literature.bib

@article{Wilson2017,
    doi = {10.1371/journal.pcbi.1005510},
    author = {Wilson, Greg and Bryan, Jennifer and Cranston, Karen and Kitzes, Justin and Nederbragt, Lex and Teal, Tracy K.},
    journal = {PLOS Computational Biology},
    publisher = {Public Library of Science},
    title = {Good enough practices in scientific computing},
    year = {2017},
    month = {06},
    volume = {13},
    url = {https://doi.org/10.1371/journal.pcbi.1005510},
    pages = {1-20},
    abstract = {Author summary Computers are now essential in all branches of science, but most researchers are never taught the equivalent of basic lab skills for research computing. As a result, data can get lost, analyses can take much longer than necessary, and researchers are limited in how effectively they can work with software and data. Computing workflows need to follow the same practices as lab projects and notebooks, with organized data, documented steps, and the project structured for reproducibility, but researchers new to computing often don't know where to start. This paper presents a set of good computing practices that every researcher can adopt, regardless of their current level of computational skill. These practices, which encompass data management, programming, collaborating with colleagues, organizing projects, tracking work, and writing manuscripts, are drawn from a wide variety of published sources from our daily lives and from our work with volunteer organizations that have delivered workshops to over 11,000 people since 2010.},
    number = {6}
}

@online{TIER4,
	title = {{TIER} Protocol 4.0},
	url = {https://www.projecttier.org/tier-protocol/protocol-4-0/},
  year = {2021},
	author = {{Project TIER}},
	urldate = {2024-08-26}
}

@article{Marwick2018,
author = {Marwick, Ben and Boettiger, Carl and Mullen, Lincoln},
title = {Packaging Data Analytical Work Reproducibly Using {R} (and Friends)},
journal = {The American Statistician},
volume = {72},
number = {1},
pages = {80--88},
year = {2018},
publisher = {ASA Website},
doi = {10.1080/00031305.2017.1375986},
URL = {https://doi.org/10.1080/00031305.2017.1375986},
eprint = {https://doi.org/10.1080/00031305.2017.1375986},
abstract = { Computers are a central tool in the research process, enabling complex and large-scale data analysis. As computer-based research has increased in complexity, so have the challenges of ensuring that this research is reproducible. To address this challenge, we review the concept of the research compendium as a solution for providing a standard and easily recognizable way for organizing the digital materials of a research project to enable other researchers to inspect, reproduce, and extend the research. We investigate how the structure and tooling of software packages of the R programming language are being used to produce research compendia in a variety of disciplines. We also describe how software engineering tools and services are being used by researchers to streamline working with research compendia. Using real-world examples, we show how researchers can improve the reproducibility of their work using research compendia based on R packages and related tools. }
}

@Article{Vuorre2021,
author="Vuorre, Matti
and Crump, Matthew J. C.",
title="Sharing and organizing research products as {R} packages",
journal="Behavior Research Methods",
year="2021",
month="Apr",
day="01",
volume="53",
number="2",
pages="792--802",
abstract="A consensus on the importance of open data and reproducible code is emerging. How should data and code be shared to maximize the key desiderata of reproducibility, permanence, and accessibility? Research assets should be stored persistently in formats that are not software restrictive, and documented so that others can reproduce and extend the required computations. The sharing method should be easy to adopt by already busy researchers. We suggest the R package standard as a solution for creating, curating, and communicating research assets. The R package standard, with extensions discussed herein, provides a format for assets and metadata that satisfies the above desiderata, facilitates reproducibility, open access, and sharing of materials through online platforms like GitHub and Open Science Framework. We discuss a stack of R resources that help users create reproducible collections of research assets, from experiments to manuscripts, in the RStudio interface. We created an R package, vertical, to help researchers incorporate these tools into their workflows, and discuss its functionality at length in an online supplement. Together, these tools may increase the reproducibility and openness of psychological science.",
issn="1554-3528",
doi="10.3758/s13428-020-01436-x",
url="https://doi.org/10.3758/s13428-020-01436-x"
}

@online{Vilhuber2021,
	title = {Preparing your files for verification},
	url = {https://aeadataeditor.github.io/aea-de-guidance/preparing-for-data-deposit},
	titleaddon = {Office of the {AEA} Data Editor},
	author = {Vilhuber, Lars},
	urldate = {2024-08-26},
	date = {2021-04-08},
	langid = {english}
}

@online{VanRossum2013,
	title = {Style Guide for Python Code},
	url = {https://peps.python.org/pep-0008/},
	shorttitle = {{PEP} 8},
	abstract = {This document gives coding conventions for the Python code comprising the standard library in the main Python distribution.  Please see the companion informational {PEP} describing style guidelines for the C code in the C implementation of Python.},
	titleaddon = {Python Enhancement Proposals ({PEPs})},
	author = {van Rossum, Guido and Warsaw, Barry and Coghlan, Alyssa},
	urldate = {2024-08-27},
	date = {2013-08-01},
	langid = {english}
}

@online{Wickham2022Style,
	title = {The tidyverse style guide},
	url = {https://style.tidyverse.org/},
	author = {Wickham, Hadley},
	urldate = {2024-08-27},
	date = {2022-07-24},
	langid = {english}
}

@online{Wickham2023Design,
	title = {Tidy design principles},
	url = {https://design.tidyverse.org/},
	author = {Wickham, Hadley},
	urldate = {2024-08-27},
	date = {2023-11-20}
}

@book{Raymond2003,
	location = {Boston},
	title = {The art of {UNIX} programming: with contributions from thirteen {UNIX} pioneers, including its inventor, Ken Thompson},
	isbn = {978-0-13-142901-7},
	url = {https://www.arp242.net/the-art-of-unix-programming/},
	series = {Addison-Wesley professional computing series},
	shorttitle = {The art of {UNIX} programming},
	pagetotal = {525},
	publisher = {Addison-Wesley},
	author = {Raymond, Eric S.},
	date = {2003-09-17}
}

@online{Mineault2021,
	title = {The Good Research Code Handbook},
	rights = {Open Access},
	url = {https://goodresearch.dev/},
	author = {Mineault, Patrick and Nozawa, Kento},
	urldate = {2024-08-27},
	date = {2021-12-21},
	doi = {10.5281/ZENODO.5796873},
	howpublished = {\url{https://goodresearch.dev/}}
}

@incollection{Chacon2024,
	edition = {Second edition},
	title = {Removing a File from Every Commit},
	isbn = {978-1-4842-0077-3},
	url = {https://git-scm.com/book/en/v2/Git-Tools-Rewriting-History#_removing_file_every_commit},
	booktitle = {Pro Git},
	publisher = {Apress},
	author = {Chacon, Scott and Straub, Ben},
	urldate = {2024-08-28},
	date = {2024-08-20},
	langid = {english}
}

@online{Moller2015,
	title = {Definition of Free Cultural Works},
	url = {https://freedomdefined.org/Definition/1.1},
	author = {Möller, Erik and Hill, Benjamin Mako and Garlick, Mia and Stark, Elizabeth and Knapp, Justin Anthony and Kadlec, Petr and Stallman, Richard and Lessig, Lawrence and Beesley, Angela},
	urldate = {2024-08-28},
	date = {2015-02-17},
	langid = {english}
}

@online{FSF2024,
	title = {What is Free Software?},
	url = {https://www.gnu.org/philosophy/free-sw.html},
	author = {{Free Software Foundation}},
	urldate = {2024-08-30},
	date = {2021-02-02},
	version = {1.169}
}

@online{OSI2007,
	title = {The Open Source Definition},
	url = {https://opensource.org/osd},
	author = {{Open Source Initiative}},
	urldate = {2024-08-30},
	date = {2007-03-22},
	langid = {american},
	version = {1.9}
}

@online{OKFN2016,
	title = {The Open Definition - Open Definition - Defining Open in Open Data, Open Content and Open Knowledge},
	url = {https://opendefinition.org/},
	author = {{Open Knowledge Foundation}},
	urldate = {2024-08-30},
	date = {2016},
	version = {2.1}
}

@online{Wheeler2014,
	title = {Make Your Open Source Software {GPL}-Compatible. Or Else.},
	url = {https://dwheeler.com/essays/gpl-compatible.html},
	author = {Wheeler, David A.},
	urldate = {2024-08-31},
	date = {2014-02-16}
}

@online{Matt2009,
	title = {Why {CC} {BY}-{SA} is Unsuitable},
	url = {https://osmfoundation.org/w/index.php?title=Licence_and_Legal_FAQ/Why_CC_BY-SA_is_Unsuitable&oldid=3927},
	titleaddon = {{OpenStreetMap} Foundation},
	author = {{Matt}},
	urldate = {2024-09-02},
	date = {2009-10-23}
}

@online{Poole2017,
	title = {Use of {CC} {BY} 4.0 licensed data in {OpenStreetMap}},
	url = {https://blog.openstreetmap.org/2017/03/17/use-of-cc-by-data/},
	titleaddon = {{OpenStreetMap} Blog},
	author = {Poole, Simon},
	urldate = {2024-09-02},
	date = {2017-03-17},
	langid = {american}
}

@online{Koppor2016,
	title = {Answer to '{GPL}-Licensed {LaTeX} template - implications for resulting work?'},
	url = {https://opensource.stackexchange.com/questions/2735/gpl-licensed-latex-template-implications-for-resulting-work/4206#4206},
	shorttitle = {Answer to "{GPL}-Licensed {LaTeX} template - implications for resulting work?},
	titleaddon = {Open Source Stack Exchange},
	author = {{Koppor}},
	urldate = {2024-09-02},
	date = {2016-07-23}
}

@online{MadHatter2022,
	title = {Answer to 'Is the {PDF} output of {LaTeX} code licensed under {GPLv}3 also covered?'},
	url = {https://opensource.stackexchange.com/questions/12738/is-the-pdf-output-of-latex-code-licensed-under-gplv3-also-covered/12739#12739},
	shorttitle = {Answer to "Is the {PDF} output of {LaTeX} code licensed under {GPLv}3 also covered?},
	titleaddon = {Open Source Stack Exchange},
	author = {{MadHatter}},
	urldate = {2024-09-02},
	date = {2022-03-18}
}

@misc{Klimpel2013,
	title = {Free knowledge based on Creative Commons licenses},
	url = {https://meta.wikimedia.org/wiki/Free_knowledge_based_on_Creative_Commons_licenses},
	publisher = {Wikimedia},
	author = {Klimpel, Paul},
	urldate = {2024-09-03},
	date = {2013},
	langid = {english}
}

@online{ODI2015,
	title = {What are the impacts of non-open licences?},
	url = {https://theodi.org/insights/guides/what-are-the-impacts-of-non-open-licences/},
	abstract = {This guide outlines the key considerations that inform licensing decisions},
	author = {{Open Data Institute}},
	urldate = {2024-09-03},
	date = {2015-09-22},
	langid = {english}
}

@online{CC2024FAQ,
	title = {Answer to 'Can {I} combine material under different Creative Commons licenses in my work?' in Frequently Asked Questions},
	url = {https://creativecommons.org/faq/#can-i-combine-material-under-different-creative-commons-licenses-in-my-work},
	author = {{Creative Commons}},
	urldate = {2024-09-03},
	date = {2024-06-03},
	langid = {english}
}

@article{Morin2012,
	title = {A Quick Guide to Software Licensing for the Scientist-Programmer},
	volume = {8},
	issn = {1553-7358},
	url = {https://dx.plos.org/10.1371/journal.pcbi.1002598},
	doi = {10.1371/journal.pcbi.1002598},
	pages = {e1002598},
	number = {7},
	journaltitle = {{PLoS} Computational Biology},
	shortjournal = {{PLoS} Comput Biol},
	author = {Morin, Andrew and Urban, Jennifer and Sliz, Piotr},
	editor = {Lewitter, Fran},
	urldate = {2024-09-03},
	date = {2012-07-26},
	langid = {english}
}

@report{Lammerhirt2017,
	title = {Avoiding data use silos: How governments can simplify the open licensing landscape},
	rights = {{CC}-{BY}-4.0},
	url = {https://web.archive.org/web/20231002141440/https://research.okfn.org/avoiding-data-use-silos/},
	shorttitle = {Avoiding data use silos},
	institution = {Open Knowledge International},
	author = {Lämmerhirt, Danny},
	urldate = {2024-09-03},
	date = {2017-12}
}

@online{Morrison2024,
	title = {Which open data license?},
	url = {https://forum.openmod.org/t/which-open-data-license/2611},
	shorttitle = {Which open data license?},
	titleaddon = {Open Energy Modelling Initiative forum},
	author = {Morrison, Robbie},
	urldate = {2024-09-03},
	date = {2024-08-27},
	langid = {british},
	note = {Section: Licensing}
}

@online{Stallman2022Version,
	title = {For Clarity's Sake, Please Don't Say “Licensed under {GNU} {GPL} 2”!},
	url = {https://www.gnu.org/licenses/identify-licenses-clearly.html},
	author = {Stallman, Richard},
	urldate = {2024-09-03},
	date = {2022-01-22}
}

@incollection{Wickham2023PackagesDependency,
	edition = {Second edition},
	title = {When should you take a dependency?},
	isbn = {978-1-09-813494-5},
	url = {https://r-pkgs.org/dependencies-mindset-background.html#sec-dependencies-pros-cons},
	booktitle = {R Packages},
	publisher = {O'Reilly Media},
	author = {Wickham, Hadley and Bryan, Jennifer},
	urldate = {2024-08-27},
	date = {2023-07-23}
}

@incollection{Wickham2023PackagesLicense,
	edition = {Second edition},
	title = {Licensing},
	isbn = {978-1-09-813494-5},
	url = {https://r-pkgs.org/license.html},
	booktitle = {R Packages},
	publisher = {O'Reilly Media},
	author = {Wickham, Hadley and Bryan, Jennifer},
	urldate = {2024-09-03},
	date = {2023-07-23}
}

@online{CC2013,
	title = {Considerations for licensors and licensees},
	url = {https://creativecommons.org/share-your-work/licensing-considerations/version4/},
	author = {{Creative Commons}},
	urldate = {2024-09-03},
	date = {2013-11-25},
	langid = {american}
}

@online{Rumsey2022,
	title = {Exclusive licence to publish – now here’s a thing},
	url = {https://www.coalition-s.org/blog/exclusive-licence-to-publish-now-heres-a-thing/},
	titleaddon = {{Plan S}},
	author = {Rumsey, Sally and Labastida, Ignasi},
	urldate = {2024-09-03},
	date = {2022-07-25},
	langid = {english}
}

@article{Suber2022,
	title = {Publishing Without Exclusive Rights},
	volume = {25},
	rights = {https://creativecommons.org/licenses/by/4.0},
	issn = {1080-2711},
	url = {https://journals.publishing.umich.edu/jep/article/id/1869/},
	doi = {10.3998/jep.1869},
	number = {1},
	journaltitle = {The Journal of Electronic Publishing},
	author = {Suber, Peter},
	urldate = {2024-09-03},
	date = {2022-04-26}
}

@online{Elson2016,
	title = {Retaining copyright for figures in academic publications to allow easy citation and reuse},
	url = {https://medium.com/@malte.elson/retaining-copyright-for-figures-in-academic-publications-to-allow-easy-citation-and-reuse-77c6e2b511fe},
	abstract = {tl;dr
1. Scientists routinely cannot reuse or quote figures in publications, even their own, due to copyright agreements.
2. Figures can be…},
	titleaddon = {Medium},
	author = {Elson, Malte},
	urldate = {2024-09-03},
	date = {2016-11-11},
	langid = {english}
}

@online{CC2024Certificate,
	title = {Creative Commons Certificate for Educators, Academic Librarians, and Open Culture},
	url = {https://certificates.creativecommons.org/cccertedu/},
	author = {{Creative Commons}},
	urldate = {2024-09-03},
	date = {2024},
	langid = {english}
}

@book{Grassmuck2004,
	location = {Bonn},
	edition = {2., korrigierte Aufl},
	title = {Freie Software: zwischen Privat- und Gemeineigentum},
	isbn = {978-3-89331-569-7},
	url = {https://freie-software.bpb.de/},
	series = {Schriftenreihe},
	shorttitle = {Freie Software},
	number = {458},
	publisher = {Bundeszentrale für politische Bildung},
	author = {Grassmuck, Volker},
	urldate = {2024-09-03},
	date = {2004},
	langid = {de},
}

@collection{Kreutzer2014,
	location = {Bonn},
	title = {Open Content: a practical guide to using Creative Commons Licences},
	isbn = {978-3-940785-57-2},
	url = {https://meta.wikimedia.org/wiki/Open_Content_-_A_Practical_Guide_to_Using_Creative_Commons_Licences},
	shorttitle = {Open Content},
	pagetotal = {78},
	publisher = {German Comm. for {UNESCO}},
	editor = {Kreutzer, Till and {Deutsche UNESCO-Kommission}},
	urldate = {2024-09-03},
	date = {2014}
}

@online{CC2015,
	title = {{ShareAlike} compatibility analysis: {GPL}},
	url = {https://wiki.creativecommons.org/index.php?title=ShareAlike_compatibility_analysis:_GPL&oldid=114476},
	author = {{Creative Commons}},
	urldate = {2024-09-03},
	date = {2015-08-08}
}

@misc{Jackson2018,
	title = {Software Deposit: Where To Deposit Software},
	rights = {Creative Commons Attribution 4.0, Open Access},
	url = {https://softwaresaved.github.io/software-deposit-guidance/},
	shorttitle = {Software Deposit},
	abstract = {There are myriad digital repositories where you can deposit your research software so that the exact versions of your software upon which you have published your research results are retained and remain available for future inspection and use, both by yourself and by other researchers. These digital repositories may be provided by your institution, recommended, or mandated, by funders or publishers, or provided as a service to research communities by third-party organisations. This guide provides advice on choosing where to deposit your software.},
	author = {Jackson, Michael and {The Software Sustainability Institute}},
	urldate = {2024-09-04},
	date = {2018-08-07},
	langid = {english},
	doi = {10.5281/zenodo.1327329},
	keywords = {digital preservation, repositories, research outputs, research software, software sustainability, software sustainability institute},
	howpublished = {\url{https://softwaresaved.github.io/software-deposit-guidance/WhereToDepositSoftware.html}}
}

@article{Daquin2023,
	title = {{FAIREST}: A Framework for Assessing Research Repositories},
	volume = {5},
	issn = {2641-435X},
	url = {https://direct.mit.edu/dint/article/5/1/202/113179/FAIREST-A-Framework-for-Assessing-Research},
	doi = {10.1162/dint_a_00159},
	shorttitle = {{FAIREST}},
	abstract = {{ABSTRACT}
            The open science movement has gained significant momentum within the last few years. This comes along with the need to store and share research artefacts, such as publications and research data. For this purpose, research repositories need to be established. A variety of solutions exist for implementing such repositories, covering diverse features, ranging from custom depositing workflows to social media-like functions.
            In this article, we introduce the {FAIREST} principles, a framework inspired by the well-known {FAIR} principles, but designed to provide a set of metrics for assessing and selecting solutions for creating digital repositories for research artefacts. The goal is to support decision makers in choosing such a solution when planning for a repository, especially at an institutional level. The metrics included are therefore based on two pillars: (1) an analysis of established features and functionalities, drawn from existing dedicated, general purpose and commonly used solutions, and (2) a literature review on general requirements for digital repositories for research artefacts and related systems. We further describe an assessment of 11 widespread solutions, with the goal to provide an overview of the current landscape of research data repository solutions, identifying gaps and research challenges to be addressed.},
	pages = {202--241},
	number = {1},
	journaltitle = {Data Intelligence},
	author = {d'Aquin, Mathieu and Kirstein, Fabian and Oliveira, Daniela and Schimmler, Sonja and Urbanek, Sebastian},
	urldate = {2024-09-04},
	date = {2023-03-08},
	langid = {english}
}

@article{Garijo2022,
	title = {Nine best practices for research software registries and repositories},
	volume = {8},
	rights = {https://creativecommons.org/licenses/by/4.0/},
	issn = {2376-5992},
	url = {https://peerj.com/articles/cs-1023},
	doi = {10.7717/peerj-cs.1023},
	abstract = {Scientific software registries and repositories improve software findability and research transparency, provide information for software citations, and foster preservation of computational methods in a wide range of disciplines. Registries and repositories play a critical role by supporting research reproducibility and replicability, but developing them takes effort and few guidelines are available to help prospective creators of these resources. To address this need, the
              {FORCE}11 Software Citation Implementation Working Group
              convened a Task Force to distill the experiences of the managers of existing resources in setting expectations for all stakeholders. In this article, we describe the resultant best practices which include defining the scope, policies, and rules that govern individual registries and repositories, along with the background, examples, and collaborative work that went into their development. We believe that establishing specific policies such as those presented here will help other scientific software registries and repositories better serve their users and their disciplines.},
	pages = {e1023},
	journaltitle = {{PeerJ} Computer Science},
	author = {Garijo, Daniel and Ménager, Hervé and Hwang, Lorraine and Trisovic, Ana and Hucka, Michael and Morrell, Thomas and Allen, Alice and {Task Force on Best Practices for Software Registries} and {SciCodes Consortium}},
	urldate = {2024-09-04},
	date = {2022-08-08},
	langid = {english}
}

@report{Arguillas2022,
	title = {10 Things for Curating Reproducible and {FAIR} Research},
	url = {https://curating4reproducibility.org/10things/},
	abstract = {This document, "10 Things for Curating Reproducible and {FAIR} Research," describes the key issues of curating reproducible and {FAIR} research ({CURE}-{FAIR}). It lists standards-based guidelines for ten practices, focusing primarily on research compendia produced by quantitative data-driven social science.


The "10 {CURE}-{FAIR} Things" are intended primarily for data curators and information professionals who are charged with publication and archival of {FAIR} and computationally reproducible research. Often the first re-users of the research compendium, they have the opportunity to verify that a computation can be executed and that it can reproduce pre-specified results. Secondarily, the "10 {CURE}-{FAIR} Things" will be of interest to researchers, publishers, editors, reviewers, and others who have a stake in creating, using, sharing, publishing, or preserving reproducible research.},
	author = {Arguillas, Florio and Christian, Thu-Mai and Gooch, Mandy and Honeyman, Tom and Peer, Limor and {CURE-FAIR WG}},
	institution = {Research Data Alliance},
	urldate = {2024-09-04},
	date = {2022-06-27},
	doi = {10.15497/RDA00074},
	howpublished = {\url{https://curating4reproducibility.org/10things/}}
}

@inreference{Wikipedia2024,
	title = {{GNU} General Public License – Linking and derived works},
	rights = {Creative Commons Attribution-{ShareAlike} License},
	url = {https://en.wikipedia.org/w/index.php?title=GNU_General_Public_License&oldid=1244139410#Linking_and_derived_works},
	abstract = {The {GNU} General Public Licenses ({GNU} {GPL} or simply {GPL}) are a series of widely used free software licenses, or copyleft licenses, that guarantee end users the freedoms to run, study, share, and modify the software. The license was the first copyleft for general use and was originally written by Richard Stallman, the founder of the Free Software Foundation ({FSF}), for the {GNU} Project. The license grants the recipients of a computer program the rights of the Free Software Definition. The licenses in the {GPL} series are all copyleft licenses, which means that any derivative work must be distributed under the same or equivalent license terms. It is more restrictive than the Lesser General Public License and even further distinct from the more widely-used permissive software licenses such as {BSD}, {MIT}, and Apache.
Historically, the {GPL} license family has been one of the most popular software licenses in the free and open-source software ({FOSS}) domain. Prominent free software programs licensed under the {GPL} include the Linux kernel and the {GNU} Compiler Collection ({GCC}). David A. Wheeler argues that the copyleft provided by the {GPL} was crucial to the success of Linux-based systems, giving the programmers who contributed to the kernel the assurance that their work would benefit the whole world and remain free, rather than being exploited by software companies that would not have to give anything back to the community.
In 2007, the third version of the license ({GPLv}3) was released to address some perceived problems with the second version ({GPLv}2) which were discovered during the latter's long-time usage.
To keep the license current, the {GPL} license includes an optional "any later version" clause, allowing users to choose between the original terms or the terms in new versions as updated by the {FSF}. Software projects licensed with the optional "or later" clause include the {GNU} Project, while the Linux kernel, for instance, is licensed under {GPLv}2 only.
The "or any later version" clause is sometimes known as a "lifeboat clause" since it allows combinations between different versions of {GPL}-licensed software to maintain compatibility.},
	booktitle = {Wikipedia},
	publisher = {Wikipedia, The Free Encyclopedia},
	author = {{Wikipedia contributors}},
	urldate = {2024-09-06},
	date = {2024-09-05},
	langid = {english},
	note = {Page Version {ID}: 1244139410}
}

@book{APA2020,
	location = {Washington},
	title = {Publication manual of the American Psychological Association},
	edition = {7th ed.},
	isbn = {978-1-4338-3217-8 978-1-4338-3218-5 978-1-4338-3215-4 978-1-4338-3216-1},
	publisher = {American Psychological Association},
	urldate = {2024-09-12},
	date = {2020},
	langid = {english},
	doi = {10.1037/0000165-000},
}

@report{ScienceEurope2021,
	title = {Practical Guide to the International Alignment of Research Data Management - Extended Edition},
	rights = {Creative Commons Attribution 4.0 International, Open Access},
	url = {https://zenodo.org/record/4915861},
	doi = {10.5281/ZENODO.4915861},
	abstract = {This resource offers targeted guidance for organisations, scientific communities, as well as individual researchers, to organise research data and preserve it appropriately Originally released in 2019, and following its successful uptake by many organisations, the extended edition features a brand-new rubric to facilitate the evaluation of a data management plan ({DMP}). The guide also presents core requirements for {DMPs}, criteria for the selection of trustworthy repositories, and guidance for researchers to comply with organisational requirements.},
	author = {{Science Europe}},
	urldate = {2024-09-18},
	date = {2021-01-27},
	note = {Publisher: Zenodo},
	keywords = {{RDM}, Research Data, Research Data Management},
	howpublished = {\url{https://scienceeurope.org/our-resources/practical-guide-to-the-international-alignment-of-research-data-management/}}
}

@online{Stallman2022NoLimit,
	title = {Why programs must not limit the freedom to run them},
	url = {https://www.gnu.org/philosophy/programs-must-not-limit-freedom-to-run.html},
	author = {Stallman, Richard},
	urldate = {2024-09-21},
	date = {2022-09-06},
}

@online{Moller2023,
	title = {The case for Free use: reasons not to use a Creative Commons -{NC} license},
	url = {https://freedomdefined.org/index.php?title=Licenses/NC&oldid=27327},
	author = {Möller, Erik},
	urldate = {2024-09-21},
	date = {2023-12-15},
	langid = {english},
}

@online{Fogel2006,
	title = {The Surprising History of Copyright and The Promise of a Post-Copyright World},
	url = {https://questioncopyright.org/promise/},
	titleaddon = {Question Copyright},
	author = {Fogel, Karl},
	urldate = {2024-09-21},
	date = {2006-05-27},
	langid = {american},
}
@online{UKGovernment2020,
	title = {Quality assurance of code for analysis and research},
	url = {https://best-practice-and-impact.github.io/qa-of-code-guidance/},
	urldate = {2024-11-26},
	author = {{UK Government Analytical Community}},
	year = {2020},
}
@incollection{Buckheit1995,
	location = {New York, {NY}},
	title = {{WaveLab} and Reproducible Research},
	volume = {103},
	isbn = {978-0-387-94564-4 978-1-4612-2544-7},
	url = {http://link.springer.com/10.1007/978-1-4612-2544-7_5},
	pages = {55--81},
	booktitle = {Wavelets and Statistics},
	publisher = {Springer New York},
	author = {Buckheit, Jonathan B. and Donoho, David L.},
	editor = {Antoniadis, Anestis and Oppenheim, Georges},
	editorb = {Bickel, P. and Diggle, P. and Fienberg, S. and Krickeberg, K. and Olkin, I. and Wermuth, N. and Zeger, S.},
	editorbtype = {redactor},
	urldate = {2024-11-27},
	date = {1995},
	doi = {10.1007/978-1-4612-2544-7_5},
	note = {Series Title: Lecture Notes in Statistics},
}
@article{Gentleman2007,
	title = {Statistical Analyses and Reproducible Research},
	volume = {16},
	issn = {1061-8600, 1537-2715},
	doi = {10.1198/106186007X178663},
	pages = {1--23},
	number = {1},
	journaltitle = {Journal of Computational and Graphical Statistics},
	shortjournal = {Journal of Computational and Graphical Statistics},
	author = {Gentleman, Robert and Temple Lang, Duncan},
	urldate = {2024-11-27},
	date = {2007-03},
	langid = {english},
}
@article{Ince2012,
	title = {The case for open computer programs},
	volume = {482},
	issn = {0028-0836, 1476-4687},
	url = {https://www.nature.com/articles/nature10836},
	doi = {10.1038/nature10836},
	pages = {485--488},
	number = {7386},
	journaltitle = {Nature},
	shortjournal = {Nature},
	author = {Ince, Darrel C. and Hatton, Leslie and Graham-Cumming, John},
	urldate = {2023-10-24},
	date = {2012-02},
	langid = {english},
}
@book{NASEM2019,
	location = {Washington, D.C.},
	title = {Reproducibility and Replicability in Science},
	isbn = {978-0-309-48616-3},
	publisher = {National Academies Press},
	author = {{National Academies of Sciences, Engineering, and Medicine}},
	urldate = {2024-11-27},
	date = {2019-09-20},
	doi = {10.17226/25303},
}
@article{Knuth1984,
	title = {Literate Programming},
	volume = {27},
	issn = {0010-4620, 1460-2067},
	doi = {10.1093/comjnl/27.2.97},
	pages = {97--111},
	number = {2},
	journaltitle = {The Computer Journal},
	shortjournal = {The Computer Journal},
	author = {Knuth, D. E.},
	urldate = {2024-11-27},
	date = {1984-02-01},
	langid = {english},
}
@incollection{Leisch2002,
	location = {Heidelberg},
	title = {Sweave: Dynamic Generation of Statistical Reports Using Literate Data Analysis},
	isbn = {978-3-7908-1517-7 978-3-642-57489-4},
	url = {http://link.springer.com/10.1007/978-3-642-57489-4_89},
	shorttitle = {Sweave},
	pages = {575--580},
	booktitle = {Compstat},
	publisher = {Physica-Verlag {HD}},
	author = {Leisch, Friedrich},
	editor = {Härdle, Wolfgang and Rönz, Bernd},
	urldate = {2024-11-27},
	date = {2002},
	langid = {english},
	doi = {10.1007/978-3-642-57489-4_89},
}
@book{Xie2015,
	location = {Boca Raton, {FL}},
	edition = {Second edition},
	title = {Dynamic documents with {R} and knitr},
	isbn = {978-1-4987-1697-0 978-1-315-36070-6 978-1-4987-8739-0 978-1-315-38248-7},
	series = {The R series},
	abstract = {Quickly and Easily Write Dynamic Documents Suitable for both beginners and advanced users, Dynamic Documents with R and knitr, Second Edition makes writing statistical reports easier by integrating computing directly with reporting. Reports range from homework, projects, exams, books, blogs, and web pages to virtually any documents related to statistical graphics, computing, and data analysis. The book covers basic applications for beginners while guiding power users in understanding the extensibility of the knitr package. New to the Second Edition A new chapter that introduces R Markdown v2 Changes that reflect improvements in the knitr package New sections on generating tables, defining custom printing methods for objects in code chunks, the C/Fortran engines, the Stan engine, running engines in a persistent session, and starting a local server to serve dynamic documents Boost Your Productivity in Statistical Report Writing and Make Your Scientific Computing with R Reproducible Like its highly praised predecessor, this edition shows you how to improve your efficiency in writing reports. The book takes you from program output to publication-quality reports, helping you fine-tune every aspect of your report},
	pagetotal = {1},
	publisher = {{CRC} Press},
	author = {Xie, Yihui},
	date = {2015},
}
@inproceedings{Kluyver2016,
       booktitle = {Positioning and Power in Academic Publishing: Players, Agents and Agendas},
          editor = {Fernando Loizides and Birgit Scmidt},
           title = {Jupyter Notebooks – a publishing format for reproducible computational workflows},
          author = {Thomas Kluyver and Benjamin Ragan-Kelley and Fernando P{\'e}rez and Brian Granger and Matthias Bussonnier and Jonathan Frederic and Kyle Kelley and Jessica Hamrick and Jason Grout and Sylvain Corlay and Paul Ivanov and Dami{\'a}n Avila and Safia Abdalla and Carol Willing and {Jupyter development team}},
       publisher = {IOS Press},
         address = {Netherlands},
            year = {2016},
           pages = {87--90},
             doi = {10.3233/978-1-61499-649-1-87},
        abstract = {It is increasingly necessary for researchers in all fields to write computer code, and in order to reproduce research results, it is important that this code is published. We present Jupyter notebooks, a document format for publishing code, results and explanations in a form that is both readable and executable. We discuss various tools and use cases for notebook documents.}
}
@online{apsillers2019,
	title = {Answer to "Does "the {GPL} doesn't cover the output of a program" also apply if the output is source code?"},
	url = {https://opensource.stackexchange.com/a/8060/34940},
	shorttitle = {Answer to "Does "the {GPL} doesn't cover the output of a program" also apply if the output is source code?},
	titleaddon = {Open Source Stack Exchange},
	author = {apsillers},
	urldate = {2024-11-28},
	date = {2019-03-11},
}
@book{Fowler1999,
	title = {Refactoring: Improving the Design of Existing Code},
	shorttitle = {Refactoring},
	publisher = {Addison-Wesley},
	author = {Fowler, Martin and Beck, Kent and Opdyke, William and Roberts, Don},
	date = {1999},
}
@misc{Brown2016,
  author       = {Brown, Louise and
                  Crusoe, Michael R. and
                  Miļajevs, Dmitrijs and
                  Romanowska, Iza},
  title        = {{Should you cite this particular piece of software?}},
  year         = 2016,
  doi          = {10.5281/zenodo.2559142},
  url          = {https://mr-c.github.io/shouldacite/},
	howpublished = {\url{https://mr-c.github.io/shouldacite/}}
}
@article{Starr2015,
	title = {Achieving human and machine accessibility of cited data in scholarly publications},
	volume = {1},
	issn = {2376-5992},
	doi = {10.7717/peerj-cs.1},
	pages = {e1},
	journaltitle = {{PeerJ} Computer Science},
	author = {Starr, Joan and Castro, Eleni and Crosas, Mercè and Dumontier, Michel and Downs, Robert R. and Duerr, Ruth and Haak, Laurel L. and Haendel, Melissa and Herman, Ivan and Hodson, Simon and Hourclé, Joe and Kratz, John Ernest and Lin, Jennifer and Nielsen, Lars Holm and Nurnberger, Amy and Proell, Stefan and Rauber, Andreas and Sacchi, Simone and Smith, Arthur and Taylor, Mike and Clark, Tim},
	urldate = {2024-11-28},
	date = {2015-05-27},
	langid = {english},
}
@article{Smith2016,
	title = {Software citation principles},
	volume = {2},
	rights = {http://creativecommons.org/licenses/by/4.0/},
	issn = {2376-5992},
	url = {https://peerj.com/articles/cs-86},
	doi = {10.7717/peerj-cs.86},
	abstract = {Software is a critical part of modern research and yet there is little support across the scholarly ecosystem for its acknowledgement and citation. Inspired by the activities of the {FORCE}11 working group focused on data citation, this document summarizes the recommendations of the {FORCE}11 Software Citation Working Group and its activities between June 2015 and April 2016. Based on a review of existing community practices, the goal of the working group was to produce a consolidated set of citation principles that may encourage broad adoption of a consistent policy for software citation across disciplines and venues. Our work is presented here as a set of software citation principles, a discussion of the motivations for developing the principles, reviews of existing community practice, and a discussion of the requirements these principles would place upon different stakeholders. Working examples and possible technical solutions for how these principles can be implemented will be discussed in a separate paper.},
	pages = {e86},
	journaltitle = {{PeerJ} Computer Science},
	author = {Smith, Arfon M. and Katz, Daniel S. and Niemeyer, Kyle E. and {FORCE11 Software Citation Working Group}},
	urldate = {2024-11-28},
	date = {2016-09-19},
	langid = {english},
}
@online{Villa2016Copyleft,
	title = {Copyleft, attribution, and data: other considerations},
	url = {https://lu.is/2016/09/copyleft-attribution-and-data-other-considerations/},
	shorttitle = {Copyleft, attribution, and data},
	abstract = {Public licenses for databases don’t work well. Before going into solutions to that problem, though, I wanted to talk briefly about some things that are important to consider when thinking abo…},
	titleaddon = {Luis Villa: Open Tech and Policy},
	author = {Villa, Luis},
	urldate = {2024-12-04},
	date = {2016-09-21},
	langid = {american},
}
@online{Villa2016CC0,
	title = {Public licenses and data: So what to do instead?},
	url = {https://lu.is/2016/09/public-licenses-and-data-so-what-to-do-instead/},
	shorttitle = {Public licenses and data},
	abstract = {I just explained why open and copyleft licensing, which work fairly well in the software context, might not be legally workable, or practically a good idea, around data. So what to do instead? tl;d…},
	titleaddon = {Luis Villa: Open Tech and Policy},
	author = {Villa, Luis},
	urldate = {2024-12-04},
	date = {2016-09-26},
	langid = {american},
}
@online{Vezina2020,
	title = {Why Sharing Academic Publications Under “No Derivatives” Licenses is Misguided},
	url = {https://creativecommons.org/2020/04/21/academic-publications-under-no-derivatives-licenses-is-misguided/},
	abstract = {Using “No Derivatives” ({ND}) licenses on academic publications is ill-advised for policing academic fraud and unhelpful to the dissemination of research.},
	titleaddon = {Creative Commons},
	author = {Vézina, Brigitte},
	urldate = {2024-12-04},
	date = {2020-04-21},
	langid = {american},
}
@online{WikimediaCommons2009,
	title = {Licensing/Justifications},
	url = {https://commons.wikimedia.org/w/index.php?title=Commons:Licensing/Justifications&oldid=917608913},
	titleaddon = {Wikimedia Commons},
	author = {{Wikimedia Commons contributors}},
	urldate = {2024-12-04},
	date = {2009-06-30},
	langid = {english},
}

@misc{UKRN2023,
	title = {Rights Retention Strategy: a Primer from {UKRN}},
	rights = {https://creativecommons.org/licenses/by/4.0/legalcode},
	url = {https://osf.io/2ajsg},
	doi = {10.31219/osf.io/2ajsg},
	shorttitle = {Rights Retention Strategy},
	abstract = {This guide describes how authors can retain rights on their “author’s accepted manuscripts” using the Rights Retention Strategy.},
	publisher = {Open Science Framework},
	author = {{UK Reproducibility Network} and Eglen, Stephen},
	urldate = {2024-12-10},
	date = {2023-04-18},
}

@online{SPARC2006,
	title = {Author Rights: Using the {SPARC} Author Addendum},
	url = {https://sparcopen.org/our-work/author-rights/brochure-html/},
	shorttitle = {Author Rights},
	author = {{SPARC}},
	urldate = {2024-12-10},
	date = {2006},
	langid = {american},
}