OhdsiShinyAppBuilder

OhdsiShinyAppBuilder is part of HADES.

Introduction

Create shiny apps using modules from OhdsiShinyModules or custom modules

Examples

To create a shiny viewer to explore CohortDiagnostic results, Characterization results, PatientLevelPrediction results and CohortMethod results:

# install dependencies
remotes::install_github('ohdsi/ResultModelManager')
remotes::install_github('ohdsi/OhdsiShinyAppBuilder')

library(dplyr)
library(OhdsiShinyAppBuilder)

# STEP 1: create a config by first creating an empty config initializeModuleConfig()
#         and then adding a shiny module using addModuleConfig()

# Note: the common OHDSI analyses have default config settings (e.g., createDefaultAboutConfig() )

config <- initializeModuleConfig() %>%
  addModuleConfig(
    createDefaultAboutConfig()
  )  %>%
  addModuleConfig(
    createDefaultCohortDiagnosticsConfig()
  ) %>%
  addModuleConfig(
    createDefaultCharacterizationConfig()
  ) %>%
  addModuleConfig(
    createDefaultPredictionConfig()
  ) %>%
  addModuleConfig(
    createDefaultEstimationConfig()
  )

# Step 2: specify the connection details to the results database 
#          using DatabaseConnector::createConnectionDetails 
connectionDetails <- DatabaseConnector::createConnectionDetails(
 # add details to the result database
)

# Step 3: create a connection handler using the ResultModelManager package
connection <- ResultModelManager::ConnectionHandler$new(connectionDetails)

# Step 4: now run the shiny app based on the config file and view the results
#         at the specified connection
OhdsiShinyAppBuilder::viewShiny(
config = config, 
connection = connection
)

# Note - if you have non-standard table prefixes you may need 
#   to specify them in createDefaultResultDatabaseSettings()
OhdsiShinyAppBuilder::viewShiny(
config = config, 
connection = connection,  
resultDatabaseSettings = createDefaultResultDatabaseSettings()
)

If the connection works and there is results in the database, then an interactive shiny app will open.

Running a on a shiny server

If running the shiny app on a server, you create the config as in Example 1, but instead of OhdsiShinyAppBuilder::viewShiny use:

OhdsiShinyAppBuilder::createShinyApp(config = config, connection = connection)

Technology

OhdsiShinyAppBuilder is an R package.

System Requirements

Running the package requires R.

Installation

1. See the instructions here for configuring your R environment, including Java.

2. In R, use the following commands to download and install OhdsiShinyAppBuilder:

install.packages("remotes")
remotes::install_github("ohdsi/OhdsiShinyAppBuilder")

User Documentation

Documentation can be found on the package website.

Support

• Developer questions/comments/feedback: OHDSI Forum
• We use the GitHub issue tracker for all bugs/issues/enhancements

Contributing

Read here how you can contribute to this package.

License

OhdsiShinyAppBuilder is licensed under Apache License 2.0.

Development

OhdsiShinyAppBuilder is being developed in R Studio.

Development status

Under development

Acknowledgements