Develop (#324)

- merged cohortmethod/sccs/evidence synth into estimation module
- improved characterization module
- bug fixes
- updated modules for latest HADES

Co-authored-by: nhall6 <nhall6@its.jnj.com>
Co-authored-by: Jamie Gilbert <JGilber2@its.jnj.com>
Co-authored-by: Frank DeFalco <fdefalco@ohdsi.org>
Co-authored-by: Nathan Hall <106178605+nhall6@users.noreply.github.com>
Co-authored-by: Chris Knoll <cknoll@ohdsi.org>
Co-authored-by: Anthony Sena <asena5@its.jnj.com>

DESCRIPTION

@@ -1,8 +1,11 @@
 Package: OhdsiShinyModules
 Type: Package
 Title: Repository of Shiny Modules for OHDSI Result Viewers
-Version: 2.1.5
-Author: Jenna Reps
+Version: 3.0.0
+Authors@R: c(
+  person("Jenna", "Reps", email = "jreps@its.jnj.com", role = c("aut", "cre")),
+  person("Nathan", "Hall", role = c("aut")),
+  person("Jamie", "Gibert", role = c("aut")))
 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 .
 License: Apache License 2.0
@@ -24,18 +27,21 @@ Imports:
     htmltools,
     lubridate,
     methods,
+    openxlsx,
     ParallelLogger,
     plotly,
     purrr,
     reactable,
     readr,
+    ReportGenerator,
     RJSONIO,
     rlang,
     rmarkdown,
     scales,
     shiny, 
     shinycssloaders,
     shinydashboard,
+    shinyglide,
     shinyWidgets,
     SqlRender,
     stringi,
@@ -54,5 +60,6 @@ Suggests:
     testthat,
     withr
 Remotes:
+    ohdsi/ReportGenerator,
     ohdsi/ResultModelManager
 RoxygenNote: 7.3.1

NAMESPACE

@@ -4,18 +4,10 @@ export(LargeDataTable)
 export(aboutHelperFile)
 export(aboutServer)
 export(aboutViewer)
-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)
@@ -30,9 +22,6 @@ export(cohortMethodAttritionServer)
 export(cohortMethodAttritionViewer)
 export(cohortMethodCovariateBalanceServer)
 export(cohortMethodCovariateBalanceViewer)
-export(cohortMethodDiagnosticsSummaryServer)
-export(cohortMethodDiagnosticsSummaryViewer)
-export(cohortMethodHelperFile)
 export(cohortMethodKaplanMeierServer)
 export(cohortMethodKaplanMeierViewer)
 export(cohortMethodPopulationCharacteristicsServer)
@@ -43,12 +32,8 @@ 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)
@@ -65,11 +50,15 @@ export(databaseInformationView)
 export(datasourcesHelperFile)
 export(datasourcesServer)
 export(datasourcesViewer)
-export(evidenceSynthesisHelperFile)
-export(evidenceSynthesisServer)
-export(evidenceSynthesisViewer)
+export(estimationHelperFile)
+export(estimationServer)
+export(estimationViewer)
 export(getEnabledCdReports)
+export(getExampleConnectionDetails)
 export(getLogoImage)
+export(homeHelperFile)
+export(homeServer)
+export(homeViewer)
 export(incidenceRatesView)
 export(inclusionRulesView)
 export(indexEventBreakdownView)
@@ -103,9 +92,9 @@ export(patientLevelPredictionViewer)
 export(phevaluatorHelperFile)
 export(phevaluatorServer)
 export(phevaluatorViewer)
-export(sccsHelperFile)
-export(sccsServer)
-export(sccsView)
+export(reportHelperFile)
+export(reportServer)
+export(reportViewer)
 export(timeDistributionsView)
 export(visitContextView)
 importFrom(dplyr,"%>%")

NEWS.md

@@ -1,6 +1,19 @@
+OhdsiShinyModules v2.2.1
+========================
+- Fixed issue in DatabaseConnector check for pooled connections of sqlite databases on cohort diagnotiscs load (from main hotfix)
+
+OhdsiShinyModules v2.2.0
+========================
+- Combined cohort method, sccs and evidence synthesis into one estimation module with shared target and outcome ids
+- Characterizations now share the target id 
+- Updated tests to get them all working
+- Cleaned R check (but cohort incidence still has many notes)
+
+
 OhdsiShinyModules v2.1.5
 ========================
-Fixed issue in DatabaseConnector check for pooled connections of sqlite databases on cohort diagnotiscs load
+Fixed bug of orphan concepts report not displaying
+Fixed bug in orphan concepts where negative database ids were causing dynamic sql queries to crash
 
 OhdsiShinyModules v2.1.4
 ========================

R/OhdsiShinyModules.R

@@ -19,7 +19,9 @@
 #' OhdsiShinyModules
 #' 
 #' @description A selection of shiny modules for exploring standardized OHDSI results 
+#'
 #' @name OhdsiShinyModules
+#' @keywords internal
 #' @importFrom dplyr %>%
 #' @importFrom rlang .data
-"_PACKAGE"
+"_PACKAGE"