| Type: | Package |
| Title: | Viewing Observational Health Data Sciences and Informatics Results via 'shiny' Modules |
| Version: | 1.0.0 |
| Date: | 2024-12-09 |
| Maintainer: | Jenna Reps <jreps@its.jnj.com> |
| 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/. |
| License: | Apache License 2.0 |
| VignetteBuilder: | knitr |
| Depends: | R (≥ 3.3.0) |
| Imports: | checkmate, DatabaseConnector, devtools, dplyr, ParallelLogger (≥ 2.0.0), ResultModelManager (≥ 0.4.0), rlang, shiny, shinydashboard, utils |
| Suggests: | Eunomia, jsonlite, knitr, rmarkdown, testthat, markdown, remotes |
| RoxygenNote: | 7.3.1 |
| Encoding: | UTF-8 |
| NeedsCompilation: | no |
| Packaged: | 2024-12-09 20:37:22 UTC; jreps |
| Author: | Jenna Reps [aut, cre], Nathan Hall [aut], Josh Ide [aut], Jamie Gibert [aut] |
| Repository: | CRAN |
| Date/Publication: | 2024-12-10 21:10:11 UTC |
OhdsiShinyAppBuilder
Description
A package for creating viewers for the OHDSI shiny apps
Author(s)
Maintainer: Jenna Reps jreps@its.jnj.com
Authors:
Nathan Hall
Josh Ide
Jamie Gibert
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
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