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

• installer_R.R and installer_unix.sh

  • installation scripts in R and UNIX

• RUN.R

  • script to start shiny server

  • R --no-save < RUN.R

• synthetic_data_generator.R

  • script to generate synthetic data

  • R --no-save < synthetic_data_generator.R

• build_man_test.R

  • script to build manuals and test code (testing script)

  • R --no-save < build_man_test.R

• build_man_test_git_add.sh

  • shell script to build manuals, test code and commit to git all documentation

  • ./build_man_test_git_add.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

	
		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

    
    	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 < build_man_test.R

• Deployment instructions

Usage

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