Package 'OhdsiShinyAppBuilder'

Title: Viewing Observational Health Data Sciences and Informatics Results via 'shiny' Modules
Description: Users can build a single 'shiny' app for exploring population characterization, population-level causal effect estimation, and patient-level prediction results generated via the R analyses packages in 'HADES' (see <https://ohdsi.github.io/Hades/>). Learn more about 'OhdsiShinyAppBuilder' at <https://ohdsi.github.io/OhdsiShinyAppBuilder/>.
Authors: Jenna Reps [aut, cre], Nathan Hall [aut], Josh Ide [aut], Jamie Gibert [aut]
Maintainer: Jenna Reps <[email protected]>
License: Apache License 2.0
Version: 1.1.0
Built: 2026-07-22 19:07:31 UTC
Source: https://github.com/cran/OhdsiShinyAppBuilder

Help Index

addModuleConfig

Description

Create an R list with the config specification for one or more modules

Usage

addModuleConfig(config, moduleConfig)

Arguments

config

The current config to append the extra module to
moduleConfig

A module config to be added

Details

User specifies the settings to create a config for a module

Value

An R list with the module config settings

See Also

Other Config: initializeModuleConfig(), loadConfig(), saveConfig()

createDefaultAboutConfig

Description

Create an R list with the about config specification

Usage

createDefaultAboutConfig()

Details

User specifies the settings to create a default config for an about module

Value

An R list with the module config settings

See Also

Other ModuleConfig: createDefaultCharacterizationConfig(), createDefaultCohortDiagnosticsConfig(), createDefaultCohortGeneratorConfig(), createDefaultCohortMethodConfig(), createDefaultDatasourcesConfig(), createDefaultEstimationConfig(), createDefaultEvidenceSynthesisConfig(), createDefaultHomeConfig(), createDefaultPhevaluatorConfig(), createDefaultPredictionConfig(), createDefaultReportConfig(), createDefaultSccsConfig(), createModuleConfig()

createDefaultCharacterizationConfig

Description

Create an R list with the characterization config specification

Usage

createDefaultCharacterizationConfig()

Details

User specifies the settings to create a default config for a characterization module

Value

An R list with the module config settings

See Also

Other ModuleConfig: createDefaultAboutConfig(), createDefaultCohortDiagnosticsConfig(), createDefaultCohortGeneratorConfig(), createDefaultCohortMethodConfig(), createDefaultDatasourcesConfig(), createDefaultEstimationConfig(), createDefaultEvidenceSynthesisConfig(), createDefaultHomeConfig(), createDefaultPhevaluatorConfig(), createDefaultPredictionConfig(), createDefaultReportConfig(), createDefaultSccsConfig(), createModuleConfig()

createDefaultCohortDiagnosticsConfig

Description

Create an R list with the characterization config specification

Usage

createDefaultCohortDiagnosticsConfig()

Details

User specifies the settings to create a default config for a characterization module

Value

An R list with the module config settings

See Also

Other ModuleConfig: createDefaultAboutConfig(), createDefaultCharacterizationConfig(), createDefaultCohortGeneratorConfig(), createDefaultCohortMethodConfig(), createDefaultDatasourcesConfig(), createDefaultEstimationConfig(), createDefaultEvidenceSynthesisConfig(), createDefaultHomeConfig(), createDefaultPhevaluatorConfig(), createDefaultPredictionConfig(), createDefaultReportConfig(), createDefaultSccsConfig(), createModuleConfig()

createDefaultCohortGeneratorConfig

Description

Create an R list with the cohort generator config specification

Usage

createDefaultCohortGeneratorConfig()

Details

User specifies the settings to create a default config for a cohort generator module

Value

An R list with the module config settings

See Also

Other ModuleConfig: createDefaultAboutConfig(), createDefaultCharacterizationConfig(), createDefaultCohortDiagnosticsConfig(), createDefaultCohortMethodConfig(), createDefaultDatasourcesConfig(), createDefaultEstimationConfig(), createDefaultEvidenceSynthesisConfig(), createDefaultHomeConfig(), createDefaultPhevaluatorConfig(), createDefaultPredictionConfig(), createDefaultReportConfig(), createDefaultSccsConfig(), createModuleConfig()

createDefaultCohortMethodConfig

Description

Create an R list with the cohort method config specification (depreciated)

Usage

createDefaultCohortMethodConfig()

Details

User specifies the settings to create a default config for a cohort method module

Value

An R list with the module config settings

See Also

Other ModuleConfig: createDefaultAboutConfig(), createDefaultCharacterizationConfig(), createDefaultCohortDiagnosticsConfig(), createDefaultCohortGeneratorConfig(), createDefaultDatasourcesConfig(), createDefaultEstimationConfig(), createDefaultEvidenceSynthesisConfig(), createDefaultHomeConfig(), createDefaultPhevaluatorConfig(), createDefaultPredictionConfig(), createDefaultReportConfig(), createDefaultSccsConfig(), createModuleConfig()

createDefaultDatasourcesConfig

Description

Create an R list with the datasources config specification

Usage

createDefaultDatasourcesConfig()

Details

User specifies the settings to create a default config for a datasources module

Value

An R list with the module config settings

See Also

Other ModuleConfig: createDefaultAboutConfig(), createDefaultCharacterizationConfig(), createDefaultCohortDiagnosticsConfig(), createDefaultCohortGeneratorConfig(), createDefaultCohortMethodConfig(), createDefaultEstimationConfig(), createDefaultEvidenceSynthesisConfig(), createDefaultHomeConfig(), createDefaultPhevaluatorConfig(), createDefaultPredictionConfig(), createDefaultReportConfig(), createDefaultSccsConfig(), createModuleConfig()

createDefaultEstimationConfig

Description

Create an R list with the estimation config specification

Usage

createDefaultEstimationConfig()

Details

User specifies the settings to create a default config for an estimation module

Value

An R list with the module config settings

See Also

Other ModuleConfig: createDefaultAboutConfig(), createDefaultCharacterizationConfig(), createDefaultCohortDiagnosticsConfig(), createDefaultCohortGeneratorConfig(), createDefaultCohortMethodConfig(), createDefaultDatasourcesConfig(), createDefaultEvidenceSynthesisConfig(), createDefaultHomeConfig(), createDefaultPhevaluatorConfig(), createDefaultPredictionConfig(), createDefaultReportConfig(), createDefaultSccsConfig(), createModuleConfig()

createDefaultEvidenceSynthesisConfig

Description

Create an R list with the Evidence Synthesis config specification (depreciated)

Usage

createDefaultEvidenceSynthesisConfig()

Details

User specifies the settings to create a default config for a Evidence Synthesis module

Value

An R list with the module config settings

See Also

Other ModuleConfig: createDefaultAboutConfig(), createDefaultCharacterizationConfig(), createDefaultCohortDiagnosticsConfig(), createDefaultCohortGeneratorConfig(), createDefaultCohortMethodConfig(), createDefaultDatasourcesConfig(), createDefaultEstimationConfig(), createDefaultHomeConfig(), createDefaultPhevaluatorConfig(), createDefaultPredictionConfig(), createDefaultReportConfig(), createDefaultSccsConfig(), createModuleConfig()

createDefaultHomeConfig

Description

Create an R list with the about config specification

Usage

createDefaultHomeConfig()

Details

User specifies the settings to create a default config for an about module

Value

An R list with the module config settings

See Also

Other ModuleConfig: createDefaultAboutConfig(), createDefaultCharacterizationConfig(), createDefaultCohortDiagnosticsConfig(), createDefaultCohortGeneratorConfig(), createDefaultCohortMethodConfig(), createDefaultDatasourcesConfig(), createDefaultEstimationConfig(), createDefaultEvidenceSynthesisConfig(), createDefaultPhevaluatorConfig(), createDefaultPredictionConfig(), createDefaultReportConfig(), createDefaultSccsConfig(), createModuleConfig()

createDefaultPhevaluatorConfig

Description

Create an R list with the phevaluator config specification

Usage

createDefaultPhevaluatorConfig()

Details

User specifies the settings to create a default config for a phevaluator module

Value

An R list with the module config settings

See Also

Other ModuleConfig: createDefaultAboutConfig(), createDefaultCharacterizationConfig(), createDefaultCohortDiagnosticsConfig(), createDefaultCohortGeneratorConfig(), createDefaultCohortMethodConfig(), createDefaultDatasourcesConfig(), createDefaultEstimationConfig(), createDefaultEvidenceSynthesisConfig(), createDefaultHomeConfig(), createDefaultPredictionConfig(), createDefaultReportConfig(), createDefaultSccsConfig(), createModuleConfig()

createDefaultPredictionConfig

Description

Create an R list with the prediction config specification

Usage

createDefaultPredictionConfig()

Details

User specifies the settings to create a default config for a prediction module

Value

An R list with the module config settings

See Also

Other ModuleConfig: createDefaultAboutConfig(), createDefaultCharacterizationConfig(), createDefaultCohortDiagnosticsConfig(), createDefaultCohortGeneratorConfig(), createDefaultCohortMethodConfig(), createDefaultDatasourcesConfig(), createDefaultEstimationConfig(), createDefaultEvidenceSynthesisConfig(), createDefaultHomeConfig(), createDefaultPhevaluatorConfig(), createDefaultReportConfig(), createDefaultSccsConfig(), createModuleConfig()

createDefaultReportConfig

Description

Create an R list with the report config specification

Usage

createDefaultReportConfig()

Details

User specifies the settings to create a default config for a report module

Value

An R list with the module config settings

See Also

Other ModuleConfig: createDefaultAboutConfig(), createDefaultCharacterizationConfig(), createDefaultCohortDiagnosticsConfig(), createDefaultCohortGeneratorConfig(), createDefaultCohortMethodConfig(), createDefaultDatasourcesConfig(), createDefaultEstimationConfig(), createDefaultEvidenceSynthesisConfig(), createDefaultHomeConfig(), createDefaultPhevaluatorConfig(), createDefaultPredictionConfig(), createDefaultSccsConfig(), createModuleConfig()

createDefaultResultDatabaseSettings

Description

Create an R list with the default table prefixes and tables

Usage

createDefaultResultDatabaseSettings(
  schema = "main",
  vocabularyDatabaseSchema = schema,
  cgTablePrefix = "cg_",
  cgTable = "cohort_definition",
  databaseTable = "DATABASE_META_DATA",
  databaseTablePrefix = "",
  cdTablePrefix = "cd_",
  cTablePrefix = "c_",
  incidenceTablePrefix = "ci_",
  plpTablePrefix = "plp_",
  cmTablePrefix = "cm_",
  sccsTablePrefix = "sccs_",
  esTablePrefix = "es_",
  pvTablePrefix = "pv_"
)

Arguments

schema

The schema containing the OHDSI study results
vocabularyDatabaseSchema

The schema containing the vocabulary database
cgTablePrefix

The table prefix for cohort generator tables
cgTable

The table with the cohort definitions in cohort generator
databaseTable

The table with the database details
databaseTablePrefix

The prefix for the databaseTable
cdTablePrefix

The table prefix for the cohort diagnostic results
cTablePrefix

The table prefix for the characterization results
incidenceTablePrefix

The table prefix for the incidence results
plpTablePrefix

The table prefix for the prediction results
cmTablePrefix

The table prefix for the cohort method results
sccsTablePrefix

The table prefix for the self controlled case series results
esTablePrefix

The table prefix for the evidence synthesis method results
pvTablePrefix

The table prefix for the phevaluator results

Details

User specifies the schema name and can override default table prefixes and table names

Value

An R list with the module config settings

createDefaultSccsConfig

Description

Create an R list with the SCCS config specification (depreciated)

Usage

createDefaultSccsConfig()

Details

User specifies the settings to create a default config for a SCCS module

Value

An R list with the module config settings

See Also

Other ModuleConfig: createDefaultAboutConfig(), createDefaultCharacterizationConfig(), createDefaultCohortDiagnosticsConfig(), createDefaultCohortGeneratorConfig(), createDefaultCohortMethodConfig(), createDefaultDatasourcesConfig(), createDefaultEstimationConfig(), createDefaultEvidenceSynthesisConfig(), createDefaultHomeConfig(), createDefaultPhevaluatorConfig(), createDefaultPredictionConfig(), createDefaultReportConfig(), createModuleConfig()

createModuleConfig

Description

Create an R list with the config specification

Usage

createModuleConfig(
  moduleId = "about",
  tabName = "About",
  shinyModulePackage = "OhdsiShinyModules",
  shinyModulePackageVersion = "3.0.0",
  moduleUiFunction = "aboutViewer",
  moduleServerFunction = "aboutServer",
  moduleInfoBoxFile = "aboutHelperFile()",
  moduleIcon = "info",
  installSource = "CRAN",
  gitHubRepo = NULL
)

Arguments

moduleId

The shiny id for the tab containing the module UI
tabName

The name of the tab in the shiny app (this will be the side menu button text)
shinyModulePackage

The R package to find the server and UI functions
shinyModulePackageVersion

The minimum version of the shinyModulePackage
moduleUiFunction

The name of the UI function in the R package shinyModulePackage
moduleServerFunction

The name of the server function in the R package shinyModulePackage
moduleInfoBoxFile

The function in the R package shinyModulePackage that contains info text
moduleIcon

The icon to use for the side menu button
installSource

Either CRAN or github specifying where to install shinyModulePackage from
gitHubRepo

If installSource is github then this is the github repo containing the package e.g., 'ohdsi'

Details

User specifies the settings to create a config for a module

Value

An R list with the module config settings

See Also

Other ModuleConfig: createDefaultAboutConfig(), createDefaultCharacterizationConfig(), createDefaultCohortDiagnosticsConfig(), createDefaultCohortGeneratorConfig(), createDefaultCohortMethodConfig(), createDefaultDatasourcesConfig(), createDefaultEstimationConfig(), createDefaultEvidenceSynthesisConfig(), createDefaultHomeConfig(), createDefaultPhevaluatorConfig(), createDefaultPredictionConfig(), createDefaultReportConfig(), createDefaultSccsConfig()

createShinyApp

Description

Create a shiny app for a shiny server

Usage

createShinyApp(
  config,
  connection,
  resultDatabaseSettings = createDefaultResultDatabaseSettings(),
  connectionDetails = NULL,
  usePooledConnection = TRUE,
  studyDescription = NULL,
  title = "OHDSI Analysis Viewer",
  protocolLink = "http://ohdsi.org",
  themePackage = "OhdsiShinyAppBuilder",
  htmlHeader = "",
  reportSummaryDetails = NULL
)

Arguments

config

The json with the app config
connection

A connection to the results
resultDatabaseSettings

A list with the result schema and table prefixes
connectionDetails

A DatabaseConnector::connectionDetails connection to the results database
usePooledConnection

Use a pooled database connection or not - set to true for multi-user environments (default)
studyDescription

A human-readable character string describing the study/analysis
title

The title for the app. Defaults to: OHDSI Analysis Viewer
protocolLink

A link to a site containing the study protocol
themePackage

A package containing custom theme elements
htmlHeader

Additional HTML to add to the shiny app header
reportSummaryDetails

NULL or a data.frame with the columns reportName and reportLocation

Details

User specifies the json config and connection

Value

Shiny app instance

See Also

Other Shiny: viewShiny()

initializeModuleConfig

Description

Creates an empty config

Usage

initializeModuleConfig()

Details

An empty config that can be used to add shiny module configs to

Value

An empty list

See Also

Other Config: addModuleConfig(), loadConfig(), saveConfig()

loadConfig

Description

Load the config specification

Usage

loadConfig(configLocation)

Arguments

configLocation

The location of the config json file

Details

User specifies the config file and this function returns the R list with the config

Value

An R list with the config settings

See Also

Other Config: addModuleConfig(), initializeModuleConfig(), saveConfig()

OhdsiShinyAppBuilder

Description

A package for creating viewers for the OHDSI shiny apps

Author(s)

Maintainer: Jenna Reps [email protected]

Authors:

saveConfig

Description

Save the R list with the config specification as a json

Usage

saveConfig(configList, configLocation)

Arguments

configList

An R list with the config settings
configLocation

The location to save the config json file

Details

User saves the R list with the config as a json file

Value

An R list with the config settings

See Also

Other Config: addModuleConfig(), initializeModuleConfig(), loadConfig()

viewShiny

Description

Open the shiny app

Usage

viewShiny(
  config,
  connection,
  resultDatabaseSettings = createDefaultResultDatabaseSettings(),
  connectionDetails = NULL,
  usePooledConnection = TRUE,
  studyDescription = NULL,
  title = "OHDSI Analysis Viewer",
  protocolLink = "http://ohdsi.org",
  themePackage = "OhdsiShinyAppBuilder",
  htmlHeader = ""
)

Arguments

config

The json with the app config
connection

A connection to the results
resultDatabaseSettings

A list with the result schema and table prefixes
connectionDetails

A DatabaseConnector::connectionDetails connection to the results database
usePooledConnection

Use a pooled database connection or not - set to true for multi-user environments (default)
studyDescription

A human-readable character string describing the study/analysis
title

The title for the app. Defaults to: OHDSI Analysis Viewer
protocolLink

A link to a site containing the study protocol
themePackage

A package containing custom theme elements
htmlHeader

Additional HTML to add to the shiny app header

Details

User specifies the json config and connection

Value

The shiny app will open

See Also

Other Shiny: createShinyApp()