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Standardization #180

Merged
merged 23 commits into from
Aug 7, 2023
Merged

Standardization #180

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8a803f4
added data viewer components module and modified description-cohorts.R
nhall6 Apr 21, 2023
e6af4fd
updating component functionality
nhall6 Apr 21, 2023
aa05c9c
updating components module and functionality with target viewer from …
nhall6 Apr 27, 2023
85d59b3
Adding updated function to helpers to properly sort cohort generator …
nhall6 May 2, 2023
65c6fe2
Merge branch 'components' into standardization
jreps May 2, 2023
c204677
Fixing cohort generator attrition table and plot
nhall6 May 5, 2023
11a1829
Merge branch 'standardization' of https://github.com/OHDSI/OhdsiShiny…
nhall6 May 5, 2023
80933bf
Merge branch 'standardization' of https://github.com/OHDSI/OhdsiShiny…
jreps May 23, 2023
a7f4817
test fixes
jreps May 23, 2023
f3fcca2
adding selection options to SCCS diagnostics
jreps May 23, 2023
393bc96
added summary diagnostic to CM and SCCS
jreps May 24, 2023
c13e734
added evidence synth diagnostics
jreps May 25, 2023
b77c478
adding sticky columns
jreps May 25, 2023
a2378cf
Update estimation-diagnosticsSummary.R
jreps May 31, 2023
a32b550
prediction updates
jreps Jun 13, 2023
23af060
restructuring
jreps Jul 13, 2023
c4f0a58
standardizing modules
jreps Jul 16, 2023
60415c2
updated interface
jreps Jul 17, 2023
502e3ae
updated interface
jreps Jul 17, 2023
6703717
enabling shared db table for cohort diag
jreps Jul 17, 2023
3bb7416
updating version
jreps Jul 21, 2023
c82addd
standardizing cohort method
jreps Aug 4, 2023
00842e1
standardizing sccs
jreps Aug 4, 2023
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3 changes: 2 additions & 1 deletion DESCRIPTION
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@@ -1,7 +1,7 @@
Package: OhdsiShinyModules
Type: Package
Title: Repository of Shiny Modules for OHDSI Result Viewers
Version: 1.1.0.9000
Version: 1.2.0
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 .
Expand Down Expand Up @@ -36,6 +36,7 @@ Imports:
shinydashboard,
shinyWidgets,
SqlRender,
stringi,
stringr,
tibble,
tidyr,
Expand Down
138 changes: 71 additions & 67 deletions NAMESPACE
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Expand Up @@ -3,19 +3,56 @@
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)
Expand All @@ -24,46 +61,9 @@ 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)
Expand All @@ -72,32 +72,36 @@ export(getLogoImage)
export(incidenceRatesView)
export(inclusionRulesView)
export(indexEventBreakdownView)
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(sccsDiagnosticsSummaryServer)
export(sccsDiagnosticsSummaryViewer)
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(resultTableServer)
export(resultTableViewer)
export(sccsHelperFile)
export(sccsServer)
export(sccsView)
Expand Down
6 changes: 6 additions & 0 deletions NEWS.md
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@@ -1,3 +1,9 @@
OhdsiShinyModules v1.2.0
========================
- 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

OhdsiShinyModules v1.1.0
========================
- Udated the style for Characterization
Expand Down
12 changes: 10 additions & 2 deletions R/about-main.R
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Expand Up @@ -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(
Expand Down Expand Up @@ -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) {
Expand Down
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