Package maintenance

OHDSI · Oct 5, 2023 · 0696f1a · 0696f1a
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -8,3 +8,4 @@ docs
 .github
 deploy.sh
 compare_versions
+^.idea$
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: OhdsiShinyModules
 Type: Package
 Title: Repository of Shiny Modules for OHDSI Result Viewers
-Version: 1.2.0
+Version: 2.0.0
 Author: Jenna Reps
 Maintainer: Jenna Reps <[email protected]>
 Description: Install this package to access useful shiny modules for building shiny apps to explore results using the OHDSI tools .
@@ -11,6 +11,7 @@ LazyData: true
 Depends:
     R (>= 3.3.0)
 VignetteBuilder: knitr
+Language: EN-US
 Imports:
     checkmate,
     CirceR,

diff --git a/NEWS.md b/NEWS.md
@@ -1,9 +1,13 @@
-OhdsiShinyModules v1.2.0
+OhdsiShinyModules v2.0.0
 ========================
 - updated all models to use the same resultDatabaseSettings
 - made module function naming consistent (modules named after analysis packages)
 - made table prefix inputs consistent across modules
 - updated patientlevelprediction, cohortmethod and sccs to look similar.
+- Updated Cohort Diagnostics characterization to improve overall performance
+- Added plots for incidence in characterization module
+- Added PheValuator package
+- Numerous bug fixes (see github issues)
 
 OhdsiShinyModules v1.1.0
 ========================

diff --git a/R/OhdsiShinyModules.R b/R/OhdsiShinyModules.R
@@ -1,6 +1,6 @@
 # @file OhdsiShinyModules.R
 #
-# Copyright 2022 Observational Health Data Sciences and Informatics
+# Copyright 2023 Observational Health Data Sciences and Informatics
 #
 # This file is part of OhdsiShinyModules
 # 

diff --git a/R/about-main.R b/R/about-main.R
@@ -1,6 +1,6 @@
 # @file about-main.R
 #
-# Copyright 2022 Observational Health Data Sciences and Informatics
+# Copyright 2023 Observational Health Data Sciences and Informatics
 #
 # This file is part of PatientLevelPrediction
 #

diff --git a/R/characterization-aggregateFeatures.R b/R/characterization-aggregateFeatures.R
@@ -1,6 +1,6 @@
 # @file characterization-aggregateFeatures.R
 #
-# Copyright 2022 Observational Health Data Sciences and Informatics
+# Copyright 2023 Observational Health Data Sciences and Informatics
 #
 # This file is part of OhdsiShinyModules
 #

diff --git a/R/characterization-cohorts.R b/R/characterization-cohorts.R
@@ -1,6 +1,6 @@
 # @file characterization-timeToEvent.R
 #
-# Copyright 2022 Observational Health Data Sciences and Informatics
+# Copyright 2023 Observational Health Data Sciences and Informatics
 #
 # This file is part of OhdsiShinyModules
 #

diff --git a/R/characterization-dechallengeRechallenge.R b/R/characterization-dechallengeRechallenge.R
@@ -1,6 +1,6 @@
 # @file characterization-DechallengeRechallenge.R
 #
-# Copyright 2022 Observational Health Data Sciences and Informatics
+# Copyright 2023 Observational Health Data Sciences and Informatics
 #
 # This file is part of OhdsiShinyModules
 #

diff --git a/R/characterization-main.R b/R/characterization-main.R
@@ -1,6 +1,6 @@
 # @file characterization-main.R
 #
-# Copyright 2022 Observational Health Data Sciences and Informatics
+# Copyright 2023 Observational Health Data Sciences and Informatics
 #
 # This file is part of OhdsiShinyModules
 #

diff --git a/R/characterization-timeToEvent.R b/R/characterization-timeToEvent.R
@@ -1,6 +1,6 @@
 # @file characterization-timeToEvent.R
 #
-# Copyright 2022 Observational Health Data Sciences and Informatics
+# Copyright 2023 Observational Health Data Sciences and Informatics
 #
 # This file is part of OhdsiShinyModules
 #

diff --git a/R/cohort-diagnostics-characterization.R b/R/cohort-diagnostics-characterization.R
@@ -1,4 +1,4 @@
-# Copyright 2022 Observational Health Data Sciences and Informatics
+# Copyright 2023 Observational Health Data Sciences and Informatics
 #
 # This file is part of OhdsiShinyModules
 #

diff --git a/R/cohort-diagnostics-cohort-overlap.R b/R/cohort-diagnostics-cohort-overlap.R
@@ -1,4 +1,4 @@
-# Copyright 2022 Observational Health Data Sciences and Informatics
+# Copyright 2023 Observational Health Data Sciences and Informatics
 #
 # This file is part of OhdsiShinyModules
 #

diff --git a/R/cohort-diagnostics-compareCharacterization.R b/R/cohort-diagnostics-compareCharacterization.R
@@ -1,4 +1,4 @@
-# Copyright 2022 Observational Health Data Sciences and Informatics
+# Copyright 2023 Observational Health Data Sciences and Informatics
 #
 # This file is part of PatientLevelPrediction
 #

diff --git a/R/cohort-diagnostics-conceptsInDataSource.R b/R/cohort-diagnostics-conceptsInDataSource.R
@@ -1,4 +1,4 @@
-# Copyright 2022 Observational Health Data Sciences and Informatics
+# Copyright 2023 Observational Health Data Sciences and Informatics
 #
 # This file is part of PatientLevelPrediction
 #

diff --git a/R/cohort-diagnostics-counts.R b/R/cohort-diagnostics-counts.R
@@ -1,4 +1,4 @@
-# Copyright 2022 Observational Health Data Sciences and Informatics
+# Copyright 2023 Observational Health Data Sciences and Informatics
 #
 # This file is part of PatientLevelPrediction
 #

diff --git a/R/cohort-diagnostics-databaseInformation.R b/R/cohort-diagnostics-databaseInformation.R
@@ -1,4 +1,4 @@
-# Copyright 2022 Observational Health Data Sciences and Informatics
+# Copyright 2023 Observational Health Data Sciences and Informatics
 #
 # This file is part of PatientLevelPrediction
 #

diff --git a/R/cohort-diagnostics-definition.R b/R/cohort-diagnostics-definition.R
@@ -1,4 +1,4 @@
-# Copyright 2022 Observational Health Data Sciences and Informatics
+# Copyright 2023 Observational Health Data Sciences and Informatics
 #
 # This file is part of PatientLevelPrediction
 #

diff --git a/R/cohort-diagnostics-incidenceRates.R b/R/cohort-diagnostics-incidenceRates.R
@@ -1,4 +1,4 @@
-# Copyright 2022 Observational Health Data Sciences and Informatics
+# Copyright 2023 Observational Health Data Sciences and Informatics
 #
 # This file is part of PatientLevelPrediction
 #

diff --git a/R/cohort-diagnostics-inclusionRules.R b/R/cohort-diagnostics-inclusionRules.R
@@ -1,4 +1,4 @@
-# Copyright 2022 Observational Health Data Sciences and Informatics
+# Copyright 2023 Observational Health Data Sciences and Informatics
 #
 # This file is part of PatientLevelPrediction
 #

diff --git a/R/cohort-diagnostics-indexEventBreakdown.R b/R/cohort-diagnostics-indexEventBreakdown.R
@@ -1,4 +1,4 @@
-# Copyright 2022 Observational Health Data Sciences and Informatics
+# Copyright 2023 Observational Health Data Sciences and Informatics
 #
 # This file is part of PatientLevelPrediction
 #

diff --git a/R/cohort-diagnostics-main-ui.R b/R/cohort-diagnostics-main-ui.R
@@ -1,4 +1,4 @@
-# Copyright 2022 Observational Health Data Sciences and Informatics
+# Copyright 2023 Observational Health Data Sciences and Informatics
 #
 # This file is part of PatientLevelPrediction
 #
@@ -250,4 +250,4 @@ cohortDiagnosticsView <- function(id = "DiagnosticsExplorer") {
       )
     )
   )
-}
+}
diff --git a/R/cohort-diagnostics-main.R b/R/cohort-diagnostics-main.R
@@ -1,4 +1,4 @@
-# Copyright 2022 Observational Health Data Sciences and Informatics
+# Copyright 2023 Observational Health Data Sciences and Informatics
 #
 # This file is part of CohortDiagnostics
 #

diff --git a/R/cohort-diagnostics-orphanConcepts.R b/R/cohort-diagnostics-orphanConcepts.R
@@ -1,4 +1,4 @@
-# Copyright 2022 Observational Health Data Sciences and Informatics
+# Copyright 2023 Observational Health Data Sciences and Informatics
 #
 # This file is part of PatientLevelPrediction
 #

diff --git a/R/cohort-diagnostics-shared.R b/R/cohort-diagnostics-shared.R
@@ -1,4 +1,4 @@
-# Copyright 2022 Observational Health Data Sciences and Informatics
+# Copyright 2023 Observational Health Data Sciences and Informatics
 #
 # This file is part of CohortDiagnostics
 #

diff --git a/R/cohort-diagnostics-timeDistributions.R b/R/cohort-diagnostics-timeDistributions.R
@@ -1,4 +1,4 @@
-# Copyright 2022 Observational Health Data Sciences and Informatics
+# Copyright 2023 Observational Health Data Sciences and Informatics
 #
 # This file is part of PatientLevelPrediction
 #

diff --git a/R/cohort-diagnostics-visitContext.R b/R/cohort-diagnostics-visitContext.R
@@ -1,4 +1,4 @@
-# Copyright 2022 Observational Health Data Sciences and Informatics
+# Copyright 2023 Observational Health Data Sciences and Informatics
 #
 # This file is part of PatientLevelPrediction
 #

diff --git a/R/cohort-generator-main.R b/R/cohort-generator-main.R
@@ -1,6 +1,6 @@
 # @file cohortgenerator-main.R
 #
-# Copyright 2022 Observational Health Data Sciences and Informatics
+# Copyright 2023 Observational Health Data Sciences and Informatics
 #
 # This file is part of PatientLevelPrediction
 #

diff --git a/R/cohort-method-attrition.R b/R/cohort-method-attrition.R
@@ -1,6 +1,6 @@
 # @file cohort-method-attrition
 #
-# Copyright 2022 Observational Health Data Sciences and Informatics
+# Copyright 2023 Observational Health Data Sciences and Informatics
 #
 # This file is part of OhdsiShinyModules
 #

diff --git a/R/cohort-method-covariateBalance.R b/R/cohort-method-covariateBalance.R
@@ -1,6 +1,6 @@
 # @file cohort-method-covariateBalance
 #
-# Copyright 2022 Observational Health Data Sciences and Informatics
+# Copyright 2023 Observational Health Data Sciences and Informatics
 #
 # This file is part of OhdsiShinyModules
 #

diff --git a/R/cohort-method-diagnosticsSummary.R b/R/cohort-method-diagnosticsSummary.R
@@ -1,6 +1,6 @@
 # @file cohort-method-diagnosticsSummary
 #
-# Copyright 2022 Observational Health Data Sciences and Informatics
+# Copyright 2023 Observational Health Data Sciences and Informatics
 #
 # This file is part of OhdsiShinyModules
 #
@@ -401,4 +401,4 @@ getCmDiagnosticsData <- function(
   return(
     result
   )
-}
+}
diff --git a/R/cohort-method-full-result.R b/R/cohort-method-full-result.R
@@ -160,4 +160,4 @@ cohortMethodFullResultServer <- function(
 
     }
   )
-}
+}
diff --git a/R/cohort-method-kaplainMeier.R b/R/cohort-method-kaplainMeier.R
@@ -1,6 +1,6 @@
 # @file cohort-method-kaplainMeier
 #
-# Copyright 2022 Observational Health Data Sciences and Informatics
+# Copyright 2023 Observational Health Data Sciences and Informatics
 #
 # This file is part of OhdsiShinyModules
 #

diff --git a/R/cohort-method-main.R b/R/cohort-method-main.R
@@ -1,6 +1,6 @@
 # @file cohort-method-main.R
 #
-# Copyright 2022 Observational Health Data Sciences and Informatics
+# Copyright 2023 Observational Health Data Sciences and Informatics
 #
 # This file is part of PatientLevelPrediction
 #

diff --git a/R/cohort-method-populationCharacteristics.R b/R/cohort-method-populationCharacteristics.R
@@ -1,6 +1,6 @@
 # @file cohort-method-populationCharacteristics
 #
-# Copyright 2022 Observational Health Data Sciences and Informatics
+# Copyright 2023 Observational Health Data Sciences and Informatics
 #
 # This file is part of OhdsiShinyModules
 #

diff --git a/R/cohort-method-power.R b/R/cohort-method-power.R
@@ -1,6 +1,6 @@
 # @file cohort-method-power
 #
-# Copyright 2022 Observational Health Data Sciences and Informatics
+# Copyright 2023 Observational Health Data Sciences and Informatics
 #
 # This file is part of OhdsiShinyModules
 #

diff --git a/R/cohort-method-propensityModel.R b/R/cohort-method-propensityModel.R
@@ -1,6 +1,6 @@
 # @file cohort-method-propensityModel
 #
-# Copyright 2022 Observational Health Data Sciences and Informatics
+# Copyright 2023 Observational Health Data Sciences and Informatics
 #
 # This file is part of OhdsiShinyModules
 #

diff --git a/R/cohort-method-propensityScoreDistribution.R b/R/cohort-method-propensityScoreDistribution.R
@@ -1,6 +1,6 @@
 # @file cohort-method-propensityScoreDistribution
 #
-# Copyright 2022 Observational Health Data Sciences and Informatics
+# Copyright 2023 Observational Health Data Sciences and Informatics
 #
 # This file is part of OhdsiShinyModules
 #

diff --git a/R/cohort-method-resultSummary.R b/R/cohort-method-resultSummary.R
@@ -1,6 +1,6 @@
 # @file cohort-method-resultSummary
 #
-# Copyright 2022 Observational Health Data Sciences and Informatics
+# Copyright 2023 Observational Health Data Sciences and Informatics
 #
 # This file is part of OhdsiShinyModules
 #
@@ -356,4 +356,4 @@ FROM
   return(
     result
   )
-}
+}
diff --git a/R/cohort-method-systematicError.R b/R/cohort-method-systematicError.R
@@ -1,6 +1,6 @@
 # @file cohort-method-systematicError
 #
-# Copyright 2022 Observational Health Data Sciences and Informatics
+# Copyright 2023 Observational Health Data Sciences and Informatics
 #
 # This file is part of OhdsiShinyModules
 #

diff --git a/R/components-inputselection.R b/R/components-inputselection.R
@@ -268,4 +268,4 @@ inputSelectionDfServer <- function(
 
     }
   )
-}
+}
diff --git a/R/components-largeTableViewer.R b/R/components-largeTableViewer.R
@@ -352,4 +352,4 @@ largeTableServer <- function(id,
       }
     )
   })
-}
+}
diff --git a/R/data-diagnostic-drill.R b/R/data-diagnostic-drill.R
@@ -1,6 +1,6 @@
 # @file data-diagnostic-drill.R
 #
-# Copyright 2022 Observational Health Data Sciences and Informatics
+# Copyright 2023 Observational Health Data Sciences and Informatics
 #
 # This file is part of OhdsiShinyModules
 #
@@ -344,4 +344,4 @@ getDbDataDiagnosticsDatabases <- function(
   } else{
     return(c())
   }
-}
+}
diff --git a/R/data-diagnostic-main.R b/R/data-diagnostic-main.R
@@ -1,6 +1,6 @@
 # @file data-diagnostic-main.R
 #
-# Copyright 2022 Observational Health Data Sciences and Informatics
+# Copyright 2023 Observational Health Data Sciences and Informatics
 #
 # This file is part of OhdsiShinyModules
 #

diff --git a/R/data-diagnostic-summary.R b/R/data-diagnostic-summary.R
@@ -1,6 +1,6 @@
 # @file data-diagnostic-summary.R
 #
-# Copyright 2022 Observational Health Data Sciences and Informatics
+# Copyright 2023 Observational Health Data Sciences and Informatics
 #
 # This file is part of OhdsiShinyModules
 #

diff --git a/R/datasources-main.R b/R/datasources-main.R
@@ -1,6 +1,6 @@
 # @file datasources-main.R
 #
-# Copyright 2022 Observational Health Data Sciences and Informatics
+# Copyright 2023 Observational Health Data Sciences and Informatics
 #
 # This file is part of OhdsiShinyModules
 #

diff --git a/R/evidence-synth-main.R b/R/evidence-synth-main.R
@@ -1066,4 +1066,4 @@ getColDefsESDiag <- function(
   result <- append(fixedColumns, styleList)
 
   return(result)
-}
+}
diff --git a/R/helpers-elements.R b/R/helpers-elements.R
@@ -19,4 +19,4 @@ reactableCsvDownloadButton <- function(ns,
                   tooltip = "Note, will not download live values filtered in table, groupings, or any graphical/stylstic elements")
     )
   )
-}
+}
diff --git a/R/helpers-sccsPlots.R b/R/helpers-sccsPlots.R
@@ -641,4 +641,4 @@ renderDiagnosticsSummary <- function(diagnosticsSummary) {
     Status = c(diagnosticsSummary$mdrrDiagnostic, diagnosticsSummary$timeTrendDiagnostic, diagnosticsSummary$preExposureDiagnostic, diagnosticsSummary$easeDiagnostic)
   ) %>%
     return()
-}
+}
diff --git a/R/patient-level-prediction-calibration.R b/R/patient-level-prediction-calibration.R
@@ -1,6 +1,6 @@
 # @file patient-level-prediction-calibration.R
 #
-# Copyright 2022 Observational Health Data Sciences and Informatics
+# Copyright 2023 Observational Health Data Sciences and Informatics
 #
 # This file is part of OhdsiShinyModules
 #