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