https://github.com/neelsoumya/dssurvivalshiny

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.
https://github.com/neelsoumya/dssurvivalshiny

clinical-informatics clinical-information-system data-documentation datashield meta-analysis

Last synced: about 2 months ago
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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.

• Host: GitHub
• URL: https://github.com/neelsoumya/dssurvivalshiny
• Owner: neelsoumya
• License: gpl-3.0
• Created: 2021-01-07T12:06:18.000Z (almost 4 years ago)
• Default Branch: master
• Last Pushed: 2024-05-14T09:32:51.000Z (8 months ago)
• Last Synced: 2024-05-14T11:43:14.599Z (8 months ago)
• Topics: clinical-informatics, clinical-information-system, data-documentation, datashield, meta-analysis
• Language: R
• Homepage:
• Size: 11.7 MB
• Stars: 1
• Watchers: 1
• Forks: 0
• Open Issues: 1
• Metadata Files:
  • Readme: README.md
  • Contributing: CONTRIBUTING.md
  • License: LICENSE.md
  • Citation: CITATION.cff

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README

        


## 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

	

```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

	![Screenshot of GUI](screenshot.png)

		

* Presentations

   * presentation folder

## Citation

   * Forthcoming

## Contact

 

   * Soumya Banerjee

     

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

   * [email protected]

   

* 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 < build_man_test.R

* Deployment instructions

### Usage ###

```R

R --no-save < RUN.R

```	

   

### Who do I talk to? ###

* Soumya Banerjee

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

* [email protected]

* DataSHIELD

    * DataSHIELD is a platform that enables the non-disclosive analysis of distributed sensitive data 

    * https://github.com/datashield

[![License](https://img.shields.io/badge/license-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0.html)