Introduction

This is a package with miscellaneous tools, a set of computational tools and a graphical user interface (GUI) for privacy preserving federated survival model meta-analysis using the DataSHIELD platform. The primary function is to enable data and model documentation.

• inst/shinyApp

  • folder with all R files

• installerR.R and installerunix.sh

  • installation scripts in R and UNIX

• RUN.R

  • script to start shiny server
  • R --no-save < RUN.R

• syntheticdatagenerator.R

  • script to generate synthetic data
  • R --no-save < syntheticdatagenerator.R

• buildmantest.R

  • script to build manuals and test code (testing script)
  • R --no-save < buildmantest.R
    

• buildmantestgitadd.sh

  • shell script to build manuals, test code and commit to git all documentation
  • ./buildmantestgitadd.sh

• vignettes

  • tutorials and vignettes

• misc

  • miscellaneous scripts for basic scripts and tutorials

• NAMESPACE, DESCRIPTION

  • files for package

• Dockerfile, shiny-server.conf, shiny-server.sh

  • files for Docker and vagrant
  • adapted from
    • https://github.com/isglobal-brge/ShinyDataSHIELD
  • see the following for more on how to run and compile
    • https://blog.zenika.com/2014/10/07/setting-up-a-development-environment-using-docker-and-vagrant/
    • https://data2knowledge.atlassian.net/wiki/spaces/DSDEV/pages/367656962/Vagrant
    • https://data2knowledge.atlassian.net/wiki/spaces/DSDEV/pages/12943447/Build+your+own+DataSHIELD+VMs
    • https://docs.github.com/en/packages/guides/configuring-docker-for-use-with-github-packages

• Link to demo website

  • Demo GUI shiny server

    • forthcoming

  • Demo VM running on Cambridge server

    • Forthcoming
      

  • Opal server

    • https://opal-demo.obiba.org/ui/index.html#!admin

  • Synthetic data

    • Forthcoming

Usage

Install ShinySurvivalDataSHIELD package, load package and run

```R

    install.packages('devtools')

    library(devtools)

    devtools::install_github('neelsoumya/dsSurvivalShiny')

    library(dsSurvivalShiny)

    dsSurvivalShiny::app()

    OR

    R --no-save < installer_R.R

    R --no-save < RUN.R

```

• Screenshot of graphical user interface

  

• Presentations

  • presentation folder

Citation

• Forthcoming

Contact

• Soumya Banerjee

• https://github.com/neelsoumya/dsSurvivalShiny

• sb2333@cam.ac.uk

  • Acknowledgements

• DataSHIELD technical team

What is this repository for?

• Quick summary

  • GUI for data and model documentation and meta-analysis of federated survival models

How do I get set up?

• Summary of installation

```R

    install.packages('devtools')

    library(devtools)

    devtools::install_github('neelsoumya/dsSurvivalShiny')

    library(dsSurvivalShiny)

    dsSurvivalShiny::app()

    OR

    R --no-save < installer_R.R

    R --no-save < RUN.R

```

• Configuration

• How to run tests

  • R --no-save < buildmantest.R

• Deployment instructions

Usage

R R --no-save < RUN.R

Who do I talk to?

• Soumya Banerjee

• https://sites.google.com/site/neelsoumya/Home

• sb2333@cam.ac.uk

• DataSHIELD

  • DataSHIELD is a platform that enables the non-disclosive analysis of distributed sensitive data
  • https://github.com/datashield