Merge pull request #197 from OHDSI/develop

Release candidate
OHDSI · Oct 6, 2023 · be1d48e · be1d48e
2 parents 619fed2 + 46977ca
commit be1d48e
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Showing 342 changed files with 27,635 additions and 12,455 deletions.
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -8,3 +8,4 @@ docs
 .github
 deploy.sh
 compare_versions
+^.idea$
diff --git a/.gitignore b/.gitignore
@@ -3,3 +3,5 @@
 .RData
 .Ruserdata
 /.idea/
+rsconnect/rconnect.jnj.com/NHall6/phevaluator_v01.dcf
+errorReportSql.txt
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: OhdsiShinyModules
 Type: Package
 Title: Repository of Shiny Modules for OHDSI Result Viewers
-Version: 1.1.0
+Version: 2.0.0
 Author: Jenna Reps
 Maintainer: Jenna Reps <reps@ohdsi.org>
 Description: Install this package to access useful shiny modules for building shiny apps to explore results using the OHDSI tools .
@@ -11,9 +11,11 @@ LazyData: true
 Depends:
     R (>= 3.3.0)
 VignetteBuilder: knitr
+Language: EN-US
 Imports:
     checkmate,
     CirceR,
+    cowplot,
     DatabaseConnector,
     dplyr,
     DT,
@@ -36,16 +38,17 @@ Imports:
     shinydashboard,
     shinyWidgets,
     SqlRender,
+    stringi,
     stringr,
     tibble,
     tidyr,
     tidyselect,
     tippy,
-    RColorBrewer
+    RColorBrewer,
+    markdown
 Suggests:
     kableExtra,
     knitr,
-    markdown,
     ResultModelManager,
     RSQLite,
     testthat,

diff --git a/NAMESPACE b/NAMESPACE
@@ -1,21 +1,59 @@
 # Generated by roxygen2: do not edit by hand
 
+export(LargeDataTable)
 export(aboutHelperFile)
 export(aboutServer)
 export(aboutViewer)
-export(characterizationView)
+export(characterizationAggregateFeaturesServer)
+export(characterizationAggregateFeaturesViewer)
+export(characterizationDechallengeRechallengeServer)
+export(characterizationDechallengeRechallengeViewer)
+export(characterizationHelperFile)
+export(characterizationIncidenceServer)
+export(characterizationIncidenceViewer)
+export(characterizationServer)
+export(characterizationTableServer)
+export(characterizationTableViewer)
+export(characterizationTimeToEventServer)
+export(characterizationTimeToEventViewer)
+export(characterizationViewer)
 export(cohortCountsView)
 export(cohortDefinitionsView)
+export(cohortDiagCharacterizationView)
 export(cohortDiagnosticsHelperFile)
-export(cohortDiagnosticsSever)
+export(cohortDiagnosticsServer)
 export(cohortDiagnosticsView)
 export(cohortGeneratorHelperFile)
 export(cohortGeneratorServer)
 export(cohortGeneratorViewer)
+export(cohortMethodAttritionServer)
+export(cohortMethodAttritionViewer)
+export(cohortMethodCovariateBalanceServer)
+export(cohortMethodCovariateBalanceViewer)
+export(cohortMethodDiagnosticsSummaryServer)
+export(cohortMethodDiagnosticsSummaryViewer)
+export(cohortMethodHelperFile)
+export(cohortMethodKaplanMeierServer)
+export(cohortMethodKaplanMeierViewer)
+export(cohortMethodPopulationCharacteristicsServer)
+export(cohortMethodPopulationCharacteristicsViewer)
+export(cohortMethodPowerServer)
+export(cohortMethodPowerViewer)
+export(cohortMethodPropensityModelServer)
+export(cohortMethodPropensityModelViewer)
+export(cohortMethodPropensityScoreDistServer)
+export(cohortMethodPropensityScoreDistViewer)
+export(cohortMethodResultSummaryServer)
+export(cohortMethodResultSummaryViewer)
+export(cohortMethodServer)
+export(cohortMethodSystematicErrorServer)
+export(cohortMethodSystematicErrorViewer)
+export(cohortMethodViewer)
 export(cohortOverlapView)
 export(compareCohortCharacterizationView)
 export(conceptsInDataSourceView)
 export(createCdDatabaseDataSource)
+export(createCustomColDefList)
 export(dataDiagnosticDrillServer)
 export(dataDiagnosticDrillViewer)
 export(dataDiagnosticHelperFile)
@@ -24,46 +62,9 @@ export(dataDiagnosticSummaryServer)
 export(dataDiagnosticSummaryViewer)
 export(dataDiagnosticViewer)
 export(databaseInformationView)
-export(descriptionAggregateFeaturesServer)
-export(descriptionAggregateFeaturesViewer)
-export(descriptionDechallengeRechallengeServer)
-export(descriptionDechallengeRechallengeViewer)
-export(descriptionHelperFile)
-export(descriptionIncidenceServer)
-export(descriptionIncidenceViewer)
-export(descriptionServer)
-export(descriptionTableServer)
-export(descriptionTableViewer)
-export(descriptionTimeToEventServer)
-export(descriptionTimeToEventViewer)
-export(descriptionViewer)
-export(estimationAttritionServer)
-export(estimationAttritionViewer)
-export(estimationCovariateBalanceServer)
-export(estimationCovariateBalanceViewer)
-export(estimationDiagnosticsSummaryServer)
-export(estimationDiagnosticsSummaryViewer)
-export(estimationForestPlotServer)
-export(estimationForestPlotViewer)
-export(estimationHelperFile)
-export(estimationKaplanMeierServer)
-export(estimationKaplanMeierViewer)
-export(estimationPopulationCharacteristicsServer)
-export(estimationPopulationCharacteristicsViewer)
-export(estimationPowerServer)
-export(estimationPowerViewer)
-export(estimationPropensityModelServer)
-export(estimationPropensityModelViewer)
-export(estimationPropensityScoreDistServer)
-export(estimationPropensityScoreDistViewer)
-export(estimationResultsTableServer)
-export(estimationResultsTableViewer)
-export(estimationServer)
-export(estimationSubgroupsServer)
-export(estimationSubgroupsViewer)
-export(estimationSystematicErrorServer)
-export(estimationSystematicErrorViewer)
-export(estimationViewer)
+export(datasourcesHelperFile)
+export(datasourcesServer)
+export(datasourcesViewer)
 export(evidenceSynthesisHelperFile)
 export(evidenceSynthesisServer)
 export(evidenceSynthesisViewer)
@@ -72,30 +73,36 @@ export(getLogoImage)
 export(incidenceRatesView)
 export(inclusionRulesView)
 export(indexEventBreakdownView)
+export(largeTableServer)
+export(largeTableView)
+export(makeButtonLabel)
 export(orpahanConceptsView)
-export(predictionCalibrationServer)
-export(predictionCalibrationViewer)
-export(predictionCovariateSummaryServer)
-export(predictionCovariateSummaryViewer)
-export(predictionCutoffServer)
-export(predictionCutoffViewer)
-export(predictionDesignSummaryServer)
-export(predictionDesignSummaryViewer)
-export(predictionDiagnosticsServer)
-export(predictionDiagnosticsViewer)
-export(predictionDiscriminationServer)
-export(predictionDiscriminationViewer)
-export(predictionHelperFile)
-export(predictionModelSummaryServer)
-export(predictionModelSummaryViewer)
-export(predictionNbServer)
-export(predictionNbViewer)
-export(predictionServer)
-export(predictionSettingsServer)
-export(predictionSettingsViewer)
-export(predictionValidationServer)
-export(predictionValidationViewer)
-export(predictionViewer)
+export(patientLevelPredictionCalibrationServer)
+export(patientLevelPredictionCalibrationViewer)
+export(patientLevelPredictionCovariateSummaryServer)
+export(patientLevelPredictionCovariateSummaryViewer)
+export(patientLevelPredictionCutoffServer)
+export(patientLevelPredictionCutoffViewer)
+export(patientLevelPredictionDesignSummaryServer)
+export(patientLevelPredictionDesignSummaryViewer)
+export(patientLevelPredictionDiagnosticsServer)
+export(patientLevelPredictionDiagnosticsViewer)
+export(patientLevelPredictionDiscriminationServer)
+export(patientLevelPredictionDiscriminationViewer)
+export(patientLevelPredictionHelperFile)
+export(patientLevelPredictionModelSummaryServer)
+export(patientLevelPredictionModelSummaryViewer)
+export(patientLevelPredictionNbServer)
+export(patientLevelPredictionNbViewer)
+export(patientLevelPredictionServer)
+export(patientLevelPredictionSettingsServer)
+export(patientLevelPredictionSettingsViewer)
+export(patientLevelPredictionValidationServer)
+export(patientLevelPredictionValidationViewer)
+export(patientLevelPredictionViewer)
+export(phevaluatorHelperFile)
+export(phevaluatorServer)
+export(phevaluatorViewer)
 export(sccsHelperFile)
 export(sccsServer)
 export(sccsView)

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,14 @@
+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
 ========================
 - Udated the style for Characterization

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
 #
@@ -42,7 +42,9 @@ aboutHelperFile <- function(){
 #' The user interface to the home page module
 #'
 #' @export
-aboutViewer <- function(id = 'homepage') {
+aboutViewer <- function(
+    id = 'homepage'
+    ) {
   ns <- shiny::NS(id)
 
   shinydashboard::box(
@@ -71,12 +73,18 @@ aboutViewer <- function(id = 'homepage') {
 #' The user specifies the id for the module
 #'
 #' @param id  the unique reference id for the module
+#' @param connectionHandler a connection to the database with the results
+#' @param resultDatabaseSettings a list containing the characterization result schema, dbms, tablePrefix, databaseTable and cgTablePrefix
 #' 
 #' @return
 #' The server for the shiny app home
 #'
 #' @export
-aboutServer <- function(id = 'homepage') {
+aboutServer <- function(
+    id = 'homepage',
+    connectionHandler = NULL,
+    resultDatabaseSettings = NULL
+    ) {
   shiny::moduleServer(
     id,
     function(input, output, session) {