references.bib

%%% reproducibility crisis

@article{allison2016,
	title = {Reproducibility: {A} tragedy of errors},
	volume = {530},
	copyright = {2016 Nature Publishing Group},
	issn = {1476-4687},
	shorttitle = {Reproducibility},
	url = {https://www.nature.com/articles/530027a},
	doi = {10.1038/530027a},
	abstract = {Mistakes in peer-reviewed papers are easy to find but hard to fix, report David B. Allison and colleagues.},
	language = {en},
	number = {7588},
	urldate = {2023-03-22},
	journal = {Nature},
	author = {Allison, David B. and Brown, Andrew W. and George, Brandon J. and Kaiser, Kathryn A.},
	month = feb,
	year = {2016},
	note = {Number: 7588
Publisher: Nature Publishing Group},
	keywords = {Communication, Peer review, Publishing},
	pages = {27--29}
}

@misc{bastian2016,
	title = {Reproducibility {Crisis} {Timeline}: {Milestones} in {Tackling} {Research} {Reliability}},
	shorttitle = {Reproducibility {Crisis} {Timeline}},
	url = {https://absolutelymaybe.plos.org/2016/12/05/reproducibility-crisis-timeline-milestones-in-tackling-research-reliability/},
	abstract = {It’s not a new story, although “the reproducibility crisis” may seem to be. For life sciences, I think it started in the…},
	language = {en-US},
	urldate = {2023-03-22},
	journal = {Absolutely Maybe (PLOS)},
	author = {Bastian, Hilda},
	month = dec,
	year = {2016}
}

@article{ioannidis2005,
	title = {Why {Most} {Published} {Research} {Findings} {Are} {False}},
	volume = {2},
	issn = {1549-1277},
	url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1182327/},
	doi = {10.1371/journal.pmed.0020124},
	abstract = {There is increasing concern that most current published research findings are false. The probability that a research claim is true may depend on study power and bias, the number of other studies on the same question, and, importantly, the ratio of true to no relationships among the relationships probed in each scientific field. In this framework, a research finding is less likely to be true when the studies conducted in a field are smaller; when effect sizes are smaller; when there is a greater number and lesser preselection of tested relationships; where there is greater flexibility in designs, definitions, outcomes, and analytical modes; when there is greater financial and other interest and prejudice; and when more teams are involved in a scientific field in chase of statistical significance. Simulations show that for most study designs and settings, it is more likely for a research claim to be false than true. Moreover, for many current scientific fields, claimed research findings may often be simply accurate measures of the prevailing bias. In this essay, I discuss the implications of these problems for the conduct and interpretation of research., Published research findings are sometimes refuted by subsequent evidence, says Ioannidis, with ensuing confusion and disappointment.},
	number = {8},
	urldate = {2023-03-22},
	journal = {PLoS Medicine},
	author = {Ioannidis, John P. A.},
	month = aug,
	year = {2005},
	pmid = {16060722},
	pmcid = {PMC1182327},
	pages = {e124}
}

@article{steen2011,
	title = {Retractions in the scientific literature: is the incidence of research fraud increasing?},
	volume = {37},
	copyright = {© 2011, Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.},
	issn = {0306-6800, 1473-4257},
	shorttitle = {Retractions in the scientific literature},
	url = {https://jme.bmj.com/content/37/4/249},
	doi = {10.1136/jme.2010.040923},
	abstract = {{\textless}h3{\textgreater}Background{\textless}/h3{\textgreater} {\textless}p{\textgreater}Scientific papers are retracted for many reasons including fraud (data fabrication or falsification) or error (plagiarism, scientific mistake, ethical problems). Growing attention to fraud in the lay press suggests that the incidence of fraud is increasing.{\textless}/p{\textgreater}{\textless}h3{\textgreater}Methods{\textless}/h3{\textgreater} {\textless}p{\textgreater}The reasons for retracting 742 English language research papers retracted from the PubMed database between 2000 and 2010 were evaluated. Reasons for retraction were initially dichotomised as fraud or error and then analysed to determine specific reasons for retraction.{\textless}/p{\textgreater}{\textless}h3{\textgreater}Results{\textless}/h3{\textgreater} {\textless}p{\textgreater}Error was more common than fraud (73.5\% of papers were retracted for error (or an undisclosed reason) vs 26.6\% retracted for fraud). Eight reasons for retraction were identified; the most common reason was scientific mistake in 234 papers (31.5\%), but 134 papers (18.1\%) were retracted for ambiguous reasons. Fabrication (including data plagiarism) was more common than text plagiarism. Total papers retracted per year have increased sharply over the decade (r=0.96; p\<0.001), as have retractions specifically for fraud (r=0.89; p\<0.001). Journals now reach farther back in time to retract, both for fraud (r=0.87; p\<0.001) and for scientific mistakes (r=0.95; p\<0.001). Journals often fail to alert the naïve reader; 31.8\% of retracted papers were not noted as retracted in any way.{\textless}/p{\textgreater}{\textless}h3{\textgreater}Conclusions{\textless}/h3{\textgreater} {\textless}p{\textgreater}Levels of misconduct appear to be higher than in the past. This may reflect either a real increase in the incidence of fraud or a greater effort on the part of journals to police the literature. However, research bias is rarely cited as a reason for retraction.{\textless}/p{\textgreater}},
	language = {en},
	number = {4},
	urldate = {2023-03-22},
	journal = {Journal of Medical Ethics},
	author = {Steen, R. Grant},
	month = apr,
	year = {2011},
	pmid = {21186208},
	note = {Publisher: Institute of Medical Ethics
Section: Research ethics},
	keywords = {data fabrication, data falsification, fraud, Plagiarism, professional misconduct, scientific research},
	pages = {249--253},
}

@article{whitfield2021,
	title = {Replication {Crisis}},
	volume = {43},
	issn = {0260-9592},
	url = {https://www.lrb.co.uk/the-paper/v43/n19/john-whitfield/replication-crisis},
	abstract = {If a brutally competitive environment helped the best work rise to the top, there might be an argument that the misery...},
	language = {en},
	number = {19},
	urldate = {2023-03-22},
	journal = {London Review of Books},
	author = {Whitfield, John},
	collaborator = {Ritchie, Stuart},
	month = oct,
	year = {2021},
	note = {ISBN: 9781847925657
reviewed-title: Science Fictions: Exposing Fraud, Bias, Negligence and Hype in Science},
	keywords = {Academia, Science technology and mathematics}
}

%%% reproducible research

@book{desquilbet2019,
  TITLE = {{Vers une recherche reproductible}},
  AUTHOR = {Desquilbet, Lo{\"i}c L. and Granger, Sabrina and Hejblum, Boris and Legrand, Arnaud and Pernot, Pascal and Rougier, Nicolas P. and de Castro Guerra, Elisa and Courbin-Coulaud, Martine and Duvaux, Ludovic and Gravier, Pierre and Le Campion, Gr{\'e}goire and Roux, Solenne and Santos, Fr{\'e}d{\'e}ric},
  URL = {https://hal.science/hal-02144142},
  EDITOR = {Unit{\'e} r{\'e}gionale de formation {\`a} l'information scientifique et technique de Bordeaux},
  PUBLISHER = {{Unit{\'e} r{\'e}gionale de formation {\`a} l'information scientifique et technique de Bordeaux}},
  PAGES = {1-161},
  YEAR = {2019},
  MONTH = May,
  KEYWORDS = {Open source ; Book sprint ; Data sharing ; Open science ; Data reusability ; Research transparency ; Replication crisis ; Reproducible research ; Standardization ; Open data ; Transparence de la recherche ; Recherche reproductible ; Standardisation ; Crise de la r{\'e}plication ; Science ouverte ; R{\'e}utilisation des donn{\'e}es},
  PDF = {https://hal.science/hal-02144142v3/file/20190614_recherche_reproductible.pdf},
  HAL_ID = {hal-02144142},
  HAL_VERSION = {v3},
}

@misc{the_turing_way2022,
	title = {The {Turing} {Way}: {A} handbook for reproducible, ethical and collaborative research},
	shorttitle = {The {Turing} {Way}},
	url = {https://zenodo.org/record/7625728},
	abstract = {The Turing Way: A handbook for reproducible, ethical and collaborative research The Turing Way December 2022 Latest The Turing Way is an open source community-driven guide to reproducible, ethical, inclusive and collaborative data science. The Turing Way book is collaboratively developed by its diverse community of researchers, learners, educators, and other stakeholders. The Turing Way project is openly developed and any and all questions, comments and recommendations are welcome at our github repository: https://github.com/alan-turing-institute/the-turing-way. In 2020, the project underwent a major overhaul categorising chapters into 5 guides on reproducible research, project design, collaboration, communication and ethical research. Additionally, we added a community handbook to document all the practices designed and implemented towards the development of the project and community. This release in 2021 includes additional chapters developed by our contributors across five guides and the community handbook. In addition, all the project documents from the project are provided as they appear on The Turing Way GitHub repository including the Zenodo metadata: https://github.com/alan-turing-institute/the-turing-way. Release log v1.1.0: Zenodo metadata information and additional chapters from Book Dash Dec 2022 v1.0.3: Zenodo metadata information and additional chapters from Book Dash May 2022 v1.0.2: Zenodo metadata information and additional chapters since Book Dash November 2021 v1.0.1: Zenodo metadata information and additional chapters. v1.0.0: Five guide expansion of The Turing Way with a community handbook v0.0.4: Continuous integration chapter merged to main. v0.0.3: Reproducible environments chapter merged to main. v0.0.2: Version control chapter merged to main. v0.0.1: Reproducibility chapter merged to main. Full Changelog: https://github.com/alan-turing-institute/the-turing-way/compare/v1.0.1...v1.0.3 (Previous release: https://github.com/alan-turing-institute/the-turing-way/compare/v0.0.3...v1.0.1) v1.1.0},
	urldate = {2023-03-22},
	publisher = {Zenodo},
	author = {{The Turing Way Community}},
	month = jul,
	year = {2022},
	doi = {10.5281/zenodo.7625728},
	keywords = {collaboration, community, data science, ethics, handbook, reproducibility, research practices}
}

%%% data repository

@misc{zenodo,
  doi = {10.25495/7GXK-RD71},
  url = {https://www.zenodo.org/},
  author = {{European Organization For Nuclear Research} and {OpenAIRE}},
  keywords = {FOS: Physical sciences, Publication, Dataset},
  language = {en},
  title = {Zenodo},
  publisher = {CERN},
  year = {2013}
}

@article{foster2017,
	title = {Open {Science} {Framework} ({OSF})},
	volume = {105},
	issn = {1536-5050},
	url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5370619/},
	doi = {10.5195/jmla.2017.88},
	number = {2},
	urldate = {2023-03-22},
	journal = {Journal of the Medical Library Association : JMLA},
	author = {Foster, Erin D. and Deardorff, Ariel},
	month = apr,
	year = {2017},
	pmid = {null},
	pmcid = {PMC5370619},
	pages = {203--206}
}

%%% open access

@article{ancion2022,
	title = {Action {Plan} for {Diamond} {Open} {Access}},
	url = {https://zenodo.org/record/6282403},
	doi = {10.5281/zenodo.6282403},
	abstract = {Science Europe, cOAlition S, OPERAS, and the French National Research Agency (ANR) present an Action Plan for Diamond Open Access to further develop and expand a sustainable, community-driven Diamond OA scholarly communication ecosystem. It focuses on efficiency, quality standards, capacity building, and sustainability, and it addresses the alignment and development of common resources for the whole Diamond OA ecosystem, including journals and platforms, while respecting the cultural, multilingual, and disciplinary diversity that constitutes the strength of the sector. The Action Plan intends to create an inclusive worldwide community that has the tools to strengthen existing Diamond OA journals and platforms and increase their visibility.},
	language = {eng},
	urldate = {2023-03-22},
	author = {Ancion, Zoé and Borrell-Damián, Lidia and Mounier, Pierre and Rooryck, Johan and Saenen, Bregt},
	month = mar,
	year = {2022},
	note = {Publisher: Zenodo},
	keywords = {Diamond Open Access, Open Access}
}

@techreport{planS,
  TITLE = {{Recommendations for Plan S implementation by the ANR}},
  AUTHOR = {Publications, Coll{\`e}ge and {\'E}dition Scientifique Ouverte, Groupe d'Expertise and Construire La Bibliodiversit{\'e}, Groupe Projet},
  URL = {https://hal-lara.archives-ouvertes.fr/hal-03640413},
  TYPE = {Research Report},
  PAGES = {8 p.},
  INSTITUTION = {{Comit{\'e} pour la science ouverte}},
  YEAR = {2019},
  MONTH = Jan,
  DOI = {10.52949/18},
  KEYWORDS = {bibliodiversity ; open access ; open science ; scientific publication ; Plan S ; open archive ; copyright ; recommendations ; diamond journal ; bibliodversit{\'e} ; acc{\`e}s ouvert ; science ouverte ; publication scientifique ; Plan S ; archive ouverte ; droit d'auteur ; recommandations ; mod{\`e}le diamant},
  PDF = {https://hal-lara.archives-ouvertes.fr/hal-03640413/file/Plan-S-Pre%CC%81conisations-EN-2019.pdf},
  HAL_ID = {hal-03640413},
  HAL_VERSION = {v1},
}

%%% programming

@article{knuth1984,
	title = {Literate programming},
	volume = {27},
	number = {2},
	journal = {The Computer Journal},
	author = {Knuth, Donald Ervin},
	year = {1984},
	note = {Publisher: Oxford University Press},
	pages = {97--111}
}


%%% software

@Manual{rmarkdown,
  title = {{rmarkdown}: Dynamic Documents for {R}},
    author = {JJ Allaire and Yihui Xie and Jonathan McPherson and
      Javier Luraschi and Kevin Ushey and Aron Atkins and Hadley
      Wickham and Joe Cheng and Winston Chang and Richard Iannone},
    year = {2023},
    note = {R package version 2.20},
    url = {https://pkgs.rstudio.com/rmarkdown/},
}

%%% licence

@misc{ccby4,
	title = {Creative {Commons} — {Attribution} 4.0 {International} — {CC} {BY} 4.0},
	url = {https://creativecommons.org/licenses/by/4.0/legalcode},
	urldate = {2023-03-22}
}


@software{quarto,
author = {Allaire, J.J. and Teague, Charles and Scheidegger, Carlos and Xie, Yihui and Dervieux, Christophe},
doi = {10.5281/zenodo.5960048},
month = {1},
title = {{Quarto}},
url = {https://github.com/quarto-dev/quarto-cli},
version = {1.2},
year = {2022}
}

@software{pandoc,
author = {MacFarlane, John and Krewinkel, Albert and Rosenthal, Jesse},
title = {{Pandoc}},
url = {https://github.com/jgm/pandoc}
}