Merge pull request #312 from OHDSI/prerelease

Prerelease

DESCRIPTION

@@ -1,8 +1,11 @@
 Package: OhdsiShinyModules
 Type: Package
 Title: Repository of Shiny Modules for OHDSI Result Viewers
-Version: 2.1.5.9000
-Author: Jenna Reps
+Version: 3.0.0
+Authors@R: c(
+  person("Jenna", "Reps", email = "[email protected]", role = c("aut", "cre")),
+  person("Nathan", "Hall", role = c("aut")),
+  person("Jamie", "Gibert", role = c("aut")))
 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 .
 License: Apache License 2.0
@@ -24,6 +27,7 @@ Imports:
     htmltools,
     lubridate,
     methods,
+    openxlsx,
     ParallelLogger,
     plotly,
     purrr,
@@ -56,7 +60,6 @@ Suggests:
     testthat,
     withr
 Remotes:
-    ohdsi/CirceR,
     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)
@@ -65,9 +50,9 @@ 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)
@@ -110,8 +95,7 @@ export(phevaluatorViewer)
 export(reportHelperFile)
 export(reportServer)
 export(reportViewer)
-export(sccsHelperFile)
-export(sccsServer)
-export(sccsView)
 export(timeDistributionsView)
 export(visitContextView)
+importFrom(dplyr,"%>%")
+importFrom(rlang,.data)

NEWS.md

@@ -1,3 +1,15 @@
+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 bug of orphan concepts report not displaying

R/OhdsiShinyModules.R

@@ -20,8 +20,8 @@
 #' 
 #' @description A selection of shiny modules for exploring standardized OHDSI results 
 #'
-#' @docType package
 #' @name OhdsiShinyModules
+#' @keywords internal
 #' @importFrom dplyr %>%
 #' @importFrom rlang .data
-
+"_PACKAGE"

R/about-main.R

@@ -21,7 +21,7 @@
 #'
 #' @details
 #' Returns the location of the about helper file
-#'
+#' @family {About}
 #' @return
 #' string location of the about helper file
 #'
@@ -38,7 +38,7 @@ aboutHelperFile <- function() {
 #' The user specifies the id for the module
 #'
 #' @param id  the unique reference id for the module
-#'
+#' @family {About}
 #' @return
 #' The user interface to the home page module
 #'
@@ -100,7 +100,7 @@ targetedValueBox <- function(
 #' @param connectionHandler a connection to the database with the results
 #' @param resultDatabaseSettings a list containing the characterization result schema, dbms, tablePrefix, databaseTable and cgTablePrefix
 #' @param config the config from the app.R file that contains a list of which modules to include
-#'
+#' @family {About}
 #' @return
 #' The server for the shiny app home
 #'