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On code sharing and model documentation of published individual and agent-based models

Being able to replicate research results is the hallmark of science. Replication of research findings using computational models should, in principle, be possible. In this manuscript, we assess code sharing and model documentation practices of 7500 publications about individual-based and agent-based...

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Detalles Bibliográficos
Autores principales: Janssen, Marco A., Pritchard, Calvin, Lee, Allen
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier Ltd. 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7493807/
https://www.ncbi.nlm.nih.gov/pubmed/32958993
http://dx.doi.org/10.1016/j.envsoft.2020.104873
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author Janssen, Marco A.
Pritchard, Calvin
Lee, Allen
author_facet Janssen, Marco A.
Pritchard, Calvin
Lee, Allen
author_sort Janssen, Marco A.
collection PubMed
description Being able to replicate research results is the hallmark of science. Replication of research findings using computational models should, in principle, be possible. In this manuscript, we assess code sharing and model documentation practices of 7500 publications about individual-based and agent-based models. The code availability increased over the years, up to 18% in 2018. Model documentation does not include all the elements that could improve the transparency of the models, such as mathematical equations, flow charts, and pseudocode. We find that articles with equations and flow charts being cited more among other model papers, probably because the model documentation is more transparent. The practices of code sharing improve slowly over time, partly due to the emergence of more public repositories and archives, and code availability requirements by journals and sponsors. However, a significant change in norms and habits need to happen before computational modeling becomes a reproducible science.
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spelling pubmed-74938072020-09-17 On code sharing and model documentation of published individual and agent-based models Janssen, Marco A. Pritchard, Calvin Lee, Allen Environ Model Softw Article Being able to replicate research results is the hallmark of science. Replication of research findings using computational models should, in principle, be possible. In this manuscript, we assess code sharing and model documentation practices of 7500 publications about individual-based and agent-based models. The code availability increased over the years, up to 18% in 2018. Model documentation does not include all the elements that could improve the transparency of the models, such as mathematical equations, flow charts, and pseudocode. We find that articles with equations and flow charts being cited more among other model papers, probably because the model documentation is more transparent. The practices of code sharing improve slowly over time, partly due to the emergence of more public repositories and archives, and code availability requirements by journals and sponsors. However, a significant change in norms and habits need to happen before computational modeling becomes a reproducible science. Elsevier Ltd. 2020-12 2020-09-16 /pmc/articles/PMC7493807/ /pubmed/32958993 http://dx.doi.org/10.1016/j.envsoft.2020.104873 Text en © 2020 Elsevier Ltd. All rights reserved. Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active.
spellingShingle Article
Janssen, Marco A.
Pritchard, Calvin
Lee, Allen
On code sharing and model documentation of published individual and agent-based models
title On code sharing and model documentation of published individual and agent-based models
title_full On code sharing and model documentation of published individual and agent-based models
title_fullStr On code sharing and model documentation of published individual and agent-based models
title_full_unstemmed On code sharing and model documentation of published individual and agent-based models
title_short On code sharing and model documentation of published individual and agent-based models
title_sort on code sharing and model documentation of published individual and agent-based models
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7493807/
https://www.ncbi.nlm.nih.gov/pubmed/32958993
http://dx.doi.org/10.1016/j.envsoft.2020.104873
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