release'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GH_TOKEN }}
+      BRANCH_NAME: ${{ github.head_ref || github.ref_name }}
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      RSPM: ${{ matrix.config.rspm }}
+      #CDM5_ORACLE_CDM_SCHEMA: ${{ secrets.CDM5_ORACLE_CDM_SCHEMA }}
+      #CDM5_ORACLE_OHDSI_SCHEMA: ${{ secrets.CDM5_ORACLE_OHDSI_SCHEMA }}
+      #CDM5_ORACLE_PASSWORD: ${{ secrets.CDM5_ORACLE_PASSWORD }}
+      #CDM5_ORACLE_SERVER: ${{ secrets.CDM5_ORACLE_SERVER }}
+      #CDM5_ORACLE_USER: ${{ secrets.CDM5_ORACLE_USER }}
+      CDM5_POSTGRESQL_CDM_SCHEMA: ${{ secrets.CDM5_POSTGRESQL_CDM_SCHEMA }}
+      CDM5_POSTGRESQL_OHDSI_SCHEMA: ${{ secrets.CDM5_POSTGRESQL_OHDSI_SCHEMA }}
+      CDM5_POSTGRESQL_PASSWORD: ${{ secrets.CDM5_POSTGRESQL_PASSWORD }}
+      CDM5_POSTGRESQL_SERVER: ${{ secrets.CDM5_POSTGRESQL_SERVER }}
+      CDM5_POSTGRESQL_USER: ${{ secrets.CDM5_POSTGRESQL_USER }}
+      #CDM5_SQL_SERVER_CDM_SCHEMA: ${{ secrets.CDM5_SQL_SERVER_CDM_SCHEMA }}
+      #CDM5_SQL_SERVER_OHDSI_SCHEMA: ${{ secrets.CDM5_SQL_SERVER_OHDSI_SCHEMA }}
+      #CDM5_SQL_SERVER_PASSWORD: ${{ secrets.CDM5_SQL_SERVER_PASSWORD }}
+      #CDM5_SQL_SERVER_SERVER: ${{ secrets.CDM5_SQL_SERVER_SERVER }}
+      #CDM5_SQL_SERVER_USER: ${{ secrets.CDM5_SQL_SERVER_USER }}
+      #CDM5_REDSHIFT_CDM_SCHEMA: ${{ secrets.CDM5_REDSHIFT_CDM_SCHEMA }}
+      #CDM5_REDSHIFT_OHDSI_SCHEMA: ${{ secrets.CDM5_REDSHIFT_OHDSI_SCHEMA }}
+      #CDM5_REDSHIFT_PASSWORD: ${{ secrets.CDM5_REDSHIFT_PASSWORD }}
+      #CDM5_REDSHIFT_SERVER: ${{ secrets.CDM5_REDSHIFT_SERVER }}
+      #CDM5_REDSHIFT_USER: ${{ secrets.CDM5_REDSHIFT_USER }}
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@v1
+        with:
+          r-version: ${{ matrix.config.r }}
+
+      - uses: r-lib/actions/setup-tinytex@v1
+
+      - uses: r-lib/actions/setup-pandoc@v1
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        if: runner.os != 'Windows'
+        uses: actions/cache@v2
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+
+      - name: Install system dependencies
+        if: runner.os == 'Linux'
+        run: |
+          while read -r cmd
+          do
+            eval sudo $cmd
+          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
+
+      - name: Install libssh
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt-get install libssh-dev
+      - name: Install dependencies
+        run: |
+          remotes::install_deps(dependencies = TRUE, INSTALL_opts=c("--no-multiarch"))
+          remotes::install_cran("rcmdcheck")
+        shell: Rscript {0}
+
+      - name: Install covr
+        if: runner.os == 'macOS'
+        run: |
+          remotes::install_cran("covr")
+        shell: Rscript {0}
+
+      - name: Remove check folder if exists
+        if: runner.os == 'macOS'
+        run: unlink("check", recursive = TRUE)
+        shell: Rscript {0}
+
+      - name: Check
+        env:
+          _R_CHECK_CRAN_INCOMING_REMOTE_: false
+        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--no-multiarch"), build_args = c("--no-manual"), error_on = "warning", check_dir = "check")
+        shell: Rscript {0}
+
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@v2
+        with:
+          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
+          path: check
+
+      - name: Upload source package
+        if: success() && runner.os == 'macOS' && github.event_name != 'pull_request' && github.ref == 'refs/heads/main'
+        uses: actions/upload-artifact@v2
+        with:
+          name: package_tarball
+          path: check/*.tar.gz
+
+      - name: Test coverage
+        if: runner.os == 'macOS'
+        run: covr::codecov()
+        shell: Rscript {0}
diff --git a/DESCRIPTION b/DESCRIPTION
index b6714de50..a64d41011 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: CohortDiagnostics
 Type: Package
 Title: Diagnostics for OHDSI Cohorts
-Version: 3.1.1
-Date: 2022-07-20
+Version: 3.1.2
+Date: 2022-12-19
 Authors@R: c(
     person("Gowtham", "Rao", email = "rao@ohdsi.org", role = c("aut", "cre")),
     person("Martijn", "Schuemie", email = "schuemie@ohdsi.org", role = c("aut")),
diff --git a/NEWS.md b/NEWS.md
index 30681ca75..7c5d05a72 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,10 @@
+CohortDiagnostics 3.1.2
+=======================
+Bug Fixes:
+
+1. Removed package dependency snapshot capture as it was breaking on newer versions of R
+
+
 CohortDiagnostics 3.1.1
 =======================
 Changes:
diff --git a/R/CohortCharacterizationDiagnostics.R b/R/CohortCharacterizationDiagnostics.R
index e55132e98..690c81905 100644
--- a/R/CohortCharacterizationDiagnostics.R
+++ b/R/CohortCharacterizationDiagnostics.R
@@ -48,12 +48,15 @@ getCohortCharacteristics <- function(connectionDetails = NULL,
           covariateSettings = covariateSettings,
           aggregated = TRUE
         )
-    })
+    }
+  )
   populationSize <-
     attr(x = featureExtractionOutput, which = "metaData")$populationSize
   populationSize <-
-    dplyr::tibble(cohortId = names(populationSize) %>% as.numeric(),
-                  populationSize = populationSize)
+    dplyr::tibble(
+      cohortId = names(populationSize) %>% as.numeric(),
+      populationSize = populationSize
+    )
 
   if (!"analysisRef" %in% names(results)) {
     results$analysisRef <- featureExtractionOutput$analysisRef
@@ -82,8 +85,8 @@ getCohortCharacteristics <- function(connectionDetails = NULL,
       dplyr::mutate(p = sumValue / populationSize)
 
     if (nrow(covariates %>%
-               dplyr::filter(p > 1) %>%
-               dplyr::collect()) > 0) {
+      dplyr::filter(p > 1) %>%
+      dplyr::collect()) > 0) {
       stop(
         paste0(
           "During characterization, population size (denominator) was found to be smaller than features Value (numerator).",
@@ -98,37 +101,37 @@ getCohortCharacteristics <- function(connectionDetails = NULL,
       dplyr::rename(mean = averageValue) %>%
       dplyr::select(-populationSize)
 
-      if (FeatureExtraction::isTemporalCovariateData(featureExtractionOutput)) {
-        covariates <- covariates %>%
-          dplyr::select(
-            cohortId,
-            timeId,
-            covariateId,
-            sumValue,
-            mean,
-            sd
-          )
-          if (length(is.na(covariates$timeId)) > 0) {
-            covariates[is.na(covariates$timeId),]$timeId <- -1
-          }
-      } else {
-        covariates <- covariates %>%
-          dplyr::mutate(timeId = 0) %>%
-          dplyr::select(
-            cohortId,
-            timeId,
-            covariateId,
-            sumValue,
-            mean,
-            sd
-          )
-      }
-      if ("covariates" %in% names(results)) {
-        Andromeda::appendToTable(results$covariates, covariates)
-      } else {
-        results$covariates <- covariates
+    if (FeatureExtraction::isTemporalCovariateData(featureExtractionOutput)) {
+      covariates <- covariates %>%
+        dplyr::select(
+          cohortId,
+          timeId,
+          covariateId,
+          sumValue,
+          mean,
+          sd
+        )
+      if (length(is.na(covariates$timeId)) > 0) {
+        covariates[is.na(covariates$timeId), ]$timeId <- -1
       }
+    } else {
+      covariates <- covariates %>%
+        dplyr::mutate(timeId = 0) %>%
+        dplyr::select(
+          cohortId,
+          timeId,
+          covariateId,
+          sumValue,
+          mean,
+          sd
+        )
     }
+    if ("covariates" %in% names(results)) {
+      Andromeda::appendToTable(results$covariates, covariates)
+    } else {
+      results$covariates <- covariates
+    }
+  }
 
   if ("covariatesContinuous" %in% names(featureExtractionOutput) &&
     dplyr::pull(dplyr::count(featureExtractionOutput$covariatesContinuous)) > 0) {
@@ -151,12 +154,14 @@ getCohortCharacteristics <- function(connectionDetails = NULL,
           sd
         )
       if (length(is.na(covariates$timeId)) > 0) {
-        covariates[is.na(covariates$timeId),]$timeId <- -1
+        covariates[is.na(covariates$timeId), ]$timeId <- -1
       }
     } else {
       covariates <- covariates %>%
-        dplyr::mutate(sumValue = -1,
-                      timeId = 0) %>%
+        dplyr::mutate(
+          sumValue = -1,
+          timeId = 0
+        ) %>%
         dplyr::select(
           cohortId,
           timeId,
@@ -179,10 +184,12 @@ getCohortCharacteristics <- function(connectionDetails = NULL,
   }
 
   delta <- Sys.time() - startTime
-  ParallelLogger::logInfo("Cohort characterization took ",
-                          signif(delta, 3),
-                          " ",
-                          attr(delta, "units"))
+  ParallelLogger::logInfo(
+    "Cohort characterization took ",
+    signif(delta, 3),
+    " ",
+    attr(delta, "units")
+  )
   return(results)
 }
 
@@ -221,9 +228,10 @@ executeCohortCharacterization <- function(connection,
   )
 
   if (!incremental) {
-    for (outputFile in c(covariateValueFileName, covariateValueContFileName,
-                         covariateRefFileName, analysisRefFileName, timeRefFileName)) {
-
+    for (outputFile in c(
+      covariateValueFileName, covariateValueContFileName,
+      covariateRefFileName, analysisRefFileName, timeRefFileName
+    )) {
       if (file.exists(outputFile)) {
         ParallelLogger::logInfo("Not in incremental mode - Removing file", outputFile, " and replacing")
         unlink(outputFile)
@@ -309,10 +317,12 @@ executeCohortCharacterization <- function(connection,
     }
   }
   delta <- Sys.time() - startCohortCharacterization
-  ParallelLogger::logInfo("Running ",
-                          jobName,
-                          " took",
-                          signif(delta, 3),
-                          " ",
-                          attr(delta, "units"))
+  ParallelLogger::logInfo(
+    "Running ",
+    jobName,
+    " took",
+    signif(delta, 3),
+    " ",
+    attr(delta, "units")
+  )
 }
diff --git a/R/CohortRelationship.R b/R/CohortRelationship.R
index 00d10af4c..9ee7e252e 100644
--- a/R/CohortRelationship.R
+++ b/R/CohortRelationship.R
@@ -122,7 +122,7 @@ runCohortRelationshipDiagnostics <-
             package = utils::packageName()
           )
         )
-      
+
       DatabaseConnector::renderTranslateExecuteSql(
         connection = connection,
         tempEmulationSchema = tempEmulationSchema,
@@ -135,7 +135,7 @@ runCohortRelationshipDiagnostics <-
         cohort_database_schema = cohortDatabaseSchema,
         cohort_table = cohortTable
       )
-      
+
       DatabaseConnector::renderTranslateQuerySqlToAndromeda(
         connection = connection,
         tempEmulationSchema = tempEmulationSchema,
@@ -210,13 +210,17 @@ executeCohortRelationshipDiagnostics <- function(connection,
 
   allCohortIds <- cohortDefinitionSet %>%
     dplyr::select(cohortId, checksum) %>%
-    dplyr::rename(targetCohortId = cohortId,
-                  targetChecksum = checksum) %>%
+    dplyr::rename(
+      targetCohortId = cohortId,
+      targetChecksum = checksum
+    ) %>%
     dplyr::distinct()
   combinationsOfPossibleCohortRelationships <- allCohortIds %>%
     tidyr::crossing(allCohortIds %>%
-                      dplyr::rename(comparatorCohortId = targetCohortId,
-                                    comparatorChecksum = targetChecksum)) %>%
+      dplyr::rename(
+        comparatorCohortId = targetCohortId,
+        comparatorChecksum = targetChecksum
+      )) %>%
     dplyr::filter(targetCohortId != comparatorCohortId) %>%
     dplyr::arrange(targetCohortId, comparatorCohortId) %>%
     dplyr::mutate(checksum = paste0(targetChecksum, comparatorChecksum))
@@ -230,7 +234,7 @@ executeCohortRelationshipDiagnostics <- function(connection,
 
   if (nrow(subset) > 0) {
     if (incremental &&
-        (nrow(cohortDefinitionSet) - (length(subset$targetCohortId %>% unique()))) > 0) {
+      (nrow(cohortDefinitionSet) - (length(subset$targetCohortId %>% unique()))) > 0) {
       ParallelLogger::logInfo(
         sprintf(
           " - Skipping %s target cohorts in incremental mode because the relationships has already been computed with other cohorts.",
@@ -240,12 +244,12 @@ executeCohortRelationshipDiagnostics <- function(connection,
     }
 
     if (incremental &&
-        (nrow(combinationsOfPossibleCohortRelationships) - (
-          nrow(
-            combinationsOfPossibleCohortRelationships %>%
+      (nrow(combinationsOfPossibleCohortRelationships) - (
+        nrow(
+          combinationsOfPossibleCohortRelationships %>%
             dplyr::filter(targetCohortId %in% c(subset$targetCohortId))
-          )
-        )) > 0) {
+        )
+      )) > 0) {
       ParallelLogger::logInfo(
         sprintf(
           " - Skipping %s combinations in incremental mode because these were previously computed.",
@@ -333,7 +337,7 @@ executeCohortRelationshipDiagnostics <- function(connection,
       timeExecution(
         exportFolder,
         "runCohortRelationshipDiagnostics",
-        c(subset[start:end,]$targetCohortId %>% unique(), subset[start:end,]$comparatorCohortId %>% unique()),
+        c(subset[start:end, ]$targetCohortId %>% unique(), subset[start:end, ]$comparatorCohortId %>% unique()),
         parent = "executeCohortRelationshipDiagnostics",
         expr = {
           output <-
@@ -342,10 +346,12 @@ executeCohortRelationshipDiagnostics <- function(connection,
               cohortDatabaseSchema = cohortDatabaseSchema,
               tempEmulationSchema = tempEmulationSchema,
               cohortTable = cohortTable,
-              targetCohortIds = subset[start:end,]$targetCohortId %>% unique(),
-              comparatorCohortIds = subset[start:end,]$comparatorCohortId %>% unique(),
-              relationshipDays = dplyr::tibble(startDay = temporalStartDays,
-                                               endDay = temporalEndDays)
+              targetCohortIds = subset[start:end, ]$targetCohortId %>% unique(),
+              comparatorCohortIds = subset[start:end, ]$comparatorCohortId %>% unique(),
+              relationshipDays = dplyr::tibble(
+                startDay = temporalStartDays,
+                endDay = temporalEndDays
+              )
             )
         }
       )
@@ -364,26 +370,28 @@ executeCohortRelationshipDiagnostics <- function(connection,
       )
 
       recordTasksDone(
-        cohortId = subset[start:end,]$targetCohortId,
-        comparatorId = subset[start:end,]$comparatorCohortId,
-        targetChecksum = subset[start:end,]$targetChecksum,
-        comparatorChecksum = subset[start:end,]$comparatorChecksum,
+        cohortId = subset[start:end, ]$targetCohortId,
+        comparatorId = subset[start:end, ]$comparatorCohortId,
+        targetChecksum = subset[start:end, ]$targetChecksum,
+        comparatorChecksum = subset[start:end, ]$comparatorChecksum,
         task = "runCohortRelationship",
-        checksum = subset[start:end,]$checksum,
+        checksum = subset[start:end, ]$checksum,
         recordKeepingFile = recordKeepingFile,
         incremental = incremental
       )
       deltaIteration <- Sys.time() - startCohortRelationship
-      ParallelLogger::logInfo("    - Running Cohort Relationship iteration with batchsize ",
-                              batchSize,
-                              " from row number ",
-                              start,
-                              " to ",
-                              end,
-                              " took ",
-                              signif(deltaIteration, 3),
-                              " ",
-                              attr(deltaIteration, "units"))
+      ParallelLogger::logInfo(
+        "    - Running Cohort Relationship iteration with batchsize ",
+        batchSize,
+        " from row number ",
+        start,
+        " to ",
+        end,
+        " took ",
+        signif(deltaIteration, 3),
+        " ",
+        attr(deltaIteration, "units")
+      )
     }
   } else {
     ParallelLogger::logInfo("    - Skipping in incremental mode.")
diff --git a/R/ConceptSets.R b/R/ConceptSets.R
index 10c42f91f..36d63fae9 100644
--- a/R/ConceptSets.R
+++ b/R/ConceptSets.R
@@ -125,7 +125,7 @@ combineConceptSetsFromCohorts <- function(cohorts) {
   conceptSetCounter <- 0
 
   for (i in (1:nrow(cohorts))) {
-    cohort <- cohorts[i,]
+    cohort <- cohorts[i, ]
     sql <-
       extractConceptSetsSqlFromCohortSql(cohortSql = cohort$sql)
     json <-
@@ -197,13 +197,13 @@ mergeTempTables <-
       )
     sql <-
       SqlRender::translate(sql,
-                           targetDialect = connection@dbms,
-                           tempEmulationSchema = tempEmulationSchema
+        targetDialect = connection@dbms,
+        tempEmulationSchema = tempEmulationSchema
       )
     DatabaseConnector::executeSql(connection,
-                                  sql,
-                                  progressBar = FALSE,
-                                  reportOverallTime = FALSE
+      sql,
+      progressBar = FALSE,
+      reportOverallTime = FALSE
     )
 
     # Drop temp tables:
@@ -212,13 +212,13 @@ mergeTempTables <-
         sprintf("TRUNCATE TABLE %s;\nDROP TABLE %s;", tempTable, tempTable)
       sql <-
         SqlRender::translate(sql,
-                             targetDialect = connection@dbms,
-                             tempEmulationSchema = tempEmulationSchema
+          targetDialect = connection@dbms,
+          tempEmulationSchema = tempEmulationSchema
         )
       DatabaseConnector::executeSql(connection,
-                                    sql,
-                                    progressBar = FALSE,
-                                    reportOverallTime = FALSE
+        sql,
+        progressBar = FALSE,
+        reportOverallTime = FALSE
       )
     }
   }
@@ -261,13 +261,13 @@ instantiateUniqueConceptSets <- function(uniqueConceptSets,
     sqlSubset <-
       SqlRender::render(sqlSubset, vocabulary_database_schema = vocabularyDatabaseSchema)
     sqlSubset <- SqlRender::translate(sqlSubset,
-                                      targetDialect = connection@dbms,
-                                      tempEmulationSchema = tempEmulationSchema
+      targetDialect = connection@dbms,
+      tempEmulationSchema = tempEmulationSchema
     )
     DatabaseConnector::executeSql(connection,
-                                  sqlSubset,
-                                  progressBar = FALSE,
-                                  reportOverallTime = FALSE
+      sqlSubset,
+      progressBar = FALSE,
+      reportOverallTime = FALSE
     )
   }
   utils::setTxtProgressBar(pb, 1)
@@ -298,7 +298,7 @@ getCodeSetIds <- function(criterionList) {
     return(NULL)
   } else {
     return(dplyr::tibble(domain = names(criterionList), codeSetIds = codeSetIds)
-             %>% filter(!is.na(codeSetIds)))
+    %>% filter(!is.na(codeSetIds)))
   }
 }
 
@@ -386,8 +386,8 @@ runConceptSetDiagnostics <- function(connection,
   )
 
   uniqueConceptSets <-
-    conceptSets[!duplicated(conceptSets$uniqueConceptSetId),] %>%
-      dplyr::select(-cohortId, -conceptSetId)
+    conceptSets[!duplicated(conceptSets$uniqueConceptSetId), ] %>%
+    dplyr::select(-cohortId, -conceptSetId)
 
   timeExecution(
     exportFolder,
@@ -403,11 +403,11 @@ runConceptSetDiagnostics <- function(connection,
         tempEmulationSchema = tempEmulationSchema,
         conceptSetsTable = "#inst_concept_sets"
       )
-    })
+    }
+  )
 
   if ((runIncludedSourceConcepts && nrow(subsetIncluded) > 0) ||
     (runOrphanConcepts && nrow(subsetOrphans) > 0)) {
-
     timeExecution(
       exportFolder,
       taskName = "createConceptCountsTable",
@@ -422,7 +422,8 @@ runConceptSetDiagnostics <- function(connection,
           conceptCountsTable = conceptCountsTable,
           conceptCountsTableIsTemp = conceptCountsTableIsTemp
         )
-      })
+      }
+    )
   }
   if (runIncludedSourceConcepts) {
     timeExecution(
@@ -431,7 +432,6 @@ runConceptSetDiagnostics <- function(connection,
       cohortIds = NULL,
       parent = "runConceptSetDiagnostics",
       expr = {
-
         # Included concepts ------------------------------------------------------------------
         ParallelLogger::logInfo("Fetching included source concepts")
         # TODO: Disregard empty cohorts in tally:
@@ -465,7 +465,7 @@ runConceptSetDiagnostics <- function(connection,
                 tempEmulationSchema = tempEmulationSchema,
                 snakeCaseToCamelCase = TRUE
               ) %>%
-                tidyr::tibble()
+              tidyr::tibble()
 
             counts <- counts %>%
               dplyr::rename(uniqueConceptSetId = conceptSetId) %>%
@@ -560,7 +560,8 @@ runConceptSetDiagnostics <- function(connection,
             ))
           }
         }
-      })
+      }
+    )
   }
 
   if (runBreakdownIndexEvents) {
@@ -595,7 +596,6 @@ runConceptSetDiagnostics <- function(connection,
           cohortIds = cohort$cohortId,
           parent = "runConceptSetDiagnostics",
           expr = {
-
             cohortDefinition <-
               RJSONIO::fromJSON(cohort$json, digits = 23)
             primaryCodesetIds <-
@@ -603,7 +603,7 @@ runConceptSetDiagnostics <- function(connection,
                 cohortDefinition$PrimaryCriteria$CriteriaList,
                 getCodeSetIds
               ) %>%
-                dplyr::bind_rows()
+              dplyr::bind_rows()
             if (nrow(primaryCodesetIds) == 0) {
               warning(
                 "No primary event criteria concept sets found for cohort id: ",
@@ -612,13 +612,13 @@ runConceptSetDiagnostics <- function(connection,
               return(tidyr::tibble())
             }
             primaryCodesetIds <- primaryCodesetIds %>% dplyr::filter(domain %in%
-                                                                       c(domains$domain %>% unique()))
+              c(domains$domain %>% unique()))
             if (nrow(primaryCodesetIds) == 0) {
               warning(
                 "Primary event criteria concept sets found for cohort id: ",
                 cohort$cohortId, " but,", "\nnone of the concept sets belong to the supported domains.",
                 "\nThe supported domains are:\n", paste(domains$domain,
-                                                        collapse = ", "
+                  collapse = ", "
                 )
               )
               return(tidyr::tibble())
@@ -643,7 +643,7 @@ runConceptSetDiagnostics <- function(connection,
             primaryCodesetIds <- dplyr::bind_rows(primaryCodesetIds)
 
             getCounts <- function(row) {
-              domain <- domains[domains$domain == row$domain,]
+              domain <- domains[domains$domain == row$domain, ]
               sql <-
                 SqlRender::loadRenderTranslateSql(
                   "CohortEntryBreakdown.sql",
@@ -681,7 +681,7 @@ runConceptSetDiagnostics <- function(connection,
                   store_table = "#breakdown",
                   snakeCaseToCamelCase = TRUE
                 ) %>%
-                  tidyr::tibble()
+                tidyr::tibble()
               if (!is.null(conceptIdTable)) {
                 sql <- "INSERT INTO @concept_id_table (concept_id)
                   SELECT DISTINCT concept_id
@@ -711,8 +711,8 @@ runConceptSetDiagnostics <- function(connection,
 
             counts <-
               lapply(split(primaryCodesetIds, 1:nrow(primaryCodesetIds)), getCounts) %>%
-                dplyr::bind_rows() %>%
-                dplyr::arrange(conceptCount)
+              dplyr::bind_rows() %>%
+              dplyr::arrange(conceptCount)
 
             if (nrow(counts) > 0) {
               counts$cohortId <- cohort$cohortId
@@ -724,7 +724,8 @@ runConceptSetDiagnostics <- function(connection,
               return(dplyr::tibble())
             }
             return(counts)
-          })
+          }
+        )
       }
 
       data <-
@@ -794,7 +795,7 @@ runConceptSetDiagnostics <- function(connection,
       # [OPTIMIZATION idea] can we modify the sql to do this for all uniqueConceptSetId in one query using group by?
       data <- list()
       for (i in (1:nrow(uniqueConceptSets))) {
-        conceptSet <- uniqueConceptSets[i,]
+        conceptSet <- uniqueConceptSets[i, ]
         ParallelLogger::logInfo(
           "- Finding orphan concepts for concept set '",
           conceptSet$conceptSetName,
@@ -807,7 +808,6 @@ runConceptSetDiagnostics <- function(connection,
           parent = "runConceptSetDiagnostics",
           cohortIds = paste("concept_set-", conceptSet$name),
           expr = {
-
             data[[i]] <- .findOrphanConcepts(
               connection = connection,
               cdmDatabaseSchema = cdmDatabaseSchema,
@@ -835,7 +835,8 @@ runConceptSetDiagnostics <- function(connection,
                 reportOverallTime = FALSE
               )
             }
-          })
+          }
+        )
         sql <-
           "TRUNCATE TABLE @orphan_concept_table;\nDROP TABLE @orphan_concept_table;"
         DatabaseConnector::renderTranslateExecuteSql(
@@ -940,16 +941,16 @@ runConceptSetDiagnostics <- function(connection,
       tempEmulationSchema = tempEmulationSchema,
       snakeCaseToCamelCase = TRUE
     ) %>%
-      dplyr::tibble() %>%
-      dplyr::rename(uniqueConceptSetId = codesetId) %>%
-      dplyr::inner_join(conceptSets,
-                        by = "uniqueConceptSetId"
-      ) %>%
-      dplyr::select(
-        cohortId,
-        conceptSetId,
-        conceptId
-      )
+    dplyr::tibble() %>%
+    dplyr::rename(uniqueConceptSetId = codesetId) %>%
+    dplyr::inner_join(conceptSets,
+      by = "uniqueConceptSetId"
+    ) %>%
+    dplyr::select(
+      cohortId,
+      conceptSetId,
+      conceptId
+    )
 
   resolvedConceptIds <- makeDataExportable(
     x = resolvedConceptIds,
diff --git a/R/DataSourceInformation.R b/R/DataSourceInformation.R
index 72f66db48..de9e2b785 100644
--- a/R/DataSourceInformation.R
+++ b/R/DataSourceInformation.R
@@ -49,9 +49,11 @@ getCdmDataSourceInformation <-
       }
     }
 
-    if (!DatabaseConnector::existsTable(connection = connection,
-                                        databaseSchema = cdmDatabaseSchema,
-                                        tableName = "cdm_source")) {
+    if (!DatabaseConnector::existsTable(
+      connection = connection,
+      databaseSchema = cdmDatabaseSchema,
+      tableName = "cdm_source"
+    )) {
       warning("CDM Source table not found in CDM. Metadata on CDM source will be limited.")
       return(NULL)
     }
@@ -90,9 +92,10 @@ getCdmDataSourceInformation <-
     sourceReleaseDate <- as.Date(NA)
     if ("sourceReleaseDate" %in% colnames(cdmDataSource)) {
       if (class(cdmDataSource$sourceReleaseDate) != "Date") {
-        try(sourceReleaseDate <-
-          max(as.Date(cdmDataSource$sourceReleaseDate)),
-        silent = TRUE
+        try(
+          sourceReleaseDate <-
+            max(as.Date(cdmDataSource$sourceReleaseDate)),
+          silent = TRUE
         )
       } else {
         sourceReleaseDate <- max(as.Date(cdmDataSource$sourceReleaseDate))
diff --git a/R/ExportCharacterization.R b/R/ExportCharacterization.R
index ead0585b8..d4d344ed7 100644
--- a/R/ExportCharacterization.R
+++ b/R/ExportCharacterization.R
@@ -55,7 +55,8 @@ exportCharacterization <- function(characteristics,
         sd = round(sd, digits = 4)
       ) %>%
       dplyr::select(-cohortEntries, -cohortSubjects) %>%
-      dplyr::distinct() %>% makeDataExportable(
+      dplyr::distinct() %>%
+      makeDataExportable(
         tableName = "temporal_covariate_value",
         minCellCount = minCellCount,
         databaseId = databaseId
@@ -74,7 +75,7 @@ exportCharacterization <- function(characteristics,
         covariateId = covariateRef$covariateId
       )
 
-      analysisRef <-  makeDataExportable(
+      analysisRef <- makeDataExportable(
         x = characteristics$analysisRef,
         tableName = "temporal_analysis_ref",
         minCellCount = minCellCount
@@ -109,12 +110,12 @@ exportCharacterization <- function(characteristics,
   if (!"covariatesContinuous" %in% names(characteristics)) {
     ParallelLogger::logInfo("No continuous characterization output for submitted cohorts")
   } else if (dplyr::pull(dplyr::count(characteristics$covariateRef)) > 0) {
-     characteristics$filteredCovariatesContinous <- makeDataExportable(
-       x = characteristics$covariatesContinuous,
-       tableName = "temporal_covariate_value_dist",
-       minCellCount = minCellCount,
-       databaseId = databaseId
-     )
+    characteristics$filteredCovariatesContinous <- makeDataExportable(
+      x = characteristics$covariatesContinuous,
+      tableName = "temporal_covariate_value_dist",
+      minCellCount = minCellCount,
+      databaseId = databaseId
+    )
 
     if (dplyr::pull(dplyr::count(characteristics$filteredCovariatesContinous)) > 0) {
       writeToCsv(
diff --git a/R/InclusionRules.R b/R/InclusionRules.R
index 21e08056e..5fb8dbea0 100644
--- a/R/InclusionRules.R
+++ b/R/InclusionRules.R
@@ -44,21 +44,23 @@ getInclusionStats <- function(connection,
     ParallelLogger::logInfo("Exporting inclusion rules with CohortGenerator")
 
     timeExecution(exportFolder,
-                  "getInclusionStatsCohortGenerator",
-                  parent = "getInclusionStats",
-                  expr =
-                  {
-                    CohortGenerator::insertInclusionRuleNames(
-                      connection = connection,
-                      cohortDefinitionSet = subset,
-                      cohortDatabaseSchema = cohortDatabaseSchema,
-                      cohortInclusionTable = cohortTableNames$cohortInclusionTable
-                    )
+      "getInclusionStatsCohortGenerator",
+      parent = "getInclusionStats",
+      expr = {
+        CohortGenerator::insertInclusionRuleNames(
+          connection = connection,
+          cohortDefinitionSet = subset,
+          cohortDatabaseSchema = cohortDatabaseSchema,
+          cohortInclusionTable = cohortTableNames$cohortInclusionTable
+        )
 
-                    stats <- CohortGenerator::getCohortStats(connection = connection,
-                                                             cohortTableNames = cohortTableNames,
-                                                             cohortDatabaseSchema = cohortDatabaseSchema)
-                  })
+        stats <- CohortGenerator::getCohortStats(
+          connection = connection,
+          cohortTableNames = cohortTableNames,
+          cohortDatabaseSchema = cohortDatabaseSchema
+        )
+      }
+    )
     if (!is.null(stats)) {
       if ("cohortInclusionTable" %in% (names(stats))) {
         cohortInclusion <- makeDataExportable(
diff --git a/R/Incremental.R b/R/Incremental.R
index a54246030..34373f55b 100644
--- a/R/Incremental.R
+++ b/R/Incremental.R
@@ -179,7 +179,6 @@ writeToCsv.default <- function(data, fileName, incremental = FALSE, ...) {
       delim = ","
     )
   }
-
 }
 
 writeToCsv.tbl_Andromeda <-
@@ -210,8 +209,8 @@ writeToCsv.tbl_Andromeda <-
 
       addChunk <- function(chunk) {
         if ("timeId" %in% colnames(chunk)) {
-          if (nrow(chunk[is.na(chunk$timeId),]) > 0) {
-            chunk[is.na(chunk$timeId),]$timeId <- 0
+          if (nrow(chunk[is.na(chunk$timeId), ]) > 0) {
+            chunk[is.na(chunk$timeId), ]$timeId <- 0
           }
         } else {
           chunk$timeId <- 0
@@ -266,7 +265,7 @@ saveIncremental <- function(data, fileName, ...) {
       lazy = FALSE
     )
     if ((nrow(previousData)) > 0) {
-      if("database_id" %in% colnames(previousData)) {
+      if ("database_id" %in% colnames(previousData)) {
         previousData$database_id <- as.character(previousData$database_id)
       }
 
diff --git a/R/Private.R b/R/Private.R
index a1ed136e4..188b074ea 100644
--- a/R/Private.R
+++ b/R/Private.R
@@ -324,11 +324,13 @@ timeExecution <- function(exportFolder,
     eval(expr)
     execTime <- Sys.time() - start
   }
-  executionTimes <- data.frame(task = taskName,
-                               startTime = start,
-                               cohortIds = paste(cohortIds, collapse = ";"),
-                               executionTime = execTime,
-                               parent = paste(parent, collapse = ""))
+  executionTimes <- data.frame(
+    task = taskName,
+    startTime = start,
+    cohortIds = paste(cohortIds, collapse = ";"),
+    executionTime = execTime,
+    parent = paste(parent, collapse = "")
+  )
 
   readr::write_csv(executionTimes, file = executionTimePath, append = file.exists(executionTimePath))
   return(executionTimes)
diff --git a/R/ResultsDataModel.R b/R/ResultsDataModel.R
index 90b50118f..c908ab3ef 100644
--- a/R/ResultsDataModel.R
+++ b/R/ResultsDataModel.R
@@ -49,7 +49,7 @@ fixTableMetadataForBackwardCompatibility <- function(table, tableName) {
     if (!"metadata" %in% colnames(table)) {
       data <- list()
       for (i in (1:nrow(table))) {
-        data[[i]] <- table[i,]
+        data[[i]] <- table[i, ]
         colnamesDf <- colnames(data[[i]])
         metaDataList <- list()
         for (j in (1:length(colnamesDf))) {
@@ -99,7 +99,7 @@ checkFixColumnNames <-
     expectedNames <- tableSpecs %>%
       dplyr::select(columnName) %>%
       dplyr::anti_join(dplyr::filter(optionalNames, !columnName %in% observeredNames),
-                       by = "columnName"
+        by = "columnName"
       ) %>%
       dplyr::arrange(columnName) %>%
       dplyr::pull()
@@ -206,7 +206,7 @@ checkAndFixDuplicateRows <-
            specifications = getResultsDataModelSpecifications()) {
     primaryKeys <- specifications %>%
       dplyr::filter(tableName == !!tableName &
-                      primaryKey == "Yes") %>%
+        primaryKey == "Yes") %>%
       dplyr::select(columnName) %>%
       dplyr::pull()
     duplicatedRows <- duplicated(table[, primaryKeys])
@@ -219,7 +219,7 @@ checkAndFixDuplicateRows <-
           sum(duplicatedRows)
         )
       )
-      return(table[!duplicatedRows,])
+      return(table[!duplicatedRows, ])
     } else {
       return(table)
     }
@@ -233,7 +233,7 @@ appendNewRows <-
     if (nrow(data) > 0) {
       primaryKeys <- specifications %>%
         dplyr::filter(tableName == !!tableName &
-                        primaryKey == "Yes") %>%
+          primaryKey == "Yes") %>%
         dplyr::select(columnName) %>%
         dplyr::pull()
       newData <- newData %>%
@@ -245,14 +245,18 @@ appendNewRows <-
 # Private function for testing migrations in isolation
 .createDataModel <- function(connection, databaseSchema, tablePrefix) {
   sqlParams <- getPrefixedTableNames(tablePrefix)
-  sql <- do.call(SqlRender::loadRenderTranslateSql,
-                 c(sqlParams,
-                   list(
-                     sqlFilename = "CreateResultsDataModel.sql",
-                     packageName = utils::packageName(),
-                     dbms = connection@dbms,
-                     results_schema = databaseSchema
-                   )))
+  sql <- do.call(
+    SqlRender::loadRenderTranslateSql,
+    c(
+      sqlParams,
+      list(
+        sqlFilename = "CreateResultsDataModel.sql",
+        packageName = utils::packageName(),
+        dbms = connection@dbms,
+        results_schema = databaseSchema
+      )
+    )
+  )
   DatabaseConnector::executeSql(connection, sql)
 }
 
@@ -276,9 +280,11 @@ createResultsDataModel <- function(connectionDetails = NULL,
   on.exit(DatabaseConnector::disconnect(connection))
 
   .createDataModel(connection, databaseSchema, tablePrefix)
-  migrateDataModel(connectionDetails = connectionDetails,
-                   databaseSchema = databaseSchema,
-                   tablePrefix = tablePrefix)
+  migrateDataModel(
+    connectionDetails = connectionDetails,
+    databaseSchema = databaseSchema,
+    tablePrefix = tablePrefix
+  )
 }
 
 naToEmpty <- function(x) {
@@ -360,7 +366,7 @@ uploadResults <- function(connectionDetails,
 
     primaryKey <- specifications %>%
       filter(tableName == !!tableName &
-               primaryKey == "Yes") %>%
+        primaryKey == "Yes") %>%
       select(columnName) %>%
       pull()
 
@@ -459,8 +465,8 @@ uploadResults <- function(connectionDetails,
         if (!is.null(env$primaryKeyValuesInDb)) {
           primaryKeyValuesInChunk <- unique(chunk[env$primaryKey])
           duplicates <- inner_join(env$primaryKeyValuesInDb,
-                                   primaryKeyValuesInChunk,
-                                   by = env$primaryKey
+            primaryKeyValuesInChunk,
+            by = env$primaryKey
           )
           if (nrow(duplicates) != 0) {
             if ("database_id" %in% env$primaryKey ||
@@ -527,7 +533,6 @@ uploadResults <- function(connectionDetails,
 
 deleteFromServer <-
   function(connection, schema, tableName, keyValues, tablePrefix) {
-
     createSqlStatement <- function(i) {
       sql <- paste0(
         "DELETE FROM ",
@@ -537,7 +542,7 @@ deleteFromServer <-
         tableName,
         "\nWHERE ",
         paste(paste0(
-          colnames(keyValues), " = '", keyValues[i,], "'"
+          colnames(keyValues), " = '", keyValues[i, ], "'"
         ), collapse = " AND "),
         ";"
       )
@@ -591,9 +596,9 @@ deleteAllRecordsForDatabaseId <- function(connection,
       database_id = databaseId,
     )
     DatabaseConnector::renderTranslateExecuteSql(connection,
-                                                 sql,
-                                                 progressBar = FALSE,
-                                                 reportOverallTime = FALSE
+      sql,
+      progressBar = FALSE,
+      reportOverallTime = FALSE
     )
   }
 }
@@ -615,10 +620,11 @@ migrateDataModel <- function(connectionDetails, databaseSchema, tablePrefix = ""
 
   ParallelLogger::logInfo("Updating version number")
   updateVersionSql <- SqlRender::loadRenderTranslateSql("UpdateVersionNumber.sql",
-                                                        packageName = utils::packageName(),
-                                                        database_schema = databaseSchema,
-                                                        table_prefix = tablePrefix,
-                                                        dbms = connectionDetails$dbms)
+    packageName = utils::packageName(),
+    database_schema = databaseSchema,
+    table_prefix = tablePrefix,
+    dbms = connectionDetails$dbms
+  )
 
   connection <- DatabaseConnector::connect(connectionDetails = connectionDetails)
   on.exit(DatabaseConnector::disconnect(connection))
@@ -638,9 +644,11 @@ migrateDataModel <- function(connectionDetails, databaseSchema, tablePrefix = ""
 #' @returns Instance of ResultModelManager::DataMigrationManager that has interface for converting existing data models
 #' @export
 getDataMigrator <- function(connectionDetails, databaseSchema, tablePrefix = "") {
-  ResultModelManager::DataMigrationManager$new(connectionDetails = connectionDetails,
-                                               databaseSchema = databaseSchema,
-                                               tablePrefix = tablePrefix,
-                                               migrationPath = "migrations",
-                                               packageName = utils::packageName())
+  ResultModelManager::DataMigrationManager$new(
+    connectionDetails = connectionDetails,
+    databaseSchema = databaseSchema,
+    tablePrefix = tablePrefix,
+    migrationPath = "migrations",
+    packageName = utils::packageName()
+  )
 }
diff --git a/R/RunDiagnostics.R b/R/RunDiagnostics.R
index c2e2b1236..0746b4175 100644
--- a/R/RunDiagnostics.R
+++ b/R/RunDiagnostics.R
@@ -227,12 +227,7 @@ executeDiagnostics <- function(cohortDefinitionSet,
       incremental = callingArgs$incremental,
       temporalCovariateSettings = callingArgs$temporalCovariateSettings
     ) %>%
-      RJSONIO::toJSON(digits = 23, pretty = TRUE)
-
-  # take package dependency snapshot
-  packageDependencySnapShotJson <-
-    takepackageDependencySnapshot() %>%
-      RJSONIO::toJSON(digits = 23, pretty = TRUE)
+    RJSONIO::toJSON(digits = 23, pretty = TRUE)
 
   exportFolder <- normalizePath(exportFolder, mustWork = FALSE)
   incrementalFolder <- normalizePath(incrementalFolder, mustWork = FALSE)
@@ -253,25 +248,25 @@ executeDiagnostics <- function(cohortDefinitionSet,
   errorMessage <- checkmate::makeAssertCollection()
   checkmate::assertList(cohortTableNames, null.ok = FALSE, types = "character", add = errorMessage, names = "named")
   checkmate::assertNames(names(cohortTableNames),
-                         must.include = c(
-                           "cohortTable",
-                           "cohortInclusionTable",
-                           "cohortInclusionResultTable",
-                           "cohortInclusionStatsTable",
-                           "cohortSummaryStatsTable",
-                           "cohortCensorStatsTable"
-                         ),
-                         add = errorMessage
+    must.include = c(
+      "cohortTable",
+      "cohortInclusionTable",
+      "cohortInclusionResultTable",
+      "cohortInclusionStatsTable",
+      "cohortSummaryStatsTable",
+      "cohortCensorStatsTable"
+    ),
+    add = errorMessage
   )
   checkmate::assertDataFrame(cohortDefinitionSet, add = errorMessage)
   checkmate::assertNames(names(cohortDefinitionSet),
-                         must.include = c(
-                           "json",
-                           "cohortId",
-                           "cohortName",
-                           "sql"
-                         ),
-                         add = errorMessage
+    must.include = c(
+      "json",
+      "cohortId",
+      "cohortName",
+      "sql"
+    ),
+    add = errorMessage
   )
 
   cohortTable <- cohortTableNames$cohortTable
@@ -362,26 +357,32 @@ executeDiagnostics <- function(cohortDefinitionSet,
     # All temporal covariate settings objects must be covariateSettings
     checkmate::assert_true(all(lapply(temporalCovariateSettings, class) == c("covariateSettings")), add = errorMessage)
 
-    requiredCharacterisationSettings <- c("DemographicsGender", "DemographicsAgeGroup", "DemographicsRace",
-                                          "DemographicsEthnicity", "DemographicsIndexYear", "DemographicsIndexMonth",
-                                          "ConditionEraGroupOverlap", "DrugEraGroupOverlap", "CharlsonIndex",
-                                          "Chads2", "Chads2Vasc")
+    requiredCharacterisationSettings <- c(
+      "DemographicsGender", "DemographicsAgeGroup", "DemographicsRace",
+      "DemographicsEthnicity", "DemographicsIndexYear", "DemographicsIndexMonth",
+      "ConditionEraGroupOverlap", "DrugEraGroupOverlap", "CharlsonIndex",
+      "Chads2", "Chads2Vasc"
+    )
     presentSettings <- temporalCovariateSettings[[1]][requiredCharacterisationSettings]
     if (!all(unlist(presentSettings))) {
       warning(
         "For cohort charcterization to display standardized results the following covariates must be present in your temporalCovariateSettings: \n\n",
-        paste(requiredCharacterisationSettings, collapse = ", "))
+        paste(requiredCharacterisationSettings, collapse = ", ")
+      )
     }
 
-    requiredTimeDistributionSettings <- c("DemographicsPriorObservationTime",
-                                          "DemographicsPostObservationTime",
-                                          "DemographicsTimeInCohort")
+    requiredTimeDistributionSettings <- c(
+      "DemographicsPriorObservationTime",
+      "DemographicsPostObservationTime",
+      "DemographicsTimeInCohort"
+    )
 
     presentSettings <- temporalCovariateSettings[[1]][requiredTimeDistributionSettings]
     if (!all(unlist(presentSettings))) {
       warning(
         "For time distributions diagnostics to display standardized results the following covariates must be present in your temporalCovariateSettings: \n\n",
-        paste(requiredTimeDistributionSettings, collapse = ", "))
+        paste(requiredTimeDistributionSettings, collapse = ", ")
+      )
     }
 
     # forcefully set ConditionEraGroupStart and drugEraGroupStart to NULL
@@ -389,26 +390,32 @@ executeDiagnostics <- function(cohortDefinitionSet,
     temporalCovariateSettings[[1]]$ConditionEraGroupStart <- NULL
     temporalCovariateSettings[[1]]$DrugEraGroupStart <- NULL
 
-    checkmate::assert_integerish(x = temporalCovariateSettings[[1]]$temporalStartDays,
-                                 any.missing = FALSE,
-                                 min.len = 1,
-                                 add = errorMessage)
-    checkmate::assert_integerish(x = temporalCovariateSettings[[1]]$temporalEndDays,
-                                 any.missing = FALSE,
-                                 min.len = 1,
-                                 add = errorMessage)
+    checkmate::assert_integerish(
+      x = temporalCovariateSettings[[1]]$temporalStartDays,
+      any.missing = FALSE,
+      min.len = 1,
+      add = errorMessage
+    )
+    checkmate::assert_integerish(
+      x = temporalCovariateSettings[[1]]$temporalEndDays,
+      any.missing = FALSE,
+      min.len = 1,
+      add = errorMessage
+    )
     checkmate::reportAssertions(collection = errorMessage)
 
     # Adding required temporal windows required in results viewer
     requiredTemporalPairs <-
-      list(c(-365, 0),
-           c(-30, 0),
-           c(-365, -31),
-           c(-30, -1),
-           c(0, 0),
-           c(1, 30),
-           c(31, 365),
-           c(-9999, 9999))
+      list(
+        c(-365, 0),
+        c(-30, 0),
+        c(-365, -31),
+        c(-30, -1),
+        c(0, 0),
+        c(1, 30),
+        c(31, 365),
+        c(-9999, 9999)
+      )
     for (p1 in requiredTemporalPairs) {
       found <- FALSE
       for (i in 1:length(temporalCovariateSettings[[1]]$temporalStartDays)) {
@@ -444,17 +451,17 @@ executeDiagnostics <- function(cohortDefinitionSet,
     sort()
   cohortTableColumnNamesExpected <-
     getResultsDataModelSpecifications() %>%
-      dplyr::filter(tableName == "cohort") %>%
-      dplyr::pull(columnName) %>%
-      SqlRender::snakeCaseToCamelCase() %>%
-      sort()
+    dplyr::filter(tableName == "cohort") %>%
+    dplyr::pull(columnName) %>%
+    SqlRender::snakeCaseToCamelCase() %>%
+    sort()
   cohortTableColumnNamesRequired <-
     getResultsDataModelSpecifications() %>%
-      dplyr::filter(tableName == "cohort") %>%
-      dplyr::filter(isRequired == "Yes") %>%
-      dplyr::pull(columnName) %>%
-      SqlRender::snakeCaseToCamelCase() %>%
-      sort()
+    dplyr::filter(tableName == "cohort") %>%
+    dplyr::filter(isRequired == "Yes") %>%
+    dplyr::pull(columnName) %>%
+    SqlRender::snakeCaseToCamelCase() %>%
+    sort()
 
   expectedButNotObsevered <-
     setdiff(x = cohortTableColumnNamesExpected, y = cohortTableColumnNamesObserved)
@@ -534,8 +541,8 @@ executeDiagnostics <- function(cohortDefinitionSet,
         }
       }
       vocabularyVersion <- getVocabularyVersion(connection, vocabularyDatabaseSchema)
-
-    })
+    }
+  )
 
   cohortDefinitionSet$checksum <- computeChecksum(cohortDefinitionSet$sql)
 
@@ -570,7 +577,8 @@ executeDiagnostics <- function(cohortDefinitionSet,
         snakeCaseToCamelCase = TRUE,
         tempEmulationSchema = tempEmulationSchema
       )
-    })
+    }
+  )
   # Database metadata ---------------------------------------------
   saveDatabaseMetaData(
     databaseId = databaseId,
@@ -600,7 +608,8 @@ executeDiagnostics <- function(cohortDefinitionSet,
         minCellCount = minCellCount,
         databaseId = databaseId
       )
-    })
+    }
+  )
 
   if (nrow(cohortCounts) > 0) {
     instantiatedCohorts <- cohortCounts %>%
@@ -639,7 +648,8 @@ executeDiagnostics <- function(cohortDefinitionSet,
           minCellCount = minCellCount,
           recordKeepingFile = recordKeepingFile
         )
-      })
+      }
+    )
   }
 
   # Concept set diagnostics -----------------------------------------------
@@ -674,7 +684,8 @@ executeDiagnostics <- function(cohortDefinitionSet,
           conceptIdTable = "#concept_ids",
           recordKeepingFile = recordKeepingFile
         )
-      })
+      }
+    )
   }
 
   # Time series ----------------------------------------------------------------------
@@ -700,7 +711,8 @@ executeDiagnostics <- function(cohortDefinitionSet,
           recordKeepingFile = recordKeepingFile,
           observationPeriodDateRange = observationPeriodDateRange
         )
-      })
+      }
+    )
   }
 
 
@@ -727,7 +739,8 @@ executeDiagnostics <- function(cohortDefinitionSet,
           recordKeepingFile = recordKeepingFile,
           incremental = incremental
         )
-      })
+      }
+    )
   }
 
   # Incidence rates --------------------------------------------------------------------------------------
@@ -752,7 +765,8 @@ executeDiagnostics <- function(cohortDefinitionSet,
           recordKeepingFile = recordKeepingFile,
           incremental = incremental
         )
-      })
+      }
+    )
   }
 
   # Cohort relationship ---------------------------------------------------------------------------------
@@ -777,7 +791,8 @@ executeDiagnostics <- function(cohortDefinitionSet,
           recordKeepingFile = recordKeepingFile,
           incremental = incremental
         )
-      })
+      }
+    )
   }
 
   # Temporal Cohort characterization ---------------------------------------------------------------
@@ -813,7 +828,8 @@ executeDiagnostics <- function(cohortDefinitionSet,
           timeRefFileName = file.path(exportFolder, "temporal_time_ref.csv"),
           minCharacterizationMean = minCharacterizationMean
         )
-      })
+      }
+    )
   }
 
   # Store information from the vocabulary on the concepts used -------------------------
@@ -821,8 +837,7 @@ executeDiagnostics <- function(cohortDefinitionSet,
     exportFolder,
     "exportConceptInformation",
     parent = "executeDiagnostics",
-    expr =
-    {
+    expr = {
       exportConceptInformation(
         connection = connection,
         cdmDatabaseSchema = cdmDatabaseSchema,
@@ -831,15 +846,15 @@ executeDiagnostics <- function(cohortDefinitionSet,
         incremental = incremental,
         exportFolder = exportFolder
       )
-    })
+    }
+  )
   # Delete unique concept ID table ---------------------------------
   ParallelLogger::logTrace("Deleting concept ID table")
   timeExecution(
     exportFolder,
     "DeleteConceptIdTable",
     parent = "executeDiagnostics",
-    expr =
-    {
+    expr = {
       sql <- "TRUNCATE TABLE @table;\nDROP TABLE @table;"
       DatabaseConnector::renderTranslateExecuteSql(
         connection = connection,
@@ -849,7 +864,8 @@ executeDiagnostics <- function(cohortDefinitionSet,
         progressBar = FALSE,
         reportOverallTime = FALSE
       )
-    })
+    }
+  )
 
   # Writing metadata file
   ParallelLogger::logInfo("Retrieving metadata information and writing metadata")
@@ -925,7 +941,7 @@ executeDiagnostics <- function(cohortDefinitionSet,
     # 2
     as.character(attr(delta, "units")),
     # 3
-    packageDependencySnapShotJson,
+    "{}",
     # 4
     callingArgsJson,
     # 5
@@ -996,7 +1012,8 @@ executeDiagnostics <- function(cohortDefinitionSet,
     parent = "executeDiagnostics",
     expr = {
       writeResultsZip(exportFolder, databaseId)
-    })
+    }
+  )
 
   ParallelLogger::logInfo(
     "Computing all diagnostics took ",
diff --git a/R/Shiny.R b/R/Shiny.R
index fa4031824..d00937df1 100644
--- a/R/Shiny.R
+++ b/R/Shiny.R
@@ -58,7 +58,6 @@ launchDiagnosticsExplorer <- function(sqliteDbPath = "MergedCohortDiagnosticsDat
                                       port = 80,
                                       launch.browser = FALSE,
                                       enableAnnotation = TRUE) {
-
   if (is.null(shinyConfigPath)) {
     if (is.null(connectionDetails)) {
       sqliteDbPath <- normalizePath(sqliteDbPath)
@@ -110,34 +109,36 @@ launchDiagnosticsExplorer <- function(sqliteDbPath = "MergedCohortDiagnosticsDat
     on.exit(options("CD-shiny-config" = NULL))
   }
 
-  ensure_installed(c("checkmate",
-                     "DatabaseConnector",
-                     "dplyr",
-                     "plyr",
-                     "ggplot2",
-                     "ggiraph",
-                     "gtable",
-                     "htmltools",
-                     "lubridate",
-                     "pool",
-                     "purrr",
-                     "scales",
-                     "shiny",
-                     "shinydashboard",
-                     "shinyWidgets",
-                     "shinyjs",
-                     "shinycssloaders",
-                     "stringr",
-                     "SqlRender",
-                     "tidyr",
-                     "CirceR",
-                     "rmarkdown",
-                     "reactable",
-                     "markdownInput",
-                     "markdown",
-                     "jsonlite",
-                     "ggh4x",
-                     "yaml"))
+  ensure_installed(c(
+    "checkmate",
+    "DatabaseConnector",
+    "dplyr",
+    "plyr",
+    "ggplot2",
+    "ggiraph",
+    "gtable",
+    "htmltools",
+    "lubridate",
+    "pool",
+    "purrr",
+    "scales",
+    "shiny",
+    "shinydashboard",
+    "shinyWidgets",
+    "shinyjs",
+    "shinycssloaders",
+    "stringr",
+    "SqlRender",
+    "tidyr",
+    "CirceR",
+    "rmarkdown",
+    "reactable",
+    "markdownInput",
+    "markdown",
+    "jsonlite",
+    "ggh4x",
+    "yaml"
+  ))
 
   appDir <-
     system.file("shiny", "DiagnosticsExplorer", package = utils::packageName())
@@ -229,7 +230,7 @@ createMergedResultsFile <-
 createDiagnosticsExplorerZip <- function(outputZipfile = file.path(getwd(), "DiagnosticsExplorer.zip"),
                                          sqliteDbPath = "MergedCohortDiagnosticsData.sqlite",
                                          shinyDirectory = system.file(file.path("shiny", "DiagnosticsExplorer"),
-                                                                      package = "CohortDiagnostics"
+                                           package = "CohortDiagnostics"
                                          ),
                                          overwrite = FALSE) {
   outputZipfile <- normalizePath(outputZipfile, mustWork = FALSE)
diff --git a/R/TakePackageDependencySnapshot.R b/R/TakePackageDependencySnapshot.R
deleted file mode 100644
index 4288acb0c..000000000
--- a/R/TakePackageDependencySnapshot.R
+++ /dev/null
@@ -1,98 +0,0 @@
-# Copyright 2022 Observational Health Data Sciences and Informatics
-#
-# This file is part of CohortDiagnostics
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-#     http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-#' Take a snapshot of the R environment
-#'
-#' @details
-#' This function records all versions used in the R environment as used by runCohortDiagnostics.
-#' This function was borrowed from OhdsiRTools
-#'
-#' @return
-#' A data frame listing all the dependencies of the root package and their version numbers, in the
-#' order in which they should be installed.
-#'
-takepackageDependencySnapshot <- function() {
-  splitPackageList <- function(packageList) {
-    if (is.null(packageList)) {
-      return(c())
-    } else {
-      return(strsplit(
-        gsub(
-          "\\([^)]*\\)", "", gsub(" ", "", gsub("\n", "", packageList))
-        ),
-        ","
-      )[[1]])
-    }
-  }
-
-  fetchDependencies <-
-    function(package,
-             recursive = TRUE,
-             level = 0) {
-      description <- utils::packageDescription(package)
-      packages <- splitPackageList(description$Depends)
-      packages <- c(packages, splitPackageList(description$Imports))
-      packages <-
-        c(packages, splitPackageList(description$LinkingTo))
-      # Note: if we want to include suggests, we'll need to consider circular references packages <-
-      # c(packages, splitPackageList(description$Suggests))
-      packages <- packages[packages != "R"]
-      packages <- data.frame(
-        name = packages,
-        level = rep(
-          level,
-          length(packages)
-        ),
-        stringsAsFactors = FALSE
-      )
-      if (recursive && nrow(packages) > 0) {
-        all <-
-          lapply(packages$name,
-            fetchDependencies,
-            recursive = TRUE,
-            level = level + 1
-          )
-        dependencies <- do.call("rbind", all)
-        if (nrow(dependencies) > 0) {
-          packages <- rbind(packages, dependencies)
-          packages <- aggregate(level ~ name, packages, max)
-        }
-      }
-      return(packages)
-    }
-
-  packages <-
-    fetchDependencies("CohortDiagnostics", recursive = TRUE)
-  packages <- packages[order(-packages$level), ]
-  getVersion <- function(package) {
-    return(utils::packageDescription(package)$Version)
-  }
-  versions <-
-    sapply(c(packages$name, "CohortDiagnostics"), getVersion)
-  snapshot <- data.frame(
-    package = names(versions),
-    version = as.vector(versions),
-    stringsAsFactors = FALSE
-  )
-  s <- utils::sessionInfo()
-  rVersion <- data.frame(
-    package = "R",
-    version = paste(s$R.version$major, s$R.version$minor, sep = "."),
-    stringsAsFactors = FALSE
-  )
-  snapshot <- rbind(rVersion, snapshot)
-  return(snapshot)
-}
diff --git a/R/TimeSeries.R b/R/TimeSeries.R
index f35c23e33..682442dd2 100644
--- a/R/TimeSeries.R
+++ b/R/TimeSeries.R
@@ -124,8 +124,8 @@ runCohortTimeSeriesDiagnostics <- function(connectionDetails = NULL,
         by = clock::duration_months(3)
       )
     ) %>%
-      dplyr::mutate(periodEnd = clock::add_months(x = periodBegin, n = 3) - 1) %>%
-      dplyr::mutate(calendarInterval = "q")
+    dplyr::mutate(periodEnd = clock::add_months(x = periodBegin, n = 3) - 1) %>%
+    dplyr::mutate(calendarInterval = "q")
 
   calendarMonth <-
     dplyr::tibble(
@@ -135,8 +135,8 @@ runCohortTimeSeriesDiagnostics <- function(connectionDetails = NULL,
         by = clock::duration_months(1)
       )
     ) %>%
-      dplyr::mutate(periodEnd = clock::add_months(x = periodBegin, n = 1) - 1) %>%
-      dplyr::mutate(calendarInterval = "m")
+    dplyr::mutate(periodEnd = clock::add_months(x = periodBegin, n = 1) - 1) %>%
+    dplyr::mutate(calendarInterval = "m")
 
   calendarYear <-
     dplyr::tibble(
@@ -146,8 +146,8 @@ runCohortTimeSeriesDiagnostics <- function(connectionDetails = NULL,
         by = clock::duration_years(1)
       )
     ) %>%
-      dplyr::mutate(periodEnd = clock::add_years(x = periodBegin, n = 1) - 1) %>%
-      dplyr::mutate(calendarInterval = "y")
+    dplyr::mutate(periodEnd = clock::add_years(x = periodBegin, n = 1) - 1) %>%
+    dplyr::mutate(calendarInterval = "y")
 
   timeSeriesDateRange <- dplyr::tibble(
     periodBegin = timeSeriesMinDate,
@@ -162,9 +162,9 @@ runCohortTimeSeriesDiagnostics <- function(connectionDetails = NULL,
       calendarYear,
       timeSeriesDateRange
     ) %>% # calendarWeek
-      dplyr::distinct() %>%
-      dplyr::arrange(periodBegin, periodEnd, calendarInterval) %>%
-      dplyr::mutate(timeId = dplyr::row_number())
+    dplyr::distinct() %>%
+    dplyr::arrange(periodBegin, periodEnd, calendarInterval) %>%
+    dplyr::mutate(timeId = dplyr::row_number())
 
   ParallelLogger::logTrace(" - Inserting calendar periods")
   DatabaseConnector::insertTable(
@@ -428,7 +428,7 @@ runCohortTimeSeriesDiagnostics <- function(connectionDetails = NULL,
       )
       resultsInAndromeda$ageGroupGender <-
         resultsInAndromeda$ageGroupGender %>%
-          dplyr::mutate(seriesType = !!seriesId)
+        dplyr::mutate(seriesType = !!seriesId)
       Andromeda::appendToTable(
         resultsInAndromeda$allData,
         resultsInAndromeda$ageGroupGender
@@ -452,7 +452,7 @@ runCohortTimeSeriesDiagnostics <- function(connectionDetails = NULL,
     dplyr::collect() %>% # temporal solution till fix of bug in andromeda on handling dates
     # periodBegin gets converted to integer
     dplyr::inner_join(resultsInAndromeda$calendarPeriods %>% dplyr::collect(),
-                      by = c("timeId")
+      by = c("timeId")
     ) %>%
     dplyr::arrange(
       cohortId,
@@ -520,7 +520,6 @@ executeTimeSeriesDiagnostics <- function(connection,
                                          recordKeepingFile,
                                          observationPeriodDateRange,
                                          batchSize = getOption("CohortDiagnostics-TimeSeries-batch-size", default = 20)) {
-
   if (all(!runCohortTimeSeries, !runDataSourceTimeSeries)) {
     warning(
       "Both Datasource time series and cohort time series are set to FALSE. Skippping executeTimeSeriesDiagnostics."
@@ -566,7 +565,7 @@ executeTimeSeriesDiagnostics <- function(connection,
           )
         }
 
-        cohortIds <- subset[start:end,]$cohortId %>% unique()
+        cohortIds <- subset[start:end, ]$cohortId %>% unique()
         timeExecution(
           exportFolder,
           "runCohortTimeSeriesDiagnostics",
@@ -598,12 +597,12 @@ executeTimeSeriesDiagnostics <- function(connection,
           data = data,
           fileName = outputFile,
           incremental = TRUE,
-          cohortId = subset[start:end,]$cohortId %>% unique()
+          cohortId = subset[start:end, ]$cohortId %>% unique()
         )
         recordTasksDone(
-          cohortId = subset[start:end,]$cohortId %>% unique(),
+          cohortId = subset[start:end, ]$cohortId %>% unique(),
           task = "runCohortTimeSeries",
-          checksum = subset[start:end,]$checksum,
+          checksum = subset[start:end, ]$checksum,
           recordKeepingFile = recordKeepingFile,
           incremental = incremental
         )
@@ -623,8 +622,10 @@ executeTimeSeriesDiagnostics <- function(connection,
       recordKeepingFile = recordKeepingFile
     )
 
-    if (all(nrow(subset) == 0,
-            incremental)) {
+    if (all(
+      nrow(subset) == 0,
+      incremental
+    )) {
       ParallelLogger::logInfo("Skipping Data Source Time Series in Incremental mode.")
       return(NULL)
     }
diff --git a/docs/404.html b/docs/404.html
index 653fa5c34..3dd8ed2c3 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">CohortDiagnostics</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">3.1.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">3.1.2</span>
       </span>
     </div>
 
diff --git a/docs/articles/CreatingAStudyPackage.html b/docs/articles/CreatingAStudyPackage.html
index d7205370b..2950d8852 100644
--- a/docs/articles/CreatingAStudyPackage.html
+++ b/docs/articles/CreatingAStudyPackage.html
@@ -33,7 +33,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">CohortDiagnostics</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">3.1.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">3.1.2</span>
       </span>
     </div>
 
@@ -97,7 +97,7 @@ <h1 data-toc-skip>Creating a study package</h1>
                         <h4 data-toc-skip class="author">Gowtham A.
 Rao</h4>
             
-            <h4 data-toc-skip class="date">2022-12-06</h4>
+            <h4 data-toc-skip class="date">2022-12-19</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/OHDSI/CohortDiagnostics/blob/HEAD/vignettes/CreatingAStudyPackage.Rmd" class="external-link"><code>vignettes/CreatingAStudyPackage.Rmd</code></a></small>
       <div class="hidden name"><code>CreatingAStudyPackage.Rmd</code></div>
@@ -186,7 +186,7 @@ <h3 id="option-a-using-hydra-and-rohdsiwebapi">option A: Using Hydra and ROhdsiW
 <code class="sourceCode R"><span><span class="co"># please ensure you have the latest version of Hydra. As of 08/13/2021 - CohortDiagnostics support for Hydra is still in develop branch.</span></span>
 <span><span class="co"># please check hydra release notes and update hydra</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/Hydra"</span>, ref <span class="op">=</span> <span class="st">"develop"</span><span class="op">)</span></span>
-<span><span class="va">outputFolder</span> <span class="op">&lt;-</span> <span class="st">"d:/temp/output"</span>  <span class="co"># location where you study package will be created</span></span>
+<span><span class="va">outputFolder</span> <span class="op">&lt;-</span> <span class="st">"d:/temp/output"</span> <span class="co"># location where you study package will be created</span></span>
 <span></span>
 <span></span>
 <span><span class="co">########## Please populate the information below #####################</span></span>
@@ -208,62 +208,68 @@ <h3 id="option-a-using-hydra-and-rohdsiwebapi">option A: Using Hydra and ROhdsiW
 <span><span class="va">baseUrl</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/Sys.getenv.html" class="external-link">Sys.getenv</a></span><span class="op">(</span><span class="st">"baseUrl"</span><span class="op">)</span></span>
 <span><span class="co"># if you have security enabled, please authorize the use - example below</span></span>
 <span><span class="co"># ROhdsiWebApi::authorizeWebApi(baseUrl, 'windows')</span></span>
-<span><span class="va">cohortIds</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">22040</span>,</span>
-<span>               <span class="fl">22042</span>,</span>
-<span>               <span class="fl">22041</span>,</span>
-<span>               <span class="fl">22039</span>,</span>
-<span>               <span class="fl">22038</span>,</span>
-<span>               <span class="fl">22037</span>,</span>
-<span>               <span class="fl">22036</span>,</span>
-<span>               <span class="fl">22035</span>,</span>
-<span>               <span class="fl">22034</span>,</span>
-<span>               <span class="fl">22033</span>,</span>
-<span>               <span class="fl">22031</span>,</span>
-<span>               <span class="fl">22032</span>,</span>
-<span>               <span class="fl">22030</span>,</span>
-<span>               <span class="fl">22028</span>,</span>
-<span>               <span class="fl">22029</span><span class="op">)</span></span>
+<span><span class="va">cohortIds</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span></span>
+<span>  <span class="fl">22040</span>,</span>
+<span>  <span class="fl">22042</span>,</span>
+<span>  <span class="fl">22041</span>,</span>
+<span>  <span class="fl">22039</span>,</span>
+<span>  <span class="fl">22038</span>,</span>
+<span>  <span class="fl">22037</span>,</span>
+<span>  <span class="fl">22036</span>,</span>
+<span>  <span class="fl">22035</span>,</span>
+<span>  <span class="fl">22034</span>,</span>
+<span>  <span class="fl">22033</span>,</span>
+<span>  <span class="fl">22031</span>,</span>
+<span>  <span class="fl">22032</span>,</span>
+<span>  <span class="fl">22030</span>,</span>
+<span>  <span class="fl">22028</span>,</span>
+<span>  <span class="fl">22029</span></span>
+<span><span class="op">)</span></span>
 <span></span>
 <span></span>
 <span></span>
 <span><span class="co">################# end of user input ##############</span></span>
 <span><span class="va">webApiCohorts</span> <span class="op">&lt;-</span> <span class="fu">ROhdsiWebApi</span><span class="fu">::</span><span class="fu">getCohortDefinitionsMetaData</span><span class="op">(</span>baseUrl <span class="op">=</span> <span class="va">baseUrl</span><span class="op">)</span></span>
-<span><span class="va">studyCohorts</span> <span class="op">&lt;-</span>  <span class="va">webApiCohorts</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
-<span>        <span class="fu">dplyr</span><span class="fu">::</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">.data</span><span class="op">$</span><span class="va">id</span> <span class="op"><a href="https://rdrr.io/r/base/match.html" class="external-link">%in%</a></span> <span class="va">cohortIds</span><span class="op">)</span></span>
+<span><span class="va">studyCohorts</span> <span class="op">&lt;-</span> <span class="va">webApiCohorts</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
+<span>  <span class="fu">dplyr</span><span class="fu">::</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">.data</span><span class="op">$</span><span class="va">id</span> <span class="op"><a href="https://rdrr.io/r/base/match.html" class="external-link">%in%</a></span> <span class="va">cohortIds</span><span class="op">)</span></span>
 <span></span>
 <span><span class="co"># compile them into a data table</span></span>
 <span><span class="va">cohortDefinitionsArray</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="op">)</span></span>
 <span><span class="kw">for</span> <span class="op">(</span><span class="va">i</span> <span class="kw">in</span> <span class="op">(</span><span class="fl">1</span><span class="op">:</span><span class="fu"><a href="https://rdrr.io/r/base/nrow.html" class="external-link">nrow</a></span><span class="op">(</span><span class="va">studyCohorts</span><span class="op">)</span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span>
-<span>        <span class="va">cohortDefinition</span> <span class="op">&lt;-</span></span>
-<span>                <span class="fu">ROhdsiWebApi</span><span class="fu">::</span><span class="fu">getCohortDefinition</span><span class="op">(</span>cohortId <span class="op">=</span> <span class="va">studyCohorts</span><span class="op">$</span><span class="va">id</span><span class="op">[[</span><span class="va">i</span><span class="op">]</span><span class="op">]</span>,</span>
-<span>                                                  baseUrl <span class="op">=</span> <span class="va">baseUrl</span><span class="op">)</span></span>
-<span>        <span class="va">cohortDefinitionsArray</span><span class="op">[[</span><span class="va">i</span><span class="op">]</span><span class="op">]</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span></span>
-<span>                id <span class="op">=</span> <span class="va">studyCohorts</span><span class="op">$</span><span class="va">id</span><span class="op">[[</span><span class="va">i</span><span class="op">]</span><span class="op">]</span>,</span>
-<span>                createdDate <span class="op">=</span> <span class="va">studyCohorts</span><span class="op">$</span><span class="va">createdDate</span><span class="op">[[</span><span class="va">i</span><span class="op">]</span><span class="op">]</span>,</span>
-<span>                modifiedDate <span class="op">=</span> <span class="va">studyCohorts</span><span class="op">$</span><span class="va">createdDate</span><span class="op">[[</span><span class="va">i</span><span class="op">]</span><span class="op">]</span>,</span>
-<span>                logicDescription <span class="op">=</span> <span class="va">studyCohorts</span><span class="op">$</span><span class="va">description</span><span class="op">[[</span><span class="va">i</span><span class="op">]</span><span class="op">]</span>,</span>
-<span>                name <span class="op">=</span> <span class="fu">stringr</span><span class="fu">::</span><span class="fu"><a href="https://stringr.tidyverse.org/reference/str_trim.html" class="external-link">str_trim</a></span><span class="op">(</span><span class="fu">stringr</span><span class="fu">::</span><span class="fu"><a href="https://stringr.tidyverse.org/reference/str_trim.html" class="external-link">str_squish</a></span><span class="op">(</span><span class="va">cohortDefinition</span><span class="op">$</span><span class="va">name</span><span class="op">)</span><span class="op">)</span>,</span>
-<span>                expression <span class="op">=</span> <span class="va">cohortDefinition</span><span class="op">$</span><span class="va">expression</span></span>
-<span>        <span class="op">)</span></span>
+<span>  <span class="va">cohortDefinition</span> <span class="op">&lt;-</span></span>
+<span>    <span class="fu">ROhdsiWebApi</span><span class="fu">::</span><span class="fu">getCohortDefinition</span><span class="op">(</span></span>
+<span>      cohortId <span class="op">=</span> <span class="va">studyCohorts</span><span class="op">$</span><span class="va">id</span><span class="op">[[</span><span class="va">i</span><span class="op">]</span><span class="op">]</span>,</span>
+<span>      baseUrl <span class="op">=</span> <span class="va">baseUrl</span></span>
+<span>    <span class="op">)</span></span>
+<span>  <span class="va">cohortDefinitionsArray</span><span class="op">[[</span><span class="va">i</span><span class="op">]</span><span class="op">]</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span></span>
+<span>    id <span class="op">=</span> <span class="va">studyCohorts</span><span class="op">$</span><span class="va">id</span><span class="op">[[</span><span class="va">i</span><span class="op">]</span><span class="op">]</span>,</span>
+<span>    createdDate <span class="op">=</span> <span class="va">studyCohorts</span><span class="op">$</span><span class="va">createdDate</span><span class="op">[[</span><span class="va">i</span><span class="op">]</span><span class="op">]</span>,</span>
+<span>    modifiedDate <span class="op">=</span> <span class="va">studyCohorts</span><span class="op">$</span><span class="va">createdDate</span><span class="op">[[</span><span class="va">i</span><span class="op">]</span><span class="op">]</span>,</span>
+<span>    logicDescription <span class="op">=</span> <span class="va">studyCohorts</span><span class="op">$</span><span class="va">description</span><span class="op">[[</span><span class="va">i</span><span class="op">]</span><span class="op">]</span>,</span>
+<span>    name <span class="op">=</span> <span class="fu">stringr</span><span class="fu">::</span><span class="fu"><a href="https://stringr.tidyverse.org/reference/str_trim.html" class="external-link">str_trim</a></span><span class="op">(</span><span class="fu">stringr</span><span class="fu">::</span><span class="fu"><a href="https://stringr.tidyverse.org/reference/str_trim.html" class="external-link">str_squish</a></span><span class="op">(</span><span class="va">cohortDefinition</span><span class="op">$</span><span class="va">name</span><span class="op">)</span><span class="op">)</span>,</span>
+<span>    expression <span class="op">=</span> <span class="va">cohortDefinition</span><span class="op">$</span><span class="va">expression</span></span>
+<span>  <span class="op">)</span></span>
 <span><span class="op">}</span></span>
 <span></span>
 <span><span class="va">tempFolder</span> <span class="op">&lt;-</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>
 <span><span class="fu"><a href="https://rdrr.io/r/base/unlink.html" class="external-link">unlink</a></span><span class="op">(</span>x <span class="op">=</span> <span class="va">tempFolder</span>, recursive <span class="op">=</span> <span class="cn">TRUE</span>, force <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
 <span><span class="fu"><a href="https://rdrr.io/r/base/files2.html" class="external-link">dir.create</a></span><span class="op">(</span>path <span class="op">=</span> <span class="va">tempFolder</span>, showWarnings <span class="op">=</span> <span class="cn">FALSE</span>, recursive <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
 <span></span>
-<span><span class="va">specifications</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>id <span class="op">=</span> <span class="fl">1</span>,</span>
-<span>                       version <span class="op">=</span> <span class="va">version</span>,</span>
-<span>                       name <span class="op">=</span> <span class="va">name</span>,</span>
-<span>                       packageName <span class="op">=</span> <span class="va">packageName</span>,</span>
-<span>                       skeletonVersion <span class="op">=</span> <span class="va">skeletonVersion</span>,</span>
-<span>                       createdBy <span class="op">=</span> <span class="va">createdBy</span>,</span>
-<span>                       createdDate <span class="op">=</span> <span class="va">createdDate</span>,</span>
-<span>                       modifiedBy <span class="op">=</span> <span class="va">modifiedBy</span>,</span>
-<span>                       modifiedDate <span class="op">=</span> <span class="va">modifiedDate</span>,</span>
-<span>                       skeletonType <span class="op">=</span> <span class="va">skeletonType</span>,</span>
-<span>                       organizationName <span class="op">=</span> <span class="va">organizationName</span>,</span>
-<span>                       description <span class="op">=</span> <span class="va">description</span>,</span>
-<span>                       cohortDefinitions <span class="op">=</span> <span class="va">cohortDefinitionsArray</span><span class="op">)</span></span>
+<span><span class="va">specifications</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span></span>
+<span>  id <span class="op">=</span> <span class="fl">1</span>,</span>
+<span>  version <span class="op">=</span> <span class="va">version</span>,</span>
+<span>  name <span class="op">=</span> <span class="va">name</span>,</span>
+<span>  packageName <span class="op">=</span> <span class="va">packageName</span>,</span>
+<span>  skeletonVersion <span class="op">=</span> <span class="va">skeletonVersion</span>,</span>
+<span>  createdBy <span class="op">=</span> <span class="va">createdBy</span>,</span>
+<span>  createdDate <span class="op">=</span> <span class="va">createdDate</span>,</span>
+<span>  modifiedBy <span class="op">=</span> <span class="va">modifiedBy</span>,</span>
+<span>  modifiedDate <span class="op">=</span> <span class="va">modifiedDate</span>,</span>
+<span>  skeletonType <span class="op">=</span> <span class="va">skeletonType</span>,</span>
+<span>  organizationName <span class="op">=</span> <span class="va">organizationName</span>,</span>
+<span>  description <span class="op">=</span> <span class="va">description</span>,</span>
+<span>  cohortDefinitions <span class="op">=</span> <span class="va">cohortDefinitionsArray</span></span>
+<span><span class="op">)</span></span>
 <span></span>
 <span><span class="va">jsonFileName</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><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="va">tempFolder</span>, <span class="st">"CohortDiagnosticsSpecs.json"</span><span class="op">)</span><span class="op">)</span></span>
 <span><span class="fu"><a href="https://rdrr.io/r/base/write.html" class="external-link">write</a></span><span class="op">(</span>x <span class="op">=</span> <span class="va">specifications</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu">RJSONIO</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/RJSONIO/man/toJSON.html" class="external-link">toJSON</a></span><span class="op">(</span>pretty <span class="op">=</span> <span class="cn">TRUE</span>, digits <span class="op">=</span> <span class="fl">23</span><span class="op">)</span>, file <span class="op">=</span> <span class="va">jsonFileName</span><span class="op">)</span></span>
@@ -280,13 +286,13 @@ <h3 id="option-a-using-hydra-and-rohdsiwebapi">option A: Using Hydra and ROhdsiW
 <span><span class="co">#### get the skeleton from github</span></span>
 <span><span class="co"># download.file(url = "https://github.com/OHDSI/SkeletonCohortDiagnosticsStudy/archive/refs/heads/main.zip",</span></span>
 <span><span class="co">#                          destfile = file.path(tempFolder, 'skeleton.zip'))</span></span>
-<span><span class="co"># unzip(zipfile =  file.path(tempFolder, 'skeleton.zip'), </span></span>
+<span><span class="co"># unzip(zipfile =  file.path(tempFolder, 'skeleton.zip'),</span></span>
 <span><span class="co">#       overwrite = TRUE,</span></span>
 <span><span class="co">#       exdir = file.path(tempFolder, "skeleton")</span></span>
 <span><span class="co">#         )</span></span>
 <span><span class="co"># fileList &lt;- list.files(path = file.path(tempFolder, "skeleton"), full.names = TRUE, recursive = TRUE, all.files = TRUE)</span></span>
-<span><span class="co"># DatabaseConnector::createZipFile(zipFile = file.path(tempFolder, 'skeleton.zip'), </span></span>
-<span><span class="co">#                                  files = fileList, </span></span>
+<span><span class="co"># DatabaseConnector::createZipFile(zipFile = file.path(tempFolder, 'skeleton.zip'),</span></span>
+<span><span class="co">#                                  files = fileList,</span></span>
 <span><span class="co">#                                  rootFolder = list.dirs(file.path(tempFolder, 'skeleton'), recursive = FALSE))</span></span>
 <span></span>
 <span><span class="co">##############################################################</span></span>
@@ -301,13 +307,14 @@ <h3 id="option-a-using-hydra-and-rohdsiwebapi">option A: Using Hydra and ROhdsiW
 <span><span class="va">hydraSpecificationFromFile</span> <span class="op">&lt;-</span> <span class="fu">Hydra</span><span class="fu">::</span><span class="fu">loadSpecifications</span><span class="op">(</span>fileName <span class="op">=</span> <span class="va">jsonFileName</span><span class="op">)</span></span>
 <span><span class="fu"><a href="https://rdrr.io/r/base/unlink.html" class="external-link">unlink</a></span><span class="op">(</span>x <span class="op">=</span> <span class="va">outputFolder</span>, recursive <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
 <span><span class="fu"><a href="https://rdrr.io/r/base/files2.html" class="external-link">dir.create</a></span><span class="op">(</span>path <span class="op">=</span> <span class="va">outputFolder</span>, showWarnings <span class="op">=</span> <span class="cn">FALSE</span>, recursive <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
-<span><span class="fu">Hydra</span><span class="fu">::</span><span class="fu">hydrate</span><span class="op">(</span>specifications <span class="op">=</span> <span class="va">hydraSpecificationFromFile</span>,</span>
-<span>               outputFolder <span class="op">=</span> <span class="va">outputFolder</span></span>
+<span><span class="fu">Hydra</span><span class="fu">::</span><span class="fu">hydrate</span><span class="op">(</span></span>
+<span>  specifications <span class="op">=</span> <span class="va">hydraSpecificationFromFile</span>,</span>
+<span>  outputFolder <span class="op">=</span> <span class="va">outputFolder</span></span>
 <span><span class="op">)</span></span>
 <span></span>
 <span><span class="co"># for advanced user using skeletons outside of Hydra</span></span>
 <span><span class="co"># Hydra::hydrate(specifications = hydraSpecificationFromFile,</span></span>
-<span><span class="co">#                outputFolder = outputFolder, </span></span>
+<span><span class="co">#                outputFolder = outputFolder,</span></span>
 <span><span class="co">#                skeletonFileName = file.path(tempFolder, 'skeleton.zip')</span></span>
 <span><span class="co"># )</span></span>
 <span></span>
diff --git a/docs/articles/DatabaseModeInDiagnosticsExplorer.html b/docs/articles/DatabaseModeInDiagnosticsExplorer.html
index c0e4afcb6..409421e5e 100644
--- a/docs/articles/DatabaseModeInDiagnosticsExplorer.html
+++ b/docs/articles/DatabaseModeInDiagnosticsExplorer.html
@@ -33,7 +33,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">CohortDiagnostics</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">3.1.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">3.1.2</span>
       </span>
     </div>
 
@@ -97,7 +97,7 @@ <h1 data-toc-skip>Database mode in Diagnostics Explorer</h1>
                         <h4 data-toc-skip class="author">Gowtham
 Rao</h4>
             
-            <h4 data-toc-skip class="date">2022-12-06</h4>
+            <h4 data-toc-skip class="date">2022-12-19</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/OHDSI/CohortDiagnostics/blob/HEAD/vignettes/DatabaseModeInDiagnosticsExplorer.Rmd" class="external-link"><code>vignettes/DatabaseModeInDiagnosticsExplorer.Rmd</code></a></small>
       <div class="hidden name"><code>DatabaseModeInDiagnosticsExplorer.Rmd</code></div>
diff --git a/docs/articles/RunningCohortDiagnostics.html b/docs/articles/RunningCohortDiagnostics.html
index 19b970613..645569673 100644
--- a/docs/articles/RunningCohortDiagnostics.html
+++ b/docs/articles/RunningCohortDiagnostics.html
@@ -33,7 +33,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">CohortDiagnostics</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">3.1.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">3.1.2</span>
       </span>
     </div>
 
@@ -97,7 +97,7 @@ <h1 data-toc-skip>Running Cohort Diagnostics</h1>
                         <h4 data-toc-skip class="author">Gowtham Rao and
 James P. Gilbert</h4>
             
-            <h4 data-toc-skip class="date">2022-12-06</h4>
+            <h4 data-toc-skip class="date">2022-12-19</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/OHDSI/CohortDiagnostics/blob/HEAD/vignettes/RunningCohortDiagnostics.Rmd" class="external-link"><code>vignettes/RunningCohortDiagnostics.Rmd</code></a></small>
       <div class="hidden name"><code>RunningCohortDiagnostics.Rmd</code></div>
@@ -122,8 +122,8 @@ <h3 id="pre-requisites">pre-requisites<a class="anchor" aria-label="anchor" href
 install the <code>ROhdsiWebApi</code> package to download cohort
 definitions from an ATLAS instance:</p>
 <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><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/Eunomia'</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/ROhdsiWebApi'</span><span class="op">)</span></span></code></pre></div>
+<code class="sourceCode R"><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/Eunomia"</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/ROhdsiWebApi"</span><span class="op">)</span></span></code></pre></div>
 </div>
 </div>
 <div class="section level2">
@@ -139,10 +139,12 @@ <h2 id="configuring-the-connection-to-the-server">Configuring the connection to
 <div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://ohdsi.github.io/CohortDiagnostics" class="external-link">CohortDiagnostics</a></span><span class="op">)</span></span>
 <span></span>
-<span><span class="va">connectionDetails</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://ohdsi.github.io/DatabaseConnector/reference/createConnectionDetails.html" class="external-link">createConnectionDetails</a></span><span class="op">(</span>dbms <span class="op">=</span> <span class="st">"postgresql"</span>,</span>
-<span>                                             server <span class="op">=</span> <span class="st">"localhost/ohdsi"</span>,</span>
-<span>                                             user <span class="op">=</span> <span class="st">"joe"</span>,</span>
-<span>                                             password <span class="op">=</span> <span class="st">"supersecret"</span><span class="op">)</span></span></code></pre></div>
+<span><span class="va">connectionDetails</span> <span class="op">&lt;-</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">"postgresql"</span>,</span>
+<span>  server <span class="op">=</span> <span class="st">"localhost/ohdsi"</span>,</span>
+<span>  user <span class="op">=</span> <span class="st">"joe"</span>,</span>
+<span>  password <span class="op">=</span> <span class="st">"supersecret"</span></span>
+<span><span class="op">)</span></span></code></pre></div>
 <p>For the purposes of this example, we will use the Eunomia test CDM
 package that is in an Sqlite database stored locally.</p>
 <div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
@@ -181,10 +183,12 @@ <h3 id="loading-cohort-references-from-a-package">Loading cohort references from
 the OMOP Common Data Model format.</p>
 <div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://ohdsi.github.io/CohortDiagnostics" class="external-link">CohortDiagnostics</a></span><span class="op">)</span></span>
-<span><span class="va">cohortDefinitionSet</span> <span class="op">&lt;-</span> <span class="fu">CohortGenerator</span><span class="fu">::</span><span class="fu"><a href="https://ohdsi.github.io/CohortGenerator/reference/getCohortDefinitionSet.html" class="external-link">getCohortDefinitionSet</a></span><span class="op">(</span>settingsFileName <span class="op">=</span> <span class="st">"Cohorts.csv"</span>,</span>
-<span>                                                               jsonFolder <span class="op">=</span> <span class="st">"cohorts"</span>,</span>
-<span>                                                               sqlFolder <span class="op">=</span> <span class="st">"sql/sql_server"</span>,</span>
-<span>                                                               packageName <span class="op">=</span> <span class="st">"CohortDiagnostics"</span><span class="op">)</span></span></code></pre></div>
+<span><span class="va">cohortDefinitionSet</span> <span class="op">&lt;-</span> <span class="fu">CohortGenerator</span><span class="fu">::</span><span class="fu"><a href="https://ohdsi.github.io/CohortGenerator/reference/getCohortDefinitionSet.html" class="external-link">getCohortDefinitionSet</a></span><span class="op">(</span></span>
+<span>  settingsFileName <span class="op">=</span> <span class="st">"Cohorts.csv"</span>,</span>
+<span>  jsonFolder <span class="op">=</span> <span class="st">"cohorts"</span>,</span>
+<span>  sqlFolder <span class="op">=</span> <span class="st">"sql/sql_server"</span>,</span>
+<span>  packageName <span class="op">=</span> <span class="st">"CohortDiagnostics"</span></span>
+<span><span class="op">)</span></span></code></pre></div>
 <p>Looking at this data.frame of Cohorts you will see the sql and json
 for these cohorts:</p>
 <div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
@@ -204,11 +208,13 @@ <h3 id="loading-cohort-references-from-webapi">Loading cohort references from We
 <code class="sourceCode R"><span><span class="co"># Set up url</span></span>
 <span><span class="va">baseUrl</span> <span class="op">&lt;-</span> <span class="st">"https://atlas.hosting.com/WebAPI"</span></span>
 <span><span class="co"># list of cohort ids</span></span>
-<span><span class="va">cohortIds</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">18345</span>,<span class="fl">18346</span><span class="op">)</span></span>
+<span><span class="va">cohortIds</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">18345</span>, <span class="fl">18346</span><span class="op">)</span></span>
 <span></span>
-<span><span class="va">cohortDefinitionSet</span> <span class="op">&lt;-</span> <span class="fu">ROhdsiWebApi</span><span class="fu">::</span><span class="fu">exportCohortDefinitionSet</span><span class="op">(</span>baseUrl <span class="op">=</span> <span class="va">baseUrl</span>,</span>
-<span>                                                               cohortIds <span class="op">=</span> <span class="va">cohortIds</span>,</span>
-<span>                                                               generateStats <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div>
+<span><span class="va">cohortDefinitionSet</span> <span class="op">&lt;-</span> <span class="fu">ROhdsiWebApi</span><span class="fu">::</span><span class="fu">exportCohortDefinitionSet</span><span class="op">(</span></span>
+<span>  baseUrl <span class="op">=</span> <span class="va">baseUrl</span>,</span>
+<span>  cohortIds <span class="op">=</span> <span class="va">cohortIds</span>,</span>
+<span>  generateStats <span class="op">=</span> <span class="cn">TRUE</span></span>
+<span><span class="op">)</span></span></code></pre></div>
 <p>Consult the ROhdsiWebApi documentation for details on authentication
 to your atlas instance. Please note that in order to generate inclusion
 rules statistics (a useful diagnostic tool) the parameter
@@ -226,18 +232,22 @@ <h4 id="using-cohortgenerator-to-instantiate-cohorts">Using CohortGenerator to i
 <code class="sourceCode R"><span><span class="va">cohortTableNames</span> <span class="op">&lt;-</span> <span class="fu">CohortGenerator</span><span class="fu">::</span><span class="fu"><a href="https://ohdsi.github.io/CohortGenerator/reference/getCohortTableNames.html" class="external-link">getCohortTableNames</a></span><span class="op">(</span>cohortTable <span class="op">=</span> <span class="va">cohortTable</span><span class="op">)</span></span>
 <span></span>
 <span><span class="co"># Next create the tables on the database</span></span>
-<span><span class="fu">CohortGenerator</span><span class="fu">::</span><span class="fu"><a href="https://ohdsi.github.io/CohortGenerator/reference/createCohortTables.html" class="external-link">createCohortTables</a></span><span class="op">(</span>connectionDetails <span class="op">=</span> <span class="va">connectionDetails</span>,</span>
-<span>                                    cohortTableNames <span class="op">=</span> <span class="va">cohortTableNames</span>,</span>
-<span>                                    cohortDatabaseSchema <span class="op">=</span> <span class="st">"main"</span>,</span>
-<span>                                    incremental <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span>
+<span><span class="fu">CohortGenerator</span><span class="fu">::</span><span class="fu"><a href="https://ohdsi.github.io/CohortGenerator/reference/createCohortTables.html" class="external-link">createCohortTables</a></span><span class="op">(</span></span>
+<span>  connectionDetails <span class="op">=</span> <span class="va">connectionDetails</span>,</span>
+<span>  cohortTableNames <span class="op">=</span> <span class="va">cohortTableNames</span>,</span>
+<span>  cohortDatabaseSchema <span class="op">=</span> <span class="st">"main"</span>,</span>
+<span>  incremental <span class="op">=</span> <span class="cn">FALSE</span></span>
+<span><span class="op">)</span></span>
 <span></span>
 <span><span class="co"># Generate the cohort set</span></span>
-<span><span class="fu">CohortGenerator</span><span class="fu">::</span><span class="fu"><a href="https://ohdsi.github.io/CohortGenerator/reference/generateCohortSet.html" class="external-link">generateCohortSet</a></span><span class="op">(</span>connectionDetails<span class="op">=</span> <span class="va">connectionDetails</span>,</span>
-<span>                                   cdmDatabaseSchema <span class="op">=</span> <span class="va">cdmDatabaseSchema</span>,</span>
-<span>                                   cohortDatabaseSchema <span class="op">=</span> <span class="va">cohortDatabaseSchema</span>,</span>
-<span>                                   cohortTableNames <span class="op">=</span> <span class="va">cohortTableNames</span>,</span>
-<span>                                   cohortDefinitionSet <span class="op">=</span> <span class="va">cohortDefinitionSet</span>,</span>
-<span>                                   incremental <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div>
+<span><span class="fu">CohortGenerator</span><span class="fu">::</span><span class="fu"><a href="https://ohdsi.github.io/CohortGenerator/reference/generateCohortSet.html" class="external-link">generateCohortSet</a></span><span class="op">(</span></span>
+<span>  connectionDetails <span class="op">=</span> <span class="va">connectionDetails</span>,</span>
+<span>  cdmDatabaseSchema <span class="op">=</span> <span class="va">cdmDatabaseSchema</span>,</span>
+<span>  cohortDatabaseSchema <span class="op">=</span> <span class="va">cohortDatabaseSchema</span>,</span>
+<span>  cohortTableNames <span class="op">=</span> <span class="va">cohortTableNames</span>,</span>
+<span>  cohortDefinitionSet <span class="op">=</span> <span class="va">cohortDefinitionSet</span>,</span>
+<span>  incremental <span class="op">=</span> <span class="cn">FALSE</span></span>
+<span><span class="op">)</span></span></code></pre></div>
 <p><strong>Note, that the above code will delete an existing
 table</strong>. However, incremental mode can be used when setting the
 parameter <code>incremental = TRUE</code>.</p>
@@ -259,13 +269,14 @@ <h3 id="executing-cohort-diagnostics">Executing cohort diagnostics<a class="anch
 follows:</p>
 <div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="../reference/executeDiagnostics.html">executeDiagnostics</a></span><span class="op">(</span><span class="va">cohortDefinitionSet</span>,</span>
-<span>                   connectionDetails <span class="op">=</span> <span class="va">connectionDetails</span>,</span>
-<span>                   cohortTable <span class="op">=</span> <span class="va">cohortTable</span>,</span>
-<span>                   cohortDatabaseSchema <span class="op">=</span> <span class="va">cohortDatabaseSchema</span>,</span>
-<span>                   cdmDatabaseSchema <span class="op">=</span> <span class="va">cdmDatabaseSchema</span>,</span>
-<span>                   exportFolder <span class="op">=</span> <span class="va">exportFolder</span>,</span>
-<span>                   databaseId <span class="op">=</span> <span class="st">"MyCdm"</span>,</span>
-<span>                   minCellCount <span class="op">=</span> <span class="fl">5</span><span class="op">)</span></span></code></pre></div>
+<span>  connectionDetails <span class="op">=</span> <span class="va">connectionDetails</span>,</span>
+<span>  cohortTable <span class="op">=</span> <span class="va">cohortTable</span>,</span>
+<span>  cohortDatabaseSchema <span class="op">=</span> <span class="va">cohortDatabaseSchema</span>,</span>
+<span>  cdmDatabaseSchema <span class="op">=</span> <span class="va">cdmDatabaseSchema</span>,</span>
+<span>  exportFolder <span class="op">=</span> <span class="va">exportFolder</span>,</span>
+<span>  databaseId <span class="op">=</span> <span class="st">"MyCdm"</span>,</span>
+<span>  minCellCount <span class="op">=</span> <span class="fl">5</span></span>
+<span><span class="op">)</span></span></code></pre></div>
 </div>
 <div class="section level3">
 <h3 id="cohort-statistics-table-clean-up">Cohort Statistics Table Clean up<a class="anchor" aria-label="anchor" href="#cohort-statistics-table-clean-up"></a>
@@ -274,9 +285,11 @@ <h3 id="cohort-statistics-table-clean-up">Cohort Statistics Table Clean up<a cla
 tables. As the process is complete, these are no longer required and can
 be removed.</p>
 <div class="sourceCode" id="cb10"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="fu">CohortGenerator</span><span class="fu">::</span><span class="fu"><a href="https://ohdsi.github.io/CohortGenerator/reference/dropCohortStatsTables.html" class="external-link">dropCohortStatsTables</a></span><span class="op">(</span>connectionDetails <span class="op">=</span> <span class="va">connectionDetails</span>,</span>
-<span>                                       cohortDatabaseSchema <span class="op">=</span> <span class="va">cohortDatabaseSchema</span>,</span>
-<span>                                       cohortTableNames <span class="op">=</span> <span class="va">cohortTableNames</span><span class="op">)</span></span></code></pre></div>
+<code class="sourceCode R"><span><span class="fu">CohortGenerator</span><span class="fu">::</span><span class="fu"><a href="https://ohdsi.github.io/CohortGenerator/reference/dropCohortStatsTables.html" class="external-link">dropCohortStatsTables</a></span><span class="op">(</span></span>
+<span>  connectionDetails <span class="op">=</span> <span class="va">connectionDetails</span>,</span>
+<span>  cohortDatabaseSchema <span class="op">=</span> <span class="va">cohortDatabaseSchema</span>,</span>
+<span>  cohortTableNames <span class="op">=</span> <span class="va">cohortTableNames</span></span>
+<span><span class="op">)</span></span></code></pre></div>
 </div>
 </div>
 <div class="section level2">
diff --git a/docs/articles/ViewingResultsUsingDiagnosticsExplorer.html b/docs/articles/ViewingResultsUsingDiagnosticsExplorer.html
index 50bf23ffe..04af855d1 100644
--- a/docs/articles/ViewingResultsUsingDiagnosticsExplorer.html
+++ b/docs/articles/ViewingResultsUsingDiagnosticsExplorer.html
@@ -33,7 +33,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">CohortDiagnostics</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">3.1.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">3.1.2</span>
       </span>
     </div>
 
@@ -97,7 +97,7 @@ <h1 data-toc-skip>Viewing results using Diagnostics Explorer</h1>
                         <h4 data-toc-skip class="author">Gowtham
 Rao</h4>
             
-            <h4 data-toc-skip class="date">2022-12-06</h4>
+            <h4 data-toc-skip class="date">2022-12-19</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/OHDSI/CohortDiagnostics/blob/HEAD/vignettes/ViewingResultsUsingDiagnosticsExplorer.Rmd" class="external-link"><code>vignettes/ViewingResultsUsingDiagnosticsExplorer.Rmd</code></a></small>
       <div class="hidden name"><code>ViewingResultsUsingDiagnosticsExplorer.Rmd</code></div>
diff --git a/docs/articles/WhatIsCohortDiagnostics.html b/docs/articles/WhatIsCohortDiagnostics.html
index 2e10d13f1..28dcf0f6b 100644
--- a/docs/articles/WhatIsCohortDiagnostics.html
+++ b/docs/articles/WhatIsCohortDiagnostics.html
@@ -33,7 +33,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">CohortDiagnostics</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">3.1.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">3.1.2</span>
       </span>
     </div>
 
@@ -97,7 +97,7 @@ <h1 data-toc-skip>What is Cohort Diagnostics?</h1>
                         <h4 data-toc-skip class="author">Gowtham
 Rao</h4>
             
-            <h4 data-toc-skip class="date">2022-12-06</h4>
+            <h4 data-toc-skip class="date">2022-12-19</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/OHDSI/CohortDiagnostics/blob/HEAD/vignettes/WhatIsCohortDiagnostics.Rmd" class="external-link"><code>vignettes/WhatIsCohortDiagnostics.Rmd</code></a></small>
       <div class="hidden name"><code>WhatIsCohortDiagnostics.Rmd</code></div>
diff --git a/docs/articles/index.html b/docs/articles/index.html
index 561bf2513..1b44b4839 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">CohortDiagnostics</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">3.1.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">3.1.2</span>
       </span>
     </div>
 
diff --git a/docs/authors.html b/docs/authors.html
index 7d9c1e724..23ae44098 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">CohortDiagnostics</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">3.1.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">3.1.2</span>
       </span>
     </div>
 
diff --git a/docs/index.html b/docs/index.html
index 2bb5d9bcd..f996a2927 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -39,7 +39,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">CohortDiagnostics</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">3.1.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">3.1.2</span>
       </span>
     </div>
 
diff --git a/docs/news/index.html b/docs/news/index.html
index a6b61a274..d57c4df65 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">CohortDiagnostics</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">3.1.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">3.1.2</span>
       </span>
     </div>
 
@@ -72,6 +72,11 @@ <h1 data-toc-skip>Changelog <small></small></h1>
       <small>Source: <a href="https://github.com/OHDSI/CohortDiagnostics/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="3.1.2" id="cohortdiagnostics-312">CohortDiagnostics 3.1.2<a class="anchor" aria-label="anchor" href="#cohortdiagnostics-312"></a></h2>
+<p>Bug Fixes:</p>
+<ol style="list-style-type: decimal"><li>Removed package dependency snapshot capture as it was breaking on newer versions of R</li>
+</ol></div>
     <div class="section level2">
 <h2 class="page-header" data-toc-text="3.1.1" id="cohortdiagnostics-311">CohortDiagnostics 3.1.1<a class="anchor" aria-label="anchor" href="#cohortdiagnostics-311"></a></h2>
 <p>Changes:</p>
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 227a7fe6e..0b8c7f096 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -7,5 +7,5 @@ articles:
   RunningCohortDiagnostics: RunningCohortDiagnostics.html
   ViewingResultsUsingDiagnosticsExplorer: ViewingResultsUsingDiagnosticsExplorer.html
   WhatIsCohortDiagnostics: WhatIsCohortDiagnostics.html
-last_built: 2022-12-06T21:26Z
+last_built: 2022-12-20T00:46Z
 
diff --git a/docs/reference/CohortDiagnostics-package.html b/docs/reference/CohortDiagnostics-package.html
index 117984ced..49e7e7bff 100644
--- a/docs/reference/CohortDiagnostics-package.html
+++ b/docs/reference/CohortDiagnostics-package.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">CohortDiagnostics</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">3.1.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">3.1.2</span>
       </span>
     </div>
 
diff --git a/docs/reference/checkInputFileEncoding.html b/docs/reference/checkInputFileEncoding.html
index 188894a1a..65764abf8 100644
--- a/docs/reference/checkInputFileEncoding.html
+++ b/docs/reference/checkInputFileEncoding.html
@@ -18,7 +18,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">CohortDiagnostics</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">3.1.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">3.1.2</span>
       </span>
     </div>
 
diff --git a/docs/reference/createDiagnosticsExplorerZip.html b/docs/reference/createDiagnosticsExplorerZip.html
index c86032d9d..e80a6695b 100644
--- a/docs/reference/createDiagnosticsExplorerZip.html
+++ b/docs/reference/createDiagnosticsExplorerZip.html
@@ -20,7 +20,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">CohortDiagnostics</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">3.1.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">3.1.2</span>
       </span>
     </div>
 
diff --git a/docs/reference/createMergedResultsFile.html b/docs/reference/createMergedResultsFile.html
index 986542882..a9f04e857 100644
--- a/docs/reference/createMergedResultsFile.html
+++ b/docs/reference/createMergedResultsFile.html
@@ -19,7 +19,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">CohortDiagnostics</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">3.1.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">3.1.2</span>
       </span>
     </div>
 
diff --git a/docs/reference/createResultsDataModel.html b/docs/reference/createResultsDataModel.html
index bd171264b..1ef9b5d09 100644
--- a/docs/reference/createResultsDataModel.html
+++ b/docs/reference/createResultsDataModel.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">CohortDiagnostics</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">3.1.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">3.1.2</span>
       </span>
     </div>
 
diff --git a/docs/reference/executeDiagnostics.html b/docs/reference/executeDiagnostics.html
index 5da955790..c902b770b 100644
--- a/docs/reference/executeDiagnostics.html
+++ b/docs/reference/executeDiagnostics.html
@@ -22,7 +22,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">CohortDiagnostics</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">3.1.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">3.1.2</span>
       </span>
     </div>
 
diff --git a/docs/reference/getCdmDataSourceInformation.html b/docs/reference/getCdmDataSourceInformation.html
index e90a48a1a..cda6a62fb 100644
--- a/docs/reference/getCdmDataSourceInformation.html
+++ b/docs/reference/getCdmDataSourceInformation.html
@@ -18,7 +18,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">CohortDiagnostics</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">3.1.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">3.1.2</span>
       </span>
     </div>
 
diff --git a/docs/reference/getCohortCounts.html b/docs/reference/getCohortCounts.html
index cae29104e..124bebee4 100644
--- a/docs/reference/getCohortCounts.html
+++ b/docs/reference/getCohortCounts.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">CohortDiagnostics</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">3.1.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">3.1.2</span>
       </span>
     </div>
 
diff --git a/docs/reference/getDataMigrator.html b/docs/reference/getDataMigrator.html
index eb9ed6fb4..a5dc48237 100644
--- a/docs/reference/getDataMigrator.html
+++ b/docs/reference/getDataMigrator.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">CohortDiagnostics</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">3.1.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">3.1.2</span>
       </span>
     </div>
 
diff --git a/docs/reference/getDefaultCovariateSettings.html b/docs/reference/getDefaultCovariateSettings.html
index cb45443c6..cfa9ea96f 100644
--- a/docs/reference/getDefaultCovariateSettings.html
+++ b/docs/reference/getDefaultCovariateSettings.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">CohortDiagnostics</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">3.1.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">3.1.2</span>
       </span>
     </div>
 
diff --git a/docs/reference/getDefaultVocabularyTableNames.html b/docs/reference/getDefaultVocabularyTableNames.html
index 8c736f259..e99b3359d 100644
--- a/docs/reference/getDefaultVocabularyTableNames.html
+++ b/docs/reference/getDefaultVocabularyTableNames.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">CohortDiagnostics</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">3.1.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">3.1.2</span>
       </span>
     </div>
 
diff --git a/docs/reference/getResultsDataModelSpecifications.html b/docs/reference/getResultsDataModelSpecifications.html
index 4e0bcae52..a60460a6c 100644
--- a/docs/reference/getResultsDataModelSpecifications.html
+++ b/docs/reference/getResultsDataModelSpecifications.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">CohortDiagnostics</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">3.1.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">3.1.2</span>
       </span>
     </div>
 
diff --git a/docs/reference/index.html b/docs/reference/index.html
index d5c87ca1f..efaccf446 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">CohortDiagnostics</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">3.1.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">3.1.2</span>
       </span>
     </div>
 
@@ -135,10 +135,6 @@ <h2 id="all-functions">All functions <a href="#all-functions" class="anchor" ari
           <p><code><a href="runCohortTimeSeriesDiagnostics.html">runCohortTimeSeriesDiagnostics()</a></code> </p>
         </td>
         <td><p>Given a set of instantiated cohorts get time series for the cohorts.</p></td>
-      </tr><tr><td>
-          <p><code><a href="takepackageDependencySnapshot.html">takepackageDependencySnapshot()</a></code> </p>
-        </td>
-        <td><p>Take a snapshot of the R environment</p></td>
       </tr><tr><td>
           <p><code><a href="timeExecution.html">timeExecution()</a></code> </p>
         </td>
diff --git a/docs/reference/launchDiagnosticsExplorer.html b/docs/reference/launchDiagnosticsExplorer.html
index 8db5887fa..594919ca6 100644
--- a/docs/reference/launchDiagnosticsExplorer.html
+++ b/docs/reference/launchDiagnosticsExplorer.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">CohortDiagnostics</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">3.1.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">3.1.2</span>
       </span>
     </div>
 
diff --git a/docs/reference/migrateDataModel.html b/docs/reference/migrateDataModel.html
index f662c1c13..49ed48fce 100644
--- a/docs/reference/migrateDataModel.html
+++ b/docs/reference/migrateDataModel.html
@@ -19,7 +19,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">CohortDiagnostics</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">3.1.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">3.1.2</span>
       </span>
     </div>
 
diff --git a/docs/reference/runCohortRelationshipDiagnostics.html b/docs/reference/runCohortRelationshipDiagnostics.html
index a6cdb1028..865811640 100644
--- a/docs/reference/runCohortRelationshipDiagnostics.html
+++ b/docs/reference/runCohortRelationshipDiagnostics.html
@@ -18,7 +18,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">CohortDiagnostics</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">3.1.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">3.1.2</span>
       </span>
     </div>
 
diff --git a/docs/reference/runCohortTimeSeriesDiagnostics.html b/docs/reference/runCohortTimeSeriesDiagnostics.html
index 7cb258d32..a2ee8d540 100644
--- a/docs/reference/runCohortTimeSeriesDiagnostics.html
+++ b/docs/reference/runCohortTimeSeriesDiagnostics.html
@@ -25,7 +25,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">CohortDiagnostics</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">3.1.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">3.1.2</span>
       </span>
     </div>
 
diff --git a/docs/reference/timeExecution.html b/docs/reference/timeExecution.html
index 3453e1e6b..4660120fb 100644
--- a/docs/reference/timeExecution.html
+++ b/docs/reference/timeExecution.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">CohortDiagnostics</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">3.1.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">3.1.2</span>
       </span>
     </div>
 
diff --git a/docs/reference/uploadResults.html b/docs/reference/uploadResults.html
index cd3b0e2c4..c1e45f2a5 100644
--- a/docs/reference/uploadResults.html
+++ b/docs/reference/uploadResults.html
@@ -19,7 +19,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">CohortDiagnostics</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">3.1.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">3.1.2</span>
       </span>
     </div>
 
diff --git a/extras/CohortDiagnostics.pdf b/extras/CohortDiagnostics.pdf
index 289499bd8..3a6f10116 100644
Binary files a/extras/CohortDiagnostics.pdf and b/extras/CohortDiagnostics.pdf differ
diff --git a/inst/doc/RunningCohortDiagnostics.pdf b/inst/doc/RunningCohortDiagnostics.pdf
index 1b2c559c4..072e180de 100644
Binary files a/inst/doc/RunningCohortDiagnostics.pdf and b/inst/doc/RunningCohortDiagnostics.pdf differ
diff --git a/inst/doc/ViewingResultsUsingDiagnosticsExplorer.pdf b/inst/doc/ViewingResultsUsingDiagnosticsExplorer.pdf
index 73992ab5b..ba9aa38a2 100644
Binary files a/inst/doc/ViewingResultsUsingDiagnosticsExplorer.pdf and b/inst/doc/ViewingResultsUsingDiagnosticsExplorer.pdf differ
diff --git a/inst/doc/WhatIsCohortDiagnostics.pdf b/inst/doc/WhatIsCohortDiagnostics.pdf
index 6fb627c36..5802d638c 100644
Binary files a/inst/doc/WhatIsCohortDiagnostics.pdf and b/inst/doc/WhatIsCohortDiagnostics.pdf differ
diff --git a/inst/shiny/DiagnosticsExplorer/global.R b/inst/shiny/DiagnosticsExplorer/global.R
index 3839a9ff9..baeaf411a 100644
--- a/inst/shiny/DiagnosticsExplorer/global.R
+++ b/inst/shiny/DiagnosticsExplorer/global.R
@@ -5,7 +5,7 @@ diagExpEnv$shinyConfigPath <- getOption("CD-shiny-config", default = "config.yml
 # Source all app files in to isolated namespace
 lapply(file.path("R", list.files("R", pattern = "*.R")), source, local = diagExpEnv)
 
-diagExpEnv$appVersionNum <- "Version: 3.1.1"
+diagExpEnv$appVersionNum <- "Version: 3.1.2"
 
 if (exists("shinySettings")) {
   diagExpEnv$shinySettings <- shinySettings
@@ -20,3 +20,4 @@ if (exists("shinySettings")) {
 diagExpEnv$initializeEnvironment(diagExpEnv$shinySettings, envir = diagExpEnv)
 
 
+
diff --git a/inst/shiny/DiagnosticsExplorer/renv.lock b/inst/shiny/DiagnosticsExplorer/renv.lock
index bcdcc3e08..c7ddd6eea 100644
--- a/inst/shiny/DiagnosticsExplorer/renv.lock
+++ b/inst/shiny/DiagnosticsExplorer/renv.lock
@@ -17,6 +17,23 @@
       "Requirements": [],
       "Hash": "8f9ce74c6417d61f0782cbae5fd2b7b0"
     },
+    "CirceR": {
+      "Package": "CirceR",
+      "Version": "1.2.0",
+      "Source": "GitHub",
+      "RemoteType": "github",
+      "RemoteHost": "api.github.com",
+      "RemoteRepo": "CirceR",
+      "RemoteUsername": "OHDSI",
+      "RemoteRef": "HEAD",
+      "RemoteSha": "38bf8b44d87f759dd4ba36835ce30627b3c24e6b",
+      "Requirements": [
+        "R",
+        "RJSONIO",
+        "rJava"
+      ],
+      "Hash": "b8480aa484ebcee5551cfa77fac4b25c"
+    },
     "DBI": {
       "Package": "DBI",
       "Version": "1.1.3",
diff --git a/inst/sql/sql_server/UpdateVersionNumber.sql b/inst/sql/sql_server/UpdateVersionNumber.sql
index 9bd9a9f9a..a7ed8c9fa 100644
--- a/inst/sql/sql_server/UpdateVersionNumber.sql
+++ b/inst/sql/sql_server/UpdateVersionNumber.sql
@@ -1,6 +1,7 @@
 {DEFAULT @package_version = package_version}
-{DEFAULT @version_number = '3.1.1'}
+{DEFAULT @version_number = '3.1.2'}
 
 DELETE FROM @database_schema.@table_prefix@package_version;
 INSERT INTO @database_schema.@table_prefix@package_version (version_number) VALUES ('@version_number');
 
+
diff --git a/man/takepackageDependencySnapshot.Rd b/man/takepackageDependencySnapshot.Rd
deleted file mode 100644
index d146154cc..000000000
--- a/man/takepackageDependencySnapshot.Rd
+++ /dev/null
@@ -1,19 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/TakePackageDependencySnapshot.R
-\name{takepackageDependencySnapshot}
-\alias{takepackageDependencySnapshot}
-\title{Take a snapshot of the R environment}
-\usage{
-takepackageDependencySnapshot()
-}
-\value{
-A data frame listing all the dependencies of the root package and their version numbers, in the
-order in which they should be installed.
-}
-\description{
-Take a snapshot of the R environment
-}
-\details{
-This function records all versions used in the R environment as used by runCohortDiagnostics.
-This function was borrowed from OhdsiRTools
-}
diff --git a/tests/testthat/helper.R b/tests/testthat/helper.R
index 83f77b8bb..d3c3a5832 100644
--- a/tests/testthat/helper.R
+++ b/tests/testthat/helper.R
@@ -20,7 +20,6 @@ with_dbc_connection <- function(connection, code) {
 
 # Create a cohort definition set from test cohorts
 loadTestCohortDefinitionSet <- function(cohortIds = NULL) {
-
   if (grepl("testthat", getwd())) {
     cohortPath <- "cohorts"
   } else {
@@ -37,7 +36,7 @@ loadTestCohortDefinitionSet <- function(cohortIds = NULL) {
   if (!is.null(cohortIds)) {
     cohortDefinitionSet <- cohortDefinitionSet %>% dplyr::filter(cohortId %in% cohortIds)
   }
-  
+
   cohortDefinitionSet$checksum <- computeChecksum(cohortDefinitionSet$sql)
 
   return(cohortDefinitionSet)
@@ -86,7 +85,9 @@ createTestShinyDb <- function(connectionDetails = Eunomia::getEunomiaConnectionD
     incremental = FALSE
   )
 
-  createMergedResultsFile(dataFolder = file.path(folder, "export"),
-                          sqliteDbPath = outputPath,
-                          overwrite = TRUE)
+  createMergedResultsFile(
+    dataFolder = file.path(folder, "export"),
+    sqliteDbPath = outputPath,
+    overwrite = TRUE
+  )
 }
diff --git a/tests/testthat/setup.R b/tests/testthat/setup.R
index 799c3017c..ca43ec520 100644
--- a/tests/testthat/setup.R
+++ b/tests/testthat/setup.R
@@ -32,7 +32,7 @@ skipCdmTests <- FALSE
 
 if (dbms == "sqlite") {
   connectionDetails <- Eunomia::getEunomiaConnectionDetails(databaseFile = "testEunomia.sqlite")
-   withr::defer(
+  withr::defer(
     {
       unlink("testEunomia.sqlite", recursive = TRUE, force = TRUE)
     },
diff --git a/tests/testthat/test-Characterization.R b/tests/testthat/test-Characterization.R
index 8690ad8e7..271b7af50 100644
--- a/tests/testthat/test-Characterization.R
+++ b/tests/testthat/test-Characterization.R
@@ -5,7 +5,7 @@ test_that("Execute and export characterization", {
 
   with_dbc_connection(tConnection, {
     exportFolder <- tempfile()
-    recordKeepingFile <- tempfile(fileext="csv")
+    recordKeepingFile <- tempfile(fileext = "csv")
     dir.create(exportFolder)
     on.exit(unlink(exportFolder), add = TRUE)
     cohortTableNames <- CohortGenerator::getCohortTableNames(cohortTable = cohortTable)
@@ -17,16 +17,22 @@ test_that("Execute and export characterization", {
       incremental = FALSE
     )
 
-    on.exit({
-      CohortGenerator::dropCohortStatsTables(connection = tConnection,
-                                             cohortDatabaseSchema = cohortDatabaseSchema,
-                                             cohortTableNames = cohortTableNames)
+    on.exit(
+      {
+        CohortGenerator::dropCohortStatsTables(
+          connection = tConnection,
+          cohortDatabaseSchema = cohortDatabaseSchema,
+          cohortTableNames = cohortTableNames
+        )
 
-      DatabaseConnector::renderTranslateExecuteSql(tConnection,
-                                                   "DROP TABLE @cohortDatabaseSchema.@cohortTable",
-                                                   cohortDatabaseSchema = cohortDatabaseSchema,
-                                                   cohortTable = cohortTable)
-    }, add = TRUE)
+        DatabaseConnector::renderTranslateExecuteSql(tConnection,
+          "DROP TABLE @cohortDatabaseSchema.@cohortTable",
+          cohortDatabaseSchema = cohortDatabaseSchema,
+          cohortTable = cohortTable
+        )
+      },
+      add = TRUE
+    )
 
     # Generate the cohort set
     CohortGenerator::generateCohortSet(
@@ -50,34 +56,36 @@ test_that("Execute and export characterization", {
     )
     checkmate::expect_file_exists(file.path(exportFolder, "cohort_count.csv"))
 
-    executeCohortCharacterization(connection = tConnection,
-                                  databaseId = "Testdb",
-                                  exportFolder = exportFolder,
-                                  cdmDatabaseSchema = cdmDatabaseSchema,
-                                  cohortDatabaseSchema = cohortDatabaseSchema,
-                                  cohortTable = cohortTable,
-                                  covariateSettings = temporalCovariateSettings,
-                                  tempEmulationSchema = tempEmulationSchema,
-                                  cdmVersion = 5,
-                                  cohorts = cohortDefinitionSet[1:3,],
-                                  cohortCounts = cohortCounts,
-                                  minCellCount = 5,
-                                  instantiatedCohorts = cohortDefinitionSet$cohortId,
-                                  incremental = TRUE,
-                                  recordKeepingFile = recordKeepingFile,
-                                  task = "runTemporalCohortCharacterization",
-                                  jobName = "Temporal Cohort characterization")
-    
+    executeCohortCharacterization(
+      connection = tConnection,
+      databaseId = "Testdb",
+      exportFolder = exportFolder,
+      cdmDatabaseSchema = cdmDatabaseSchema,
+      cohortDatabaseSchema = cohortDatabaseSchema,
+      cohortTable = cohortTable,
+      covariateSettings = temporalCovariateSettings,
+      tempEmulationSchema = tempEmulationSchema,
+      cdmVersion = 5,
+      cohorts = cohortDefinitionSet[1:3, ],
+      cohortCounts = cohortCounts,
+      minCellCount = 5,
+      instantiatedCohorts = cohortDefinitionSet$cohortId,
+      incremental = TRUE,
+      recordKeepingFile = recordKeepingFile,
+      task = "runTemporalCohortCharacterization",
+      jobName = "Temporal Cohort characterization"
+    )
+
     # Check all files are created
     checkmate::expect_file_exists(file.path(exportFolder, "temporal_covariate_ref.csv"))
     checkmate::expect_file_exists(file.path(exportFolder, "temporal_analysis_ref.csv"))
     checkmate::expect_file_exists(file.path(exportFolder, "temporal_covariate_value.csv"))
     checkmate::expect_file_exists(file.path(exportFolder, "temporal_covariate_value_dist.csv"))
     checkmate::expect_file_exists(file.path(exportFolder, "temporal_time_ref.csv"))
-    
+
     recordKeepingFileData <- readr::read_csv(file = recordKeepingFile, col_types = readr::cols())
     testthat::expect_equal(object = nrow(recordKeepingFileData), expected = 3)
-    
+
     # check if subset works
     subset <- subsetToRequiredCohorts(
       cohorts = cohortDefinitionSet,
@@ -85,43 +93,46 @@ test_that("Execute and export characterization", {
       incremental = TRUE,
       recordKeepingFile = recordKeepingFile
     )
-    
-    #should not have the cohorts that were previously run
-    testthat::expect_equal(object = nrow(subset %>%
-                                           dplyr::filter(
-                                             cohortId %in% c(cohortDefinitionSet[1:3, ]$cohortId)
-                                           )),
-                           expected = 0)
-    
+
+    # should not have the cohorts that were previously run
+    testthat::expect_equal(
+      object = nrow(subset %>%
+        dplyr::filter(
+          cohortId %in% c(cohortDefinitionSet[1:3, ]$cohortId)
+        )),
+      expected = 0
+    )
+
     # finish the rest of characterization
-    executeCohortCharacterization(connection = tConnection,
-                                  databaseId = "Testdb",
-                                  exportFolder = exportFolder,
-                                  cdmDatabaseSchema = cdmDatabaseSchema,
-                                  cohortDatabaseSchema = cohortDatabaseSchema,
-                                  cohortTable = cohortTable,
-                                  covariateSettings = temporalCovariateSettings,
-                                  tempEmulationSchema = tempEmulationSchema,
-                                  cdmVersion = 5,
-                                  cohorts = cohortDefinitionSet,
-                                  cohortCounts = cohortCounts,
-                                  minCellCount = 5,
-                                  instantiatedCohorts = cohortDefinitionSet$cohortId,
-                                  incremental = TRUE,
-                                  recordKeepingFile = recordKeepingFile,
-                                  task = "runTemporalCohortCharacterization",
-                                  jobName = "Temporal Cohort characterization")
-    
+    executeCohortCharacterization(
+      connection = tConnection,
+      databaseId = "Testdb",
+      exportFolder = exportFolder,
+      cdmDatabaseSchema = cdmDatabaseSchema,
+      cohortDatabaseSchema = cohortDatabaseSchema,
+      cohortTable = cohortTable,
+      covariateSettings = temporalCovariateSettings,
+      tempEmulationSchema = tempEmulationSchema,
+      cdmVersion = 5,
+      cohorts = cohortDefinitionSet,
+      cohortCounts = cohortCounts,
+      minCellCount = 5,
+      instantiatedCohorts = cohortDefinitionSet$cohortId,
+      incremental = TRUE,
+      recordKeepingFile = recordKeepingFile,
+      task = "runTemporalCohortCharacterization",
+      jobName = "Temporal Cohort characterization"
+    )
+
     # Check no time ids are NA/NULL
     tdata <- readr::read_csv(file.path(exportFolder, "temporal_covariate_value_dist.csv"))
     expect_false(any(is.na(tdata$time_id) | is.null(tdata$time_id)))
-    
+
     tdata <- readr::read_csv(file.path(exportFolder, "temporal_covariate_value.csv"))
     expect_false(any(is.na(tdata$time_id) | is.null(tdata$time_id)))
-    
+
     # It would make no sense if there were NA values here
     tdata <- readr::read_csv(file.path(exportFolder, "temporal_time_ref.csv"))
     expect_false(any(is.na(tdata$time_id) | is.null(tdata$time_id)))
-    
   })
 })
diff --git a/tests/testthat/test-DatabaseMigrations.R b/tests/testthat/test-DatabaseMigrations.R
index 5459eee6f..1df57f481 100644
--- a/tests/testthat/test-DatabaseMigrations.R
+++ b/tests/testthat/test-DatabaseMigrations.R
@@ -1,20 +1,22 @@
 if (dbms == "postgresql") {
-  resultsDatabaseSchema <- paste0("r",
-                                  gsub("[: -]", "", Sys.time(), perl = TRUE),
-                                  sample(1:100, 1))
+  resultsDatabaseSchema <- paste0(
+    "r",
+    gsub("[: -]", "", Sys.time(), perl = TRUE),
+    sample(1:100, 1)
+  )
 
   # Always clean up
   withr::defer(
-  {
-    pgConnection <- DatabaseConnector::connect(connectionDetails = connectionDetails)
-    sql <- "DROP SCHEMA IF EXISTS @resultsDatabaseSchema CASCADE;"
-    DatabaseConnector::renderTranslateExecuteSql(
-      sql = sql,
-      resultsDatabaseSchema = resultsDatabaseSchema,
-      connection = pgConnection
-    )
-    DatabaseConnector::disconnect(pgConnection)
-  },
+    {
+      pgConnection <- DatabaseConnector::connect(connectionDetails = connectionDetails)
+      sql <- "DROP SCHEMA IF EXISTS @resultsDatabaseSchema CASCADE;"
+      DatabaseConnector::renderTranslateExecuteSql(
+        sql = sql,
+        resultsDatabaseSchema = resultsDatabaseSchema,
+        connection = pgConnection
+      )
+      DatabaseConnector::disconnect(pgConnection)
+    },
     testthat::teardown_env()
   )
 }
@@ -27,34 +29,42 @@ test_that("Database Migrations execute without error", {
 
   if (dbms == "postgresql") {
     sql <- "CREATE SCHEMA @resultsDatabaseSchema;"
-    DatabaseConnector::renderTranslateExecuteSql(sql = sql,
-                                                 resultsDatabaseSchema = resultsDatabaseSchema,
-                                                 connection = connection)
+    DatabaseConnector::renderTranslateExecuteSql(
+      sql = sql,
+      resultsDatabaseSchema = resultsDatabaseSchema,
+      connection = connection
+    )
   } else {
     resultsDatabaseSchema <- "main"
   }
 
-  migrator <- getDataMigrator(connectionDetails = connectionDetails,
-                              databaseSchema = resultsDatabaseSchema,
-                              tablePrefix = "cd_")
+  migrator <- getDataMigrator(
+    connectionDetails = connectionDetails,
+    databaseSchema = resultsDatabaseSchema,
+    tablePrefix = "cd_"
+  )
   expect_true(migrator$check())
 
-  .createDataModel(connection = connection,
-                   databaseSchema = resultsDatabaseSchema,
-                   tablePrefix = "cd_")
+  .createDataModel(
+    connection = connection,
+    databaseSchema = resultsDatabaseSchema,
+    tablePrefix = "cd_"
+  )
 
   expect_false(all(migrator$getStatus()$executed))
 
-  migrateDataModel(connectionDetails = connectionDetails,
-                   databaseSchema = resultsDatabaseSchema,
-                   tablePrefix = "cd_")
+  migrateDataModel(
+    connectionDetails = connectionDetails,
+    databaseSchema = resultsDatabaseSchema,
+    tablePrefix = "cd_"
+  )
 
   expect_true(all(migrator$getStatus()$executed))
 
   ## Reruning migrations should not cause an error
-  migrateDataModel(connectionDetails = connectionDetails,
-                   databaseSchema = resultsDatabaseSchema,
-                   tablePrefix = "cd_")
-
+  migrateDataModel(
+    connectionDetails = connectionDetails,
+    databaseSchema = resultsDatabaseSchema,
+    tablePrefix = "cd_"
+  )
 })
-
diff --git a/tests/testthat/test-ResultsDataModel.R b/tests/testthat/test-ResultsDataModel.R
index 7a0af1790..afa790962 100644
--- a/tests/testthat/test-ResultsDataModel.R
+++ b/tests/testthat/test-ResultsDataModel.R
@@ -296,12 +296,12 @@ test_that("No database file fails upload", {
   DatabaseConnector::createZipFile(testZipFile, "cohorts/CohortsToCreate.csv")
 
   expect_error(
-   uploadResults(
+    uploadResults(
       connectionDetails = connectionDetails,
       schema = "main",
       zipFileName = testZipFile,
       tablePrefix = "cd_"
     ),
-   regexp ="database metadata file not found - cannot upload results"
+    regexp = "database metadata file not found - cannot upload results"
   )
 })
diff --git a/tests/testthat/test-againstCdm.R b/tests/testthat/test-againstCdm.R
index ecb45fbef..54a2107ba 100644
--- a/tests/testthat/test-againstCdm.R
+++ b/tests/testthat/test-againstCdm.R
@@ -95,10 +95,11 @@ test_that("Cohort diagnostics in incremental mode", {
     }
 
     ## Repeat tests with incremental set to false to ensure better code coverage
-    withr::with_options(list("CohortDiagnostics-TimeSeries-batch-size" = 1,
-                             "CohortDiagnostics-FE-batch-size" = 1,
-                             "CohortDiagnostics-Relationships-batch-size" = 50),
-    {
+    withr::with_options(list(
+      "CohortDiagnostics-TimeSeries-batch-size" = 1,
+      "CohortDiagnostics-FE-batch-size" = 1,
+      "CohortDiagnostics-Relationships-batch-size" = 50
+    ), {
       executeDiagnostics(
         connectionDetails = connectionDetails,
         cdmDatabaseSchema = cdmDatabaseSchema,
diff --git a/tests/testthat/test-moduleCohortRelationship.R b/tests/testthat/test-moduleCohortRelationship.R
index 25d317fd4..8b07d5636 100644
--- a/tests/testthat/test-moduleCohortRelationship.R
+++ b/tests/testthat/test-moduleCohortRelationship.R
@@ -1,20 +1,20 @@
 test_that("Testing executeCohortRelationshipDiagnostics", {
   skip_if(skipCdmTests, "cdm settings not configured")
-  
+
   # manually create cohort table and load to table
   # for the logic to work - there has to be some overlap of the comparator cohort over target cohort
   # note - we will not be testing offset in this test. it is expected to work as it is a simple substraction
-  
+
   temporalStartDays <- c(0)
   temporalEndDays <- c(0)
-  
+
   targetCohort <- dplyr::tibble(
     cohortDefinitionId = c(1),
     subjectId = c(1),
     cohortStartDate = c(as.Date("1900-01-15")),
     cohortEndDate = c(as.Date("1900-01-31"))
   ) # target cohort always one row
-  
+
   comparatorCohort <- # all records here overlap with targetCohort
     dplyr::tibble(
       cohortDefinitionId = c(10, 10, 10),
@@ -32,7 +32,7 @@ test_that("Testing executeCohortRelationshipDiagnostics", {
         as.Date("1900-01-31")
       )
     )
-  
+
   cohort <- dplyr::bind_rows(
     targetCohort,
     comparatorCohort,
@@ -41,16 +41,16 @@ test_that("Testing executeCohortRelationshipDiagnostics", {
     comparatorCohort %>%
       dplyr::mutate(cohortDefinitionId = 20)
   )
-  
+
   connectionCohortRelationship <-
     DatabaseConnector::connect(connectionDetails)
-  
+
   # to do - with incremental = FALSE
   with_dbc_connection(connectionCohortRelationship, {
     sysTime <- as.numeric(Sys.time()) * 100000
     tableName <- paste0("cr", sysTime)
     observationTableName <- paste0("op", sysTime)
-    
+
     DatabaseConnector::insertTable(
       connection = connectionCohortRelationship,
       databaseSchema = cohortDatabaseSchema,
@@ -62,7 +62,7 @@ test_that("Testing executeCohortRelationshipDiagnostics", {
       camelCaseToSnakeCase = TRUE,
       progressBar = FALSE
     )
-    
+
     cohortDefinitionSet <-
       cohort %>%
       dplyr::select(cohortDefinitionId) %>%
@@ -78,20 +78,26 @@ test_that("Testing executeCohortRelationshipDiagnostics", {
         )
       ))) %>%
       dplyr::ungroup() %>%
-      dplyr::mutate(sql = json,
-                    checksum = CohortDiagnostics:::computeChecksum(json))
-    
-    
+      dplyr::mutate(
+        sql = json,
+        checksum = CohortDiagnostics:::computeChecksum(json)
+      )
+
+
     exportFolder <- tempdir()
     exportFile <- tempfile()
-    
-    unlink(x = exportFolder,
-           recursive = TRUE,
-           force = TRUE)
-    dir.create(path = exportFolder,
-               showWarnings = FALSE,
-               recursive = TRUE)
-    
+
+    unlink(
+      x = exportFolder,
+      recursive = TRUE,
+      force = TRUE
+    )
+    dir.create(
+      path = exportFolder,
+      showWarnings = FALSE,
+      recursive = TRUE
+    )
+
     CohortDiagnostics:::executeCohortRelationshipDiagnostics(
       connection = connectionCohortRelationship,
       databaseId = "testDataSourceName",
@@ -111,16 +117,18 @@ test_that("Testing executeCohortRelationshipDiagnostics", {
       incremental = TRUE,
       batchSize = 2
     )
-    
+
     recordKeepingFileData <-
-      readr::read_csv(file = paste0(exportFile, "recordKeeping"),
-                      col_types = readr::cols())
-    
+      readr::read_csv(
+        file = paste0(exportFile, "recordKeeping"),
+        col_types = readr::cols()
+      )
+
     # testing if check sum if written to field called targetChecksum
     testthat::expect_true("targetChecksum" %in% colnames(recordKeepingFileData))
     testthat::expect_true("comparatorChecksum" %in% colnames(recordKeepingFileData))
     testthat::expect_true("checksum" %in% colnames(recordKeepingFileData))
-    
+
     testthat::expect_equal(
       object = recordKeepingFileData %>%
         dplyr::filter(cohortId == 1) %>%
@@ -131,22 +139,26 @@ test_that("Testing executeCohortRelationshipDiagnostics", {
         dplyr::filter(cohortId == 1) %>%
         dplyr::filter(comparatorId == 10) %>%
         dplyr::mutate(
-          checksum2 = paste0(targetChecksum,
-                             comparatorChecksum)
+          checksum2 = paste0(
+            targetChecksum,
+            comparatorChecksum
+          )
         ) %>%
         dplyr::pull(checksum2)
     )
-    
-    
-    
+
+
+
     ## testing if subset works
-    allCohortIds <- cohortDefinitionSet  %>%
+    allCohortIds <- cohortDefinitionSet %>%
       dplyr::filter(cohortId %in% c(1, 10, 2)) %>%
       dplyr::select(cohortId, checksum) %>%
-      dplyr::rename(targetCohortId = cohortId,
-                    targetChecksum = checksum) %>%
+      dplyr::rename(
+        targetCohortId = cohortId,
+        targetChecksum = checksum
+      ) %>%
       dplyr::distinct()
-    
+
     combinationsOfPossibleCohortRelationships <- allCohortIds %>%
       tidyr::crossing(
         allCohortIds %>%
@@ -158,34 +170,36 @@ test_that("Testing executeCohortRelationshipDiagnostics", {
       dplyr::filter(targetCohortId != comparatorCohortId) %>%
       dplyr::arrange(targetCohortId, comparatorCohortId) %>%
       dplyr::mutate(checksum = paste0(targetChecksum, comparatorChecksum))
-    
+
     subset <- CohortDiagnostics:::subsetToRequiredCombis(
       combis = combinationsOfPossibleCohortRelationships,
       task = "runCohortRelationship",
       incremental = TRUE,
       recordKeepingFile = paste0(exportFile, "recordKeeping")
     ) %>% dplyr::tibble()
-    
+
     ### subset should not have the combinations in record keeping file
     shouldBeDfOfZeroRows <- subset %>%
       dplyr::inner_join(
         recordKeepingFileData %>%
-          dplyr::select(cohortId,
-                        comparatorId) %>%
+          dplyr::select(
+            cohortId,
+            comparatorId
+          ) %>%
           dplyr::rename(
             targetCohortId = cohortId,
             comparatorCohortId = comparatorId
           ),
         by = c("targetCohortId", "comparatorCohortId")
       )
-    
+
     testthat::expect_equal(
       object = nrow(shouldBeDfOfZeroRows),
       expected = 0,
       info = "Looks like subset and record keeping file did not match."
     )
-    
-    
+
+
     ## running again by adding cohort 2, to previously run 1 and 10
     CohortDiagnostics:::executeCohortRelationshipDiagnostics(
       connection = connectionCohortRelationship,
@@ -206,36 +220,44 @@ test_that("Testing executeCohortRelationshipDiagnostics", {
       incremental = TRUE,
       batchSize = 2
     )
-    
+
     recordKeepingFileData2 <-
-      readr::read_csv(file = paste0(exportFile, "recordKeeping"),
-                      col_types = readr::cols())
+      readr::read_csv(
+        file = paste0(exportFile, "recordKeeping"),
+        col_types = readr::cols()
+      )
     # record keeping file should have 6 combinations - for 3 cohorts
-    testthat::expect_equal(object = nrow(recordKeepingFileData2),
-                           expected = 3 * 2 * 1)
-    
-    #record keeping file should have 4 additional combinations
+    testthat::expect_equal(
+      object = nrow(recordKeepingFileData2),
+      expected = 3 * 2 * 1
+    )
+
+    # record keeping file should have 4 additional combinations
     testthat::expect_equal(
       object = recordKeepingFileData2 %>%
         dplyr::anti_join(
           recordKeepingFileData %>%
-            dplyr::select(cohortId,
-                          comparatorId),
+            dplyr::select(
+              cohortId,
+              comparatorId
+            ),
           by = c("cohortId", "comparatorId")
         ) %>%
         nrow(),
       expected = 4
     )
 
-    
+
     # check what happens for an unrelated cohort combination
-    allCohortIds <- cohortDefinitionSet  %>%
+    allCohortIds <- cohortDefinitionSet %>%
       dplyr::filter(cohortId %in% c(2, 20)) %>%
       dplyr::select(cohortId, checksum) %>%
-      dplyr::rename(targetCohortId = cohortId,
-                    targetChecksum = checksum) %>%
+      dplyr::rename(
+        targetCohortId = cohortId,
+        targetChecksum = checksum
+      ) %>%
       dplyr::distinct()
-    
+
     combinationsOfPossibleCohortRelationships <- allCohortIds %>%
       tidyr::crossing(
         allCohortIds %>%
@@ -247,34 +269,34 @@ test_that("Testing executeCohortRelationshipDiagnostics", {
       dplyr::filter(targetCohortId != comparatorCohortId) %>%
       dplyr::arrange(targetCohortId, comparatorCohortId) %>%
       dplyr::mutate(checksum = paste0(targetChecksum, comparatorChecksum))
-    
+
     subset <- CohortDiagnostics:::subsetToRequiredCombis(
       combis = combinationsOfPossibleCohortRelationships,
       task = "runCohortRelationship",
       incremental = TRUE,
       recordKeepingFile = paste0(exportFile, "recordKeeping")
     ) %>% dplyr::tibble()
-    
+
     ### subset should be two rows in subsets that are not in record keeping file
     shouldBeTwoRows <- subset %>%
       dplyr::anti_join(
         recordKeepingFileData2 %>%
-          dplyr::select(cohortId,
-                        comparatorId) %>%
+          dplyr::select(
+            cohortId,
+            comparatorId
+          ) %>%
           dplyr::rename(
             targetCohortId = cohortId,
             comparatorCohortId = comparatorId
           ),
         by = c("targetCohortId", "comparatorCohortId")
       )
-    
+
     testthat::expect_equal(
       object = nrow(shouldBeTwoRows),
       expected = 2,
       info = "Looks like subset and record keeping file did not match, Two new cohorts should have run."
     )
-    
-    
   })
 })
 
diff --git a/tests/testthat/test-moduleTimeSeries.R b/tests/testthat/test-moduleTimeSeries.R
index fa238d77c..e60d299a5 100644
--- a/tests/testthat/test-moduleTimeSeries.R
+++ b/tests/testthat/test-moduleTimeSeries.R
@@ -1,9 +1,9 @@
 test_that("Testing cohort time series execution", {
   skip_if(skipCdmTests, "cdm settings not configured")
-  
+
   connectionTimeSeries <-
     DatabaseConnector::connect(connectionDetails)
-  
+
   # to do - with incremental = FALSE
   with_dbc_connection(connectionTimeSeries, {
     cohort <- dplyr::tibble(
@@ -22,11 +22,13 @@ test_that("Testing cohort time series execution", {
         as.Date("2005-09-15")
       )
     )
-    
-    cohort <- dplyr::bind_rows(cohort,
-                               cohort %>%
-                                 dplyr::mutate(cohortDefinitionId = cohortDefinitionId * 1000))
-    
+
+    cohort <- dplyr::bind_rows(
+      cohort,
+      cohort %>%
+        dplyr::mutate(cohortDefinitionId = cohortDefinitionId * 1000)
+    )
+
     cohortDefinitionSet <-
       cohort %>%
       dplyr::select(cohortDefinitionId) %>%
@@ -42,25 +44,33 @@ test_that("Testing cohort time series execution", {
         )
       ))) %>%
       dplyr::ungroup() %>%
-      dplyr::mutate(sql = json,
-                    checksum = as.character(CohortDiagnostics:::computeChecksum(json))) %>%
+      dplyr::mutate(
+        sql = json,
+        checksum = as.character(CohortDiagnostics:::computeChecksum(json))
+      ) %>%
       dplyr::ungroup()
-    
+
     exportFolder <- tempdir()
     exportFile <- tempfile()
-    
-    unlink(x = exportFolder,
-           recursive = TRUE,
-           force = TRUE)
-    dir.create(path = exportFolder,
-               showWarnings = FALSE,
-               recursive = TRUE)
-    
+
+    unlink(
+      x = exportFolder,
+      recursive = TRUE,
+      force = TRUE
+    )
+    dir.create(
+      path = exportFolder,
+      showWarnings = FALSE,
+      recursive = TRUE
+    )
+
     cohortTable <-
-      paste0("ct_",
-             gsub("[: -]", "", Sys.time(), perl = TRUE),
-             sample(1:100, 1))
-    
+      paste0(
+        "ct_",
+        gsub("[: -]", "", Sys.time(), perl = TRUE),
+        sample(1:100, 1)
+      )
+
     DatabaseConnector::insertTable(
       connection = connectionTimeSeries,
       databaseSchema = cohortDatabaseSchema,
@@ -72,7 +82,7 @@ test_that("Testing cohort time series execution", {
       camelCaseToSnakeCase = TRUE,
       progressBar = FALSE
     )
-    
+
     CohortDiagnostics:::executeTimeSeriesDiagnostics(
       connection = connectionTimeSeries,
       tempEmulationSchema = tempEmulationSchema,
@@ -95,21 +105,23 @@ test_that("Testing cohort time series execution", {
       ),
       batchSize = 1
     )
-    
+
     recordKeepingFileData <-
-      readr::read_csv(file = paste0(exportFile, "recordKeeping"),
-                      col_types = readr::cols())
-    
+      readr::read_csv(
+        file = paste0(exportFile, "recordKeeping"),
+        col_types = readr::cols()
+      )
+
     # testing if check sum is written
     testthat::expect_true("checksum" %in% colnames(recordKeepingFileData))
-    
+
     # result
     timeSeriesResults1 <-
       readr::read_csv(
         file = file.path(exportFolder, "time_series.csv"),
         col_types = readr::cols()
       )
-    
+
     subset <- CohortDiagnostics:::subsetToRequiredCohorts(
       cohorts = cohortDefinitionSet,
       task = "runCohortTimeSeries",
@@ -117,18 +129,20 @@ test_that("Testing cohort time series execution", {
       recordKeepingFile = paste0(exportFile, "recordKeeping")
     ) %>%
       dplyr::arrange(cohortId)
-    
-    testthat::expect_equal(object = subset$cohortId,
-                           expected = c(1000, 2000))
-    
-    
+
+    testthat::expect_equal(
+      object = subset$cohortId,
+      expected = c(1000, 2000)
+    )
+
+
     # delete the previously written results file. To see if the previously executed cohorts will have results after deletion
     unlink(
       x = file.path(exportFolder, "time_series.csv"),
       recursive = TRUE,
       force = TRUE
     )
-    
+
     CohortDiagnostics:::executeTimeSeriesDiagnostics(
       connection = connectionTimeSeries,
       tempEmulationSchema = tempEmulationSchema,
@@ -155,12 +169,11 @@ test_that("Testing cohort time series execution", {
         file = file.path(exportFolder, "time_series.csv"),
         col_types = readr::cols()
       )
-    
+
     testthat::expect_equal(
       object = resultsNew$cohort_id %>% unique() %>% sort(),
       expected = c(1000, 2000)
     )
-    
   })
 })
 
@@ -175,7 +188,6 @@ test_that("Testing time series logic", {
 
   # to do - with incremental = FALSE
   with_dbc_connection(connectionTimeSeries, {
-
     # manually create cohort table and load to table
     #   Cohort table has a total of four records, with each cohort id having two each
     #   cohort 1 has one subject with two different cohort entries
@@ -250,28 +262,32 @@ test_that("Testing time series logic", {
 
 test_that("Testing Data source time series execution", {
   skip_if(skipCdmTests, "cdm settings not configured")
-  
+
   connectionTimeSeries <-
     DatabaseConnector::connect(connectionDetails)
-  
+
   # to do - with incremental = FALSE
   with_dbc_connection(connectionTimeSeries, {
-    cohortDefinitionSet = dplyr::tibble(
+    cohortDefinitionSet <- dplyr::tibble(
       cohortId = -44819062,
       # cohort id is identified by an omop concept id https://athena.ohdsi.org/search-terms/terms/44819062
       checksum = CohortDiagnostics:::computeChecksum(column = "data source time series")
     )
-    
+
     exportFolder <- tempdir()
     exportFile <- tempfile()
-    
-    unlink(x = exportFolder,
-           recursive = TRUE,
-           force = TRUE)
-    dir.create(path = exportFolder,
-               showWarnings = FALSE,
-               recursive = TRUE)
-    
+
+    unlink(
+      x = exportFolder,
+      recursive = TRUE,
+      force = TRUE
+    )
+    dir.create(
+      path = exportFolder,
+      showWarnings = FALSE,
+      recursive = TRUE
+    )
+
     executeTimeSeriesDiagnostics(
       connection = connectionTimeSeries,
       tempEmulationSchema = tempEmulationSchema,
@@ -290,22 +306,24 @@ test_that("Testing Data source time series execution", {
         observationPeriodMaxDate = as.Date("2007-12-31")
       )
     )
-    
+
     recordKeepingFileData <-
-      readr::read_csv(file = paste0(exportFile, "recordKeeping"),
-                      col_types = readr::cols())
-    
+      readr::read_csv(
+        file = paste0(exportFile, "recordKeeping"),
+        col_types = readr::cols()
+      )
+
     # testing if check sum is written
     testthat::expect_true("checksum" %in% colnames(recordKeepingFileData))
     testthat::expect_equal(object = recordKeepingFileData$cohortId, expected = -44819062)
-    
+
     # result
     dataSourceTimeSeriesResult <-
       readr::read_csv(
         file = file.path(exportFolder, "time_series.csv"),
         col_types = readr::cols()
       )
-    
+
     subset <- subsetToRequiredCohorts(
       cohorts = cohortDefinitionSet,
       task = "runDataSourceTimeSeries",
@@ -313,9 +331,10 @@ test_that("Testing Data source time series execution", {
       recordKeepingFile = paste0(exportFile, "recordKeeping")
     ) %>%
       dplyr::arrange(cohortId)
-    
-    testthat::expect_equal(object = nrow(subset),
-                           expected = 0)
+
+    testthat::expect_equal(
+      object = nrow(subset),
+      expected = 0
+    )
   })
 })
-
diff --git a/vignettes/CreatingAStudyPackage.Rmd b/vignettes/CreatingAStudyPackage.Rmd
index 8e695ec21..5794b1442 100644
--- a/vignettes/CreatingAStudyPackage.Rmd
+++ b/vignettes/CreatingAStudyPackage.Rmd
@@ -20,7 +20,8 @@ knitr::opts_chunk$set(
   cache = FALSE,
   comment = "#>",
   error = FALSE,
-  tidy = FALSE)
+  tidy = FALSE
+)
 ```
 
 # Introduction
@@ -68,7 +69,7 @@ The skeleton cohort diagnostics study package is [here](https://github.com/OHDSI
 # please ensure you have the latest version of Hydra. As of 08/13/2021 - CohortDiagnostics support for Hydra is still in develop branch.
 # please check hydra release notes and update hydra
 remotes::install_github("OHDSI/Hydra", ref = "develop")
-outputFolder <- "d:/temp/output"  # location where you study package will be created
+outputFolder <- "d:/temp/output" # location where you study package will be created
 
 
 ########## Please populate the information below #####################
@@ -90,62 +91,68 @@ library(magrittr)
 baseUrl <- Sys.getenv("baseUrl")
 # if you have security enabled, please authorize the use - example below
 # ROhdsiWebApi::authorizeWebApi(baseUrl, 'windows')
-cohortIds <- c(22040,
-               22042,
-               22041,
-               22039,
-               22038,
-               22037,
-               22036,
-               22035,
-               22034,
-               22033,
-               22031,
-               22032,
-               22030,
-               22028,
-               22029)
+cohortIds <- c(
+  22040,
+  22042,
+  22041,
+  22039,
+  22038,
+  22037,
+  22036,
+  22035,
+  22034,
+  22033,
+  22031,
+  22032,
+  22030,
+  22028,
+  22029
+)
 
 
 
 ################# end of user input ##############
 webApiCohorts <- ROhdsiWebApi::getCohortDefinitionsMetaData(baseUrl = baseUrl)
-studyCohorts <-  webApiCohorts %>%
-        dplyr::filter(.data$id %in% cohortIds)
+studyCohorts <- webApiCohorts %>%
+  dplyr::filter(.data$id %in% cohortIds)
 
 # compile them into a data table
 cohortDefinitionsArray <- list()
 for (i in (1:nrow(studyCohorts))) {
-        cohortDefinition <-
-                ROhdsiWebApi::getCohortDefinition(cohortId = studyCohorts$id[[i]],
-                                                  baseUrl = baseUrl)
-        cohortDefinitionsArray[[i]] <- list(
-                id = studyCohorts$id[[i]],
-                createdDate = studyCohorts$createdDate[[i]],
-                modifiedDate = studyCohorts$createdDate[[i]],
-                logicDescription = studyCohorts$description[[i]],
-                name = stringr::str_trim(stringr::str_squish(cohortDefinition$name)),
-                expression = cohortDefinition$expression
-        )
+  cohortDefinition <-
+    ROhdsiWebApi::getCohortDefinition(
+      cohortId = studyCohorts$id[[i]],
+      baseUrl = baseUrl
+    )
+  cohortDefinitionsArray[[i]] <- list(
+    id = studyCohorts$id[[i]],
+    createdDate = studyCohorts$createdDate[[i]],
+    modifiedDate = studyCohorts$createdDate[[i]],
+    logicDescription = studyCohorts$description[[i]],
+    name = stringr::str_trim(stringr::str_squish(cohortDefinition$name)),
+    expression = cohortDefinition$expression
+  )
 }
 
 tempFolder <- tempdir()
 unlink(x = tempFolder, recursive = TRUE, force = TRUE)
 dir.create(path = tempFolder, showWarnings = FALSE, recursive = TRUE)
 
-specifications <- list(id = 1,
-                       version = version,
-                       name = name,
-                       packageName = packageName,
-                       skeletonVersion = skeletonVersion,
-                       createdBy = createdBy,
-                       createdDate = createdDate,
-                       modifiedBy = modifiedBy,
-                       modifiedDate = modifiedDate,
-                       skeletonType = skeletonType,
-                       organizationName = organizationName,
-                       description = description,
-                       cohortDefinitions = cohortDefinitionsArray)
+specifications <- list(
+  id = 1,
+  version = version,
+  name = name,
+  packageName = packageName,
+  skeletonVersion = skeletonVersion,
+  createdBy = createdBy,
+  createdDate = createdDate,
+  modifiedBy = modifiedBy,
+  modifiedDate = modifiedDate,
+  skeletonType = skeletonType,
+  organizationName = organizationName,
+  description = description,
+  cohortDefinitions = cohortDefinitionsArray
+)
 
 jsonFileName <- paste0(file.path(tempFolder, "CohortDiagnosticsSpecs.json"))
 write(x = specifications %>% RJSONIO::toJSON(pretty = TRUE, digits = 23), file = jsonFileName)
@@ -162,13 +169,13 @@ write(x = specifications %>% RJSONIO::toJSON(pretty = TRUE, digits = 23), file =
 #### get the skeleton from github
 # download.file(url = "https://github.com/OHDSI/SkeletonCohortDiagnosticsStudy/archive/refs/heads/main.zip",
 #                          destfile = file.path(tempFolder, 'skeleton.zip'))
-# unzip(zipfile =  file.path(tempFolder, 'skeleton.zip'), 
+# unzip(zipfile =  file.path(tempFolder, 'skeleton.zip'),
 #       overwrite = TRUE,
 #       exdir = file.path(tempFolder, "skeleton")
 #         )
 # fileList <- list.files(path = file.path(tempFolder, "skeleton"), full.names = TRUE, recursive = TRUE, all.files = TRUE)
-# DatabaseConnector::createZipFile(zipFile = file.path(tempFolder, 'skeleton.zip'), 
-#                                  files = fileList, 
+# DatabaseConnector::createZipFile(zipFile = file.path(tempFolder, 'skeleton.zip'),
+#                                  files = fileList,
 #                                  rootFolder = list.dirs(file.path(tempFolder, 'skeleton'), recursive = FALSE))
 
 ##############################################################
@@ -183,17 +190,17 @@ write(x = specifications %>% RJSONIO::toJSON(pretty = TRUE, digits = 23), file =
 hydraSpecificationFromFile <- Hydra::loadSpecifications(fileName = jsonFileName)
 unlink(x = outputFolder, recursive = TRUE)
 dir.create(path = outputFolder, showWarnings = FALSE, recursive = TRUE)
-Hydra::hydrate(specifications = hydraSpecificationFromFile,
-               outputFolder = outputFolder
+Hydra::hydrate(
+  specifications = hydraSpecificationFromFile,
+  outputFolder = outputFolder
 )
 
 # for advanced user using skeletons outside of Hydra
 # Hydra::hydrate(specifications = hydraSpecificationFromFile,
-#                outputFolder = outputFolder, 
+#                outputFolder = outputFolder,
 #                skeletonFileName = file.path(tempFolder, 'skeleton.zip')
 # )
 
 
 unlink(x = tempFolder, recursive = TRUE, force = TRUE)
-
 ```
diff --git a/vignettes/DatabaseModeInDiagnosticsExplorer.Rmd b/vignettes/DatabaseModeInDiagnosticsExplorer.Rmd
index 8b6b5d195..f47afb438 100644
--- a/vignettes/DatabaseModeInDiagnosticsExplorer.Rmd
+++ b/vignettes/DatabaseModeInDiagnosticsExplorer.Rmd
@@ -20,7 +20,8 @@ knitr::opts_chunk$set(
   cache = FALSE,
   comment = "#>",
   error = FALSE,
-  tidy = FALSE)
+  tidy = FALSE
+)
 ```
 
 # Database mode
@@ -70,4 +71,4 @@ databaseTableName: "database"
 # If you wish to enable annotation - not currently reccomended in multi-user environments
 enableAnnotation: FALSE
 enableAuthorization: FALSE
-```
\ No newline at end of file
+```
diff --git a/vignettes/RunningCohortDiagnostics.Rmd b/vignettes/RunningCohortDiagnostics.Rmd
index 68eb10025..b4926203c 100644
--- a/vignettes/RunningCohortDiagnostics.Rmd
+++ b/vignettes/RunningCohortDiagnostics.Rmd
@@ -20,12 +20,12 @@ knitr::opts_chunk$set(
   cache = FALSE,
   comment = "#>",
   error = FALSE,
-  tidy = FALSE)
+  tidy = FALSE
+)
 
 # Temp folders used to run the example
 exportFolder <- tempfile("CohortDiagnosticsTestExport")
 inclusionStatisticsFolder <- tempfile("inclusionStats")
-
 ```
 # Introduction
 This vignette discusses the process of generating a results set with `CohortDiagnostics` starting with cohort generation.
@@ -37,8 +37,8 @@ For this example we will also be using the `Eunomia` test package.
 Optionally, you may install the `ROhdsiWebApi` package to download cohort definitions from an ATLAS instance:
 
 ```{r eval=FALSE}
-remotes::install_github('OHDSI/Eunomia')
-remotes::install_github('OHDSI/ROhdsiWebApi')
+remotes::install_github("OHDSI/Eunomia")
+remotes::install_github("OHDSI/ROhdsiWebApi")
 ```
 
 # Configuring the connection to the server
@@ -48,10 +48,12 @@ We need to tell R how to connect to the server where the data are. `CohortDiagno
 ```{r tidy=FALSE,eval=FALSE}
 library(CohortDiagnostics)
 
-connectionDetails <- createConnectionDetails(dbms = "postgresql",
-                                             server = "localhost/ohdsi",
-                                             user = "joe",
-                                             password = "supersecret")
+connectionDetails <- createConnectionDetails(
+  dbms = "postgresql",
+  server = "localhost/ohdsi",
+  user = "joe",
+  password = "supersecret"
+)
 ```
 For the purposes of this example, we will use the Eunomia test CDM package that is in an Sqlite database stored locally.
 ```{r results = FALSE,message = FALSE,warning=FALSE, message = FALSE,eval=FALSE}
@@ -80,10 +82,12 @@ For example, the cohort diagnostics package includes an example set of cohort sq
 
 ```{r results = FALSE,message = FALSE,warning=FALSE,eval=FALSE}
 library(CohortDiagnostics)
-cohortDefinitionSet <- CohortGenerator::getCohortDefinitionSet(settingsFileName = "Cohorts.csv",
-                                                               jsonFolder = "cohorts",
-                                                               sqlFolder = "sql/sql_server",
-                                                               packageName = "CohortDiagnostics")
+cohortDefinitionSet <- CohortGenerator::getCohortDefinitionSet(
+  settingsFileName = "Cohorts.csv",
+  jsonFolder = "cohorts",
+  sqlFolder = "sql/sql_server",
+  packageName = "CohortDiagnostics"
+)
 ```
 
 Looking at this data.frame of Cohorts you will see the sql and json for these cohorts:
@@ -102,11 +106,13 @@ The following code demonstrates how to create a set of cohort references from AT
 # Set up url
 baseUrl <- "https://atlas.hosting.com/WebAPI"
 # list of cohort ids
-cohortIds <- c(18345,18346)
+cohortIds <- c(18345, 18346)
 
-cohortDefinitionSet <- ROhdsiWebApi::exportCohortDefinitionSet(baseUrl = baseUrl,
-                                                               cohortIds = cohortIds,
-                                                               generateStats = TRUE)
+cohortDefinitionSet <- ROhdsiWebApi::exportCohortDefinitionSet(
+  baseUrl = baseUrl,
+  cohortIds = cohortIds,
+  generateStats = TRUE
+)
 ```
 Consult the ROhdsiWebApi documentation for details on authentication to your atlas instance.
 Please note that in order to generate inclusion rules statistics (a useful diagnostic tool) the parameter `generateStats`
@@ -122,18 +128,22 @@ For example,
 cohortTableNames <- CohortGenerator::getCohortTableNames(cohortTable = cohortTable)
 
 # Next create the tables on the database
-CohortGenerator::createCohortTables(connectionDetails = connectionDetails,
-                                    cohortTableNames = cohortTableNames,
-                                    cohortDatabaseSchema = "main",
-                                    incremental = FALSE)
+CohortGenerator::createCohortTables(
+  connectionDetails = connectionDetails,
+  cohortTableNames = cohortTableNames,
+  cohortDatabaseSchema = "main",
+  incremental = FALSE
+)
 
 # Generate the cohort set
-CohortGenerator::generateCohortSet(connectionDetails= connectionDetails,
-                                   cdmDatabaseSchema = cdmDatabaseSchema,
-                                   cohortDatabaseSchema = cohortDatabaseSchema,
-                                   cohortTableNames = cohortTableNames,
-                                   cohortDefinitionSet = cohortDefinitionSet,
-                                   incremental = FALSE)
+CohortGenerator::generateCohortSet(
+  connectionDetails = connectionDetails,
+  cdmDatabaseSchema = cdmDatabaseSchema,
+  cohortDatabaseSchema = cohortDatabaseSchema,
+  cohortTableNames = cohortTableNames,
+  cohortDefinitionSet = cohortDefinitionSet,
+  incremental = FALSE
+)
 ```
 **Note, that the above code will delete an existing table**.
 However, incremental mode can be used when setting the parameter `incremental = TRUE`.
@@ -154,22 +164,25 @@ exportFolder <- "export"
 Then we execute the function (using the default settings) as follows:
 ```{r results = FALSE,message = FALSE,warning=FALSE,eval=FALSE}
 executeDiagnostics(cohortDefinitionSet,
-                   connectionDetails = connectionDetails,
-                   cohortTable = cohortTable,
-                   cohortDatabaseSchema = cohortDatabaseSchema,
-                   cdmDatabaseSchema = cdmDatabaseSchema,
-                   exportFolder = exportFolder,
-                   databaseId = "MyCdm",
-                   minCellCount = 5)
+  connectionDetails = connectionDetails,
+  cohortTable = cohortTable,
+  cohortDatabaseSchema = cohortDatabaseSchema,
+  cdmDatabaseSchema = cdmDatabaseSchema,
+  exportFolder = exportFolder,
+  databaseId = "MyCdm",
+  minCellCount = 5
+)
 ```
 ## Cohort Statistics Table Clean up
 The above cohort generation process will create a number of residual tables.
 As the process is complete, these are no longer required and can be removed.
 
 ```{r eval=FALSE}
-CohortGenerator::dropCohortStatsTables(connectionDetails = connectionDetails,
-                                       cohortDatabaseSchema = cohortDatabaseSchema,
-                                       cohortTableNames = cohortTableNames)
+CohortGenerator::dropCohortStatsTables(
+  connectionDetails = connectionDetails,
+  cohortDatabaseSchema = cohortDatabaseSchema,
+  cohortTableNames = cohortTableNames
+)
 ```
 
 
diff --git a/vignettes/ViewingResultsUsingDiagnosticsExplorer.Rmd b/vignettes/ViewingResultsUsingDiagnosticsExplorer.Rmd
index 6a18b152d..ec2110c1e 100644
--- a/vignettes/ViewingResultsUsingDiagnosticsExplorer.Rmd
+++ b/vignettes/ViewingResultsUsingDiagnosticsExplorer.Rmd
@@ -20,7 +20,8 @@ knitr::opts_chunk$set(
   cache = FALSE,
   comment = "#>",
   error = FALSE,
-  tidy = FALSE)
+  tidy = FALSE
+)
 ```
 
 # Viewing the diagnostics
@@ -65,4 +66,4 @@ We recommend the use of a database system, when file size of the cohort diagnost
 
 
 # Running over the network
-If you want to run the application over the network then set `runOverNetwork = TRUE` while launching the application using 'launchDiagnosticsExplorer()'. This will make the shiny application available over your network (i.e. within your networks firewall).
\ No newline at end of file
+If you want to run the application over the network then set `runOverNetwork = TRUE` while launching the application using 'launchDiagnosticsExplorer()'. This will make the shiny application available over your network (i.e. within your networks firewall).
diff --git a/vignettes/WhatIsCohortDiagnostics.Rmd b/vignettes/WhatIsCohortDiagnostics.Rmd
index d41b2a5dc..00d97897a 100644
--- a/vignettes/WhatIsCohortDiagnostics.Rmd
+++ b/vignettes/WhatIsCohortDiagnostics.Rmd
@@ -20,7 +20,8 @@ knitr::opts_chunk$set(
   cache = FALSE,
   comment = "#>",
   error = FALSE,
-  tidy = FALSE)
+  tidy = FALSE
+)
   ```
 
 # Introduction
@@ -43,4 +44,4 @@ Features
 - Break down index events into the specific concepts that triggered them.
 - Compute overlap between two cohorts.
 - Characterize cohorts, and compare these characterizations. Perform cohort comparison and temporal comparisons. 
-- Explore patient profiles of a random sample of subjects in a cohort.
\ No newline at end of file
+- Explore patient profiles of a random sample of subjects in a cohort.