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rang: Reconstructing reproducible R computational environments

A complete declarative description of the computational environment is usually missing when researchers share their materials. Without such description, software obsolescence and missing system components can jeopardize computational reproducibility in the future, even when data and computer code ar...

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Detalles Bibliográficos
Autores principales: Chan, Chung-hong, Schoch, David
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10249795/
https://www.ncbi.nlm.nih.gov/pubmed/37289797
http://dx.doi.org/10.1371/journal.pone.0286761
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author Chan, Chung-hong
Schoch, David
author_facet Chan, Chung-hong
Schoch, David
author_sort Chan, Chung-hong
collection PubMed
description A complete declarative description of the computational environment is usually missing when researchers share their materials. Without such description, software obsolescence and missing system components can jeopardize computational reproducibility in the future, even when data and computer code are available. The R package rang is a complete solution for generating the declarative description for other researchers to automatically reconstruct the computational environment at a specific time point. The reconstruction process, based on Docker, has been tested for R code as old as 2001. The declarative description generated by rang satisfies the definition of a reproducible research compendium and can be shared as such. In this contribution, we show how rang can be used to make otherwise unexecutable code, spanning fields such as computational social science and bioinformatics, executable again. We also provide instructions on how to use rang to construct reproducible and shareable research compendia of current research. The package is currently available from CRAN (https://cran.r-project.org/web/packages/rang/index.html) and GitHub (https://github.com/chainsawriot/rang).
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spelling pubmed-102497952023-06-09 rang: Reconstructing reproducible R computational environments Chan, Chung-hong Schoch, David PLoS One Research Article A complete declarative description of the computational environment is usually missing when researchers share their materials. Without such description, software obsolescence and missing system components can jeopardize computational reproducibility in the future, even when data and computer code are available. The R package rang is a complete solution for generating the declarative description for other researchers to automatically reconstruct the computational environment at a specific time point. The reconstruction process, based on Docker, has been tested for R code as old as 2001. The declarative description generated by rang satisfies the definition of a reproducible research compendium and can be shared as such. In this contribution, we show how rang can be used to make otherwise unexecutable code, spanning fields such as computational social science and bioinformatics, executable again. We also provide instructions on how to use rang to construct reproducible and shareable research compendia of current research. The package is currently available from CRAN (https://cran.r-project.org/web/packages/rang/index.html) and GitHub (https://github.com/chainsawriot/rang). Public Library of Science 2023-06-08 /pmc/articles/PMC10249795/ /pubmed/37289797 http://dx.doi.org/10.1371/journal.pone.0286761 Text en © 2023 Chan, Schoch https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Chan, Chung-hong
Schoch, David
rang: Reconstructing reproducible R computational environments
title rang: Reconstructing reproducible R computational environments
title_full rang: Reconstructing reproducible R computational environments
title_fullStr rang: Reconstructing reproducible R computational environments
title_full_unstemmed rang: Reconstructing reproducible R computational environments
title_short rang: Reconstructing reproducible R computational environments
title_sort rang: reconstructing reproducible r computational environments
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10249795/
https://www.ncbi.nlm.nih.gov/pubmed/37289797
http://dx.doi.org/10.1371/journal.pone.0286761
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