The R Consortium R submission Pilot 2 Project is to test the concept that a Shiny application created with the R-language can be successgully bundled into a submission package and transferred successfully to FDA reviewers.

This repo tries to reproduce the same Shiny application using the Rhino framework.

This application is deployed at pilot-2-submission-rhino using Git-Backed deployment on the main branch.

.
├── app
│   ├── view
│   │   └── demographic_table.R
|   |   └── km_plot.R
|   |   └── primary_table.R
|   |   └── efficacy_table.R
|   |   └── completion_table.R
│   ├── logic
│   │   └── adam_data.R
│   │   └── eff_modles.R
│   │   └── formatters.R
│   │   └── helpers.R
│   │   └── kmplot_helpers.R
│   │   └── Tplyr_helpers.R
│   ├── data
│   │   └── adam
│   │       └── adadas.xpt
│   │       └── adlbc.xpt
│   │       └── adsl.xpt
│   │       └── adtte.xpt
│   ├── docs
│   │   └── about.md
│   ├── js
│   │   └── index.js
│   ├── static
│   │   └── favicon.ico
│   ├── styles
│   │   └── main.scss
│   └── app.R
├── tests
│   ├── cypress
│   │   └── integration
│   │       └── app.spec.js
│   ├── testthat
│   │
│   └── cypress.json
├── app.R
├── rhino_submission.Rproj
├── dependencies.R
├── renv.lock
├── rhino.yml
└── README.md

• It's a standard rhino structure. The only difference is that it's using the legacy_entrypoint: "app_dir" so there is a app.R inside the app/ directory.

• The app uses 4 ADaM datasets as XPT files to function which are present inside the app/data directory. To learn more about ADaM data formats visit here

• The different teal modules are place in their individual file inside the app/view directory.

• There are a few logic and calculation functions which are placed in the app/logic directory.

• No tests are added as of now.

• No custom CSS/JS is added as of now.

The submission of proprietary packages to FDA via the eCTD gateway only supports plain text files. We use the pkglite R package to pack and unpack this Shiny/Rhino application, so that the FDA reviewers can accept and setup the submission on their systems.

The pkglite package was built to pack R packages to .txt file, therefore we have to create a simple DESCRIPTION file with just a package name to use pkglite to pack into a plain text file.

Now, we can use the following code to pack our shiny app into a .txt file: Create a simple DESCRIPTION file, pack the app, and remove the DESCRIPTION file.

app_name <- "rhinosubmission"
renv_spec <- pkglite::file_spec(
  "renv",
  pattern = "^settings\\.dcf$|^activate\\.R$",
  format = "text", recursive = FALSE
)
tests_spec <- pkglite::file_tests()
app_spec <- pkglite::file_auto("app")
root_spec <- pkglite::file_spec(
  path = ".",
  pattern = "^\\.Rprofile$|^rhino\\.yml$|^renv\\.lock$|^dependencies\\.R$|^config\\.yml$|^app\\.R$|^README\\.md$|\\.Rproj$",
  all_files = TRUE,
  recursive = FALSE
)
write(paste0("Package: ", app_name), "DESCRIPTION", append=TRUE)
pkglite::collate(
  getwd(),
  renv_spec,
  tests_spec,
  app_spec,
  root_spec
) |> pkglite::pack()
file.remove("DESCRIPTION")

The packed .txt file can be unpacked into the shiny app with the help of pkglite

pkglite::unpack("rhinosubmission.txt")