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dssynthetic

https://github.com/tombisho/dssynthetic

Science Score: 57.0%

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Repository

Basic Info
  • Host: GitHub
  • Owner: tombisho
  • License: gpl-3.0
  • Language: R
  • Default Branch: main
  • Size: 90.8 KB
Statistics
  • Stars: 1
  • Watchers: 1
  • Forks: 1
  • Open Issues: 0
  • Releases: 2
Created over 4 years ago · Last pushed over 3 years ago
Metadata Files
Readme License Citation

README.md

dsSynthetic

Introduction

dsSynthetic is a DataSHIELD server side package for generating synthetic data.

Please also look at the corresponding client side package dsSyntheticClient

https://github.com/tombisho/dsSyntheticClient

or

https://github.com/neelsoumya/dsSyntheticClient

Installation

  • Install R Studio and the development environment as described below:

    • https://data2knowledge.atlassian.net/wiki/spaces/DSDEV/pages/12943461/Getting+started

  • Install the virtual machines as described below:

    • https://data2knowledge.atlassian.net/wiki/spaces/DSDEV/pages/931069953/Installation+Training+Hub-+DataSHIELD+v6
    • https://data2knowledge.atlassian.net/wiki/spaces/DSDEV/pages/1657634881/Testing+100+VM
    • https://data2knowledge.atlassian.net/wiki/spaces/DSDEV/pages/1657634898/Tutorial+6.1.0+100+VM

  • Install dsBase and dsSynthetic on Opal server in the Virtual Machine (type tombisho/dsSynthetic and main in the textboxes)

    See the link below on how to install a package in Opal

    https://opaldoc.obiba.org/en/latest/web-user-guide/administration/datashield.html#add-package

  • Follow the bookdown

https://tombisho.github.io/synthetic_bookdown/

which uses the Opal demo server

https://opal-sandbox.mrc-epid.cam.ac.uk/

Usage

See bookdown below for executable code and a tutorial

https://tombisho.github.io/synthetic_bookdown/

which uses the Opal demo server which has all server side packages installed

https://opal-sandbox.mrc-epid.cam.ac.uk/

Acknowledgements

Thanks to the DataSHIELD team for providing the plaform on which these functions are based.

Thanks to OBiBa and Epigeny for the Opal data warehouse which we use to run DataSHIELD

Contact

Tom R.P. Bishop and Soumya Banerjee

Citation

If you like or use this work, please cite the following manuscript

Banerjee S, Bishop TRP. dsSynthetic: Synthetic data generation for the DataSHIELD federated analysis system. BMC Res. Notes. 2022;15 (1) :230

https://bmcresnotes.biomedcentral.com/articles/10.1186/s13104-022-06111-2

or

dsSynthetic: Synthetic data generation for the DataSHIELD federated analysis system

https://osf.io/tkxqm/

License

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Banerjee"
  given-names: "Soumya"
  orcid: "https://orcid.org/0000-0001-7748-9885"
- family-names: "Bishop"
  given-names: "Tom"
  orcid: "https://orcid.org/0000-0000-0000-0000"
title: "dsSynthetic: Synthetic data generation for the DataSHIELD federated analysis system. BMC Res. Notes. 2022;15 (1) :230"
version: 1.0.0
doi: https://doi.org/10.1186/s13104-022-06111-2
date-released: 2022-6-20
url: "https://bmcresnotes.biomedcentral.com/articles/10.1186/s13104-022-06111-2"

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Dependencies

DESCRIPTION cran
  • R >= 3.5.0 depends
  • dsBase * imports
  • synthpop * imports
Dockerfile docker
  • datashield/rock-base 6.2-R4.2 build