Package 'OhdsiShinyAppBuilder'

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

---

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

---

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

---

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

---

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

---

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

---

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

---

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

---

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

---

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

---

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

---

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

---

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

---

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

---

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

---

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

Details

User specifies the json config and connection

Value

Shiny app instance

---

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

---

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

---

OhdsiShinyAppBuilder

Description

A package for creating viewers for the OHDSI shiny apps

Author(s)

Maintainer: Jenna Reps [email protected]

Authors:

• Nathan Hall

• Josh Ide

• Jamie Gibert

---

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

---

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"
)

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

Details

User specifies the json config and connection

Value

The shiny app will open

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