In OHDSI/CemConnector: OHDSI Common Evidence Model (CEM) Connector

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The common evidence explorer is a shiny application and module that can be used within other shiny applications that
use OMOP standard vocabularies.

## Launching the explorer
Using the explorer works with either a database cem connector backend or a hosted url solution.
The simplest solution is to use an API as follows. This will launch the shiny app:
```r
baseUrl <- "https://cem.ohdsi.org/"
launchCeExplorer(apiUrl = baseUrl)

Alternatively, if database credentials are known the app can launch as follows:

connectionDetails <- DatabaseConnector::createConnectionDetails("postgres", ...)
launchCeExplorer(connectionDetails = connectionDetails, cemDatabaseSchema = "cem", sourceDatabaseSchema = "cem_v3_sources", vocabularyDatabaseSchema = "vocabulary")

Consult your organisations administrator for details on connecting in database mode. Unless you are serving a large number of requests, this mode is not required.

Using the explorer shiny module

This approach allows you to import the Shiny module in to your shiny application of choice.

For example:

serverFunction <- function(input, output, session) {
  backend <- CemConnector::CemWebApiBackend$new(apiUrl = "https://cem.ohdsi.org/")
  # Define a reactive that returns a dataframe with standard ingredient concepts
  ingredientConceptInput <- shiny::reactive({ tibble::tibble(conceptId = c(21604296), includeDescendants = c(1), isExcluded = c(0)) })
  # Define a reactive that returns a dataframe with standard condtion concepts
  conditionConceptInput <- shiny::reactive({ tibble::tibble(conceptId = c(4149320), includeDescendants = c(1), isExcluded = c(0)) })
  # Define a reactive that returns an integer that for looking up higher levels in the heirarchy
  siblingLookupLevelsInput <- shiny::reactive({ 1 })

  # Call the explorer module
  ceModuleServer <- ceExplorerModule("explorer", # This ID should be unqiue and match the call to ceExplorerModuleUi
                                     backend,
                                     ingredientConceptInput = ingredientConceptInput,
                                     conditionConceptInput = conditionConceptInput,
                                     siblingLookupLevelsInput = siblingLookupLevelsInput)
}

uiFunction <- function () {
  explorerTable <- ceExplorerModuleUi("explorer") # The id for the server module and ui should be the same
  shiny::fluidPage(explorerTable)
}

shiny::shinyApp(uiFunction, serverFunction)

The reactive objects for ingredientConceptInput and conditionConceptInput must return data.frames that are either empty or contain the column names conceptId, includeDescendants and isExcluded.

OHDSI/CemConnector documentation built on Aug. 5, 2023, 2:47 p.m.