references.bib

@misc{baker2015,
  title={First results from psychology's largest reproducibility test},
  author={M Baker},
  journal={Nature News},
  year={2015},
  url = {https://doi.org/10.1038/nature.2015.17433}
}

@article{baker2016,
  title={1,500 scientists lift the lid on reproducibility},
  volume={533},
  url={http://dx.doi.org/10.1038/533452a},
  DOI={10.1038/533452a},
  number={7604},
  journal={Nature},
  publisher={Springer Science and Business Media LLC},
  author={Baker, Monya},
  year={2016},
  month={May},
  pages={452–454}
}

@article{barba2021,
  author = {Barba, Lorena A},
  doi = {10.1109/MCSE.2020.3048406},
  journal = {Computing in Science {\&} Engineering},
  number = {1},
  pages = {58--64},
  title = {{Trustworthy Computational Evidence Through Transparency and Reproducibility}},
  url = {https://ieeexplore.ieee.org/document/9364769/},
  volume = {23},
  year = {2021}
}


@misc{barthez2020,
  title={Passport For Open Science},
  author={Anne-Sophie Baker and Bernard Larrouturou},
  publisher={University of Lille},
  year={2020},
  url = {https://www.ouvrirlascience.fr/passport-for-open-science-a-practical-guide-for-phd-students/}
}



@article{baker2017,
  title={Check your chemistry},
  author={M Baker},
  journal={Nature},
  volume={548},
  number={7668},
  pages={485-488},
  year={2017},
  url={https://doi.org/10.1038/548485a}
}

@misc{barba2018,
  title={Terminologies for Reproducible Research},
  author={L Barba},
  year={2018},
  journal={arXiv preprint arXiv:1802.03311},
  url={https://arxiv.org/abs/1802.03311}
}

@book{biggs2011,
  author={John Biggs and Catherine Tang},
  title={Teaching for Quality Learning at University, 4th edition},
  year={2011},
  publisher={Open University Press},
  isbn={978-0335242757}
}


@article{bion2018,
  author = {R Bion and R Chang and J Goodman},
  title = {How R Helps Airbnb Make the Most of its Data},
  journal = {The American Statistician},
  volume = {72},
  number = {1},
  pages = {46-52},
  year  = {2018},
  publisher = {Taylor & Francis},
  doi = {10.1080/00031305.2017.1392362},
  url = {https://doi.org/10.1080/00031305.2017.1392362}
}

@article{button2013,
  title={Power failure: why small sample size undermines the reliability of neuroscience},
  author={Button, KS and Ioannidis, JPA and Mokrysz, C and Nosek, BA and Flint, J and Robinson, ESJ and Munaf{\`o}, MR},
  journal={Nature Reviews Neuroscience},
  volume={14},
  number={5},
  pages={365-376},
  year={2013},
  publisher={Nature Publishing Group},
  url={https://doi.org/10.1038/nrn3475}
}


@book{bryan2020,
  author={Jenny Bryan and Jim Hester},
  title={Happy Git and GitHub for the useR},
  year={2020},
  url={https://happygitwithr.com/}
}

@article{callaghan2014,
  title={Joint declaration of data citation principles},
  author={Callaghan, S},
  year={2014},
  url={https://www.force11.org/datacitationprinciples}
}

@incollection{claerbout1992,
  title={Electronic documents give reproducible research a new meaning},
  author={Claerbout, JF and Karrenbach, M},
  booktitle={SEG Technical Program Expanded Abstracts 1992},
  pages={601--604},
  year={1992},
  publisher={Society of Exploration Geophysicists},
  url={https://doi.org/10.1190/1.1822162}
}


@misc{cooper2019,
  title={Reproducible code},
  author={Natalie Cooper and Pen-Yuah Hsing},
  publisher={British Ecological Society},
  year={2019},
  url = {https://www.britishecologicalsociety.org/publications/guides-to/}
}

@article{donoho2009,
  title={Reproducible research in computational harmonic analysis},
  author={DL Donoho and A Maleki and IU Rahman and M Shahram and V Stodden},
  journal={Computing in Science & Engineering},
  volume={11},
  number={1},
  pages={8-18},
  year={2009},
  url={https://doi.org/10.1109/MCSE.2009.15}
}

@article{fanelli2018,
  title={Opinion: Is science really facing a reproducibility crisis, and do we need it to?},
  author={Fanelli, D},
  journal={Proceedings of the National Academy of Sciences},
  volume={115},
  number={11},
  pages={2628--2631},
  year={2018},
  publisher={National Acad Sciences},
  url={https://doi.org/10.1073/pnas.1708272114}
}

@article{granell2018,
  title = {Reproducible Research is like riding a bike},
  author = {C Granell and D Nust and FO Ostermann and R Sileryte},
  journal = {PeerJ Preprints},
  year = {2018},
  volume = {6},
  pages = {e27216v1},
  url = {https://doi.org/10.7287/peerj.preprints.27216v1}
}

@misc{granell2019,
  title={Directrices para articulos reproducibles},
  author={C Granell},
  year={2019},
  url={https://doi.org/10.17605/OSF.IO/MF9BE}
}

@article{granell2020,
  title = {Reproducibilidad en AGILE: Experiencias, logros y recomendaciones},
  author = {C Granell and B Hofer and D Nust and FO Ostermann and R Sileryte},
  journal = {Revista Cartogr{\'a}fica},
  year = {2020},
  number = {100},
  pages = {155-172},
  doi = {10.35424/rcarto.i100.668},
  url = {https://doi.org/10.35424/rcarto.i100.668}
}

@misc{harrison2018,
  title={Data management},
  author={Kate Harrison},
  publisher={British Ecological Society},
  year={2018},
  url = {https://www.britishecologicalsociety.org/publications/guides-to/}
}

@article{hong2015,
  title={Top tips to make your research irreproducible},
  author={Hong, NPC and Crick, T and Gent, IP and Kotthoff, L and Takeda, K},
  journal={arXiv preprint arXiv:1504.00062},
  eprint={1504.00062},
  year={2015},
  url={https://arxiv.org/abs/1504.00062}
}

@article{ioannidis2005,
  title = {Why most published research findings are false},
  author = {JP Ioannidis},
  journal = {PLOS Medicine},
  year = {2005},
  volume = {2},
  number = {8},
  pages = {e124},
  url = {https://doi.org/10.1371/journal.pmed.0020124}
}


@article{ioannidis2017,
  title = {The Power of Bias in Economics Research},
  author = {JP Ioannidis and TD Stanley and H Doucouliagos},
  journal = {The Economic Journal},
  year = {2017},
  volume = {127},
  number = {605},
  pages = {F236-F265},
  url = {https://doi.org/10.1111/ecoj.12461}
}

@article{jolly2012,
  title={Ten Simple Rules to Protect Your Intellectual Property},
  author={M Jolly and AC Fletcher AC and PE Bourne},
  journal={PLoS Computacional Biology},
  volume={8},
  issue={11},
  pages={e1002766},
  year={2012},
  url={https://dx.doi.org/10.1371/journal.pcbi.1002766}
}

@article{knuth1984,
  title = {Literate Programming},
  author = {DE Knuth},
  journal = {The Computer Journal},
  year = {1984},
  volume = {11},
  number = {2},
  pages = {97-111},
  url = {https://doi.org/10.1093/comjnl/27.2.97},
}


@article{leek2017,
  title = {Is Most Published Research Really False?},
  author = {JT Leek and LR Jager},
  journal = {Annual Review of Statistics and Its Application},
  year = {2017},
  volume = {4},
  pages = {109-122},
  url = {https://doi.org/10.1146/annurev-statistics-060116-054104}
}

@article{macleod2021,
  title={The MDAR (Materials Design Analysis Reporting) Framework for transparent reporting in the life sciences},
  volume={118},
  url={http://dx.doi.org/10.1073/pnas.2103238118},
  DOI={10.1073/pnas.2103238118},
  number={17},
  journal={Proceedings of the National Academy of Sciences},
  publisher={Proceedings of the National Academy of Sciences},
  author={Macleod, Malcolm and Collings, Andrew M. and Graf, Chris and Kiermer, Veronique and Mellor, David and Swaminathan, Sowmya and Sweet, Deborah and Vinson, Valda},
  year={2021},
  month={Apr},
  pages={e2103238118}
}


@article{markowetz2015,
  title={Five selfish reasons to work reproducibly},
  author={F Markowetz},
  journal={Genome Biology},
  volume={16},
  pages={274},
  year={2015},
  url={https://doi.org/10.1186/s13059-015-0850-7}
}

@article{miralles2020,
  author={Miralles, Ignacio and Granell, Carlos and D{\'i}az-Sanahuja, Laura and Van Woensel, William and Bret{\'o}n-L{\'o}pez, Juana and Mira, Adriana and Castilla, Diana and Casteleyn, Sven},
  title={Smartphone Apps for the Treatment of Mental Disorders: Systematic Review},
  journal={JMIR Mhealth Uhealth},
  year={2020},
  month={Apr},
  day={2},
  volume={8},
  number={4},
  pages={e14897},
  issn={2291-5222},
  doi={10.2196/14897},
  url={https://doi.org/10.2196/14897}
}



@article{morin2012,
  title={A Quick Guide to Software Licensing for the Scientist-Programmer},
  author={A Morin and J Urban and P Sliz},
  journal={PLoS Computacional Biology},
  volume={8},
  number={7},
  pages={e1002598},
  year={2012},
  url={https://dx.doi.org/10.1371/journal.pcbi.1002598}
}


@book{NAP2019,
  author={National Academies of Sciences, Engineering, and Medicine},
  title={Reproducibility and Replicability in Science},
  isbn={978-0-309-48616-3},
  doi={10.17226/25303},
  url={https://www.nap.edu/catalog/25303/reproducibility-and-replicability-in-science},
  year={2019},
  publisher={The National Academies Press}
}

@article{nature2021,
  author={Editorial},
  title={Good research begins long before papers get written},
  volume={593},
  url={http://dx.doi.org/10.1038/d41586-021-01167-9},
  DOI={10.1038/d41586-021-01167-9},
  number={7857},
  journal={Nature},
  publisher={Springer Science and Business Media LLC},
  year={2021},
  month={Apr},
  pages={8–8}
}


@article{nosek2020,
  author = {Nosek, Brian A. and Errington, Timothy M.},
  doi = {10.1371/journal.pbio.3000691},
  issn = {1545-7885},
  journal = {PLOS Biology},
  keywords = {Replication,Reproducible science},
  month = {mar},
  number = {3},
  pages = {e3000691},
  title = {{What is replication?}},
  url = {http://dx.doi.org/10.1371/journal.pbio.3000691 https://dx.plos.org/10.1371/journal.pbio.3000691},
  volume = {18},
  year = {2020}
}


@article{noy2019,
  title={Let go of your data},
  volume={19},
  url={http://dx.doi.org/10.1038/s41563-019-0539-5},
  doi={10.1038/s41563-019-0539-5},
  number={1},
  journal={Nature Materials},
  publisher={Springer Science and Business Media LLC},
  author={Noy, Natasha and Noy, Aleksandr}, year
  ={2019},
  month={Dec},
  pages={128–128}
}

@article{nust2018,
  title={Reproducible research and GIScience: an evaluation using AGILE conference papers},
  author={D Nust and C Granell and B Hofer and M Konkol and FO Ostermann and R Sileryte and V Cerutti},
  journal={PeerJ},
  volume={6},
  pages={e5072},
  year={2018},
  url={https://doi.org/10.7717/peerj.5072}
}

@misc{nust2019,
  title={AGILE Reproducible Paper Guidelines},
  author={D Nust and FO Ostermann and R Sileryte and B Hofer and C Granell and M Teperek and A Graser and K Broman and K Hettne},
  year={2018},
  url={https://doi.org/10.17605/OSF.IO/CB7Z8}
}

@article{nust2021,
  author = {N{\"{u}}st, Daniel and Eglen, Stephen J},
  doi = {10.12688/f1000research.51738.1},
  issn = {2046-1402},
  journal = {F1000Research},
  month = {mar},
  pages = {253},
  title = {{CODECHECK: an Open Science initiative for the independent execution of computations underlying research articles during peer review to improve reproducibility}},
  url = {https://f1000research.com/articles/10-253/v1},
  volume = {10},
  year = {2021}
}


@article{ostermann2017,
  title={Advancing science with VGI: Reproducibility and replicability of recent studies using VGI},
  author={Ostermann, FO and Granell, C},
  journal={Transactions in GIS},
  volume={21},
  number={2},
  pages={224--237},
  year={2017},
  publisher={Wiley Online Library},
  url={https://doi.org/10.1111/tgis.12195}
}


@misc{ostermann2020,
  title={Reproducible Research and GIScience: an evaluation using GIScience conference papers},
  url={http://dx.doi.org/10.31223/X5ZK5V},
  DOI={10.31223/x5zk5v},
  publisher={California Digital Library (CDL)},
  author={Ostermann, Frank and Nüst, Daniel and Granell, Carlos and Hofer, Barbara and Konkol, Markus},
  year={2020},
  month={Oct}
}

@article{parsons2019,
  title={The History and Future of Data Citation in Practice},
  author={Parsons, MA and Duerr, RE and Jones, MB},
  journal={Data Science Journal},
  volume={18},
  number={1},
  year={2019},
  publisher={Ubiquity Press},
  url={https://doi.org/10.5334/dsj-2019-052}
}

@article{peng2011,
  title = {Reproducible Research in Computational Science},
  author = {RD Peng},
  journal = {Science},
  year = {2011},
  volume = {334},
  number = {6060},
  pages = {1226-1227},
  url = {https://doi.org/10.1126/science.1213847},
}

@article{perez2016,
  title={Ten simple rules for taking advantage of Git and GitHub},
  author={Perez-Riverol, Y and Gatto, L and Wang, R and Sachsenberg, T and Uszkoreit, J and da Veiga Leprevost, F and Fufezan, C and Ternent, T and Eglen, SJ and Katz, DS and others},
  journal={PLoS computational biology},
  volume={12},
  number={7},
  year={2016},
  publisher={Public Library of Science},
  url={https://doi.org/10.1371/journal.pcbi.1004947}
}

@article{rule2019,
  title={Ten simple rules for reproducible research in Jupyter notebooks},
  author={Rule, A and Birmingham, A and Zuniga, C and Altintas, I and Huang, SC and Knight, R and Moshiri, N and Nguyen, MH and Rosenthal, SB and P{\'e}rez, F and others},
  journal={PLoS computational biology},
  volume={15},
  number={7},
  pages={ e1007007},
  year={2019},
  url={https://dx.doi.org/10.1371/journal.pcbi.1007007}
}

@article{sandve2013,
  title={Ten simple rules for reproducible computational research},
  author={GK Sandve and A Nekrutenko and J Taylor and E Hovig},
  journal={PLoS Computacional Biology},
  volume={9},
  number={10},
  pages={e1003285},
  year={2017},
  url={https://dx.doi.org/10.1371/journal.pcbi.1003285}
}

@article{smith2016,
  title={Software citation principles},
  author={Smith, AM and Katz, DS and Niemeyer, KE},
  journal={PeerJ Computer Science},
  volume={2},
  pages={e86},
  year={2016},
  publisher={PeerJ Inc.},
  url={https://doi.org/10.7717/peerj-cs.86}
}

@article{stark2018,
  title={Before reproducibility must come preproducibility},
  author={Stark, PB},
  journal={Nature},
  volume={557},
  number={7706},
  pages={613--614},
  year={2018},
  publisher={Nature Publishing Group},
  url={https://doi.org/10.1038/d41586-018-05256-0}
}

@article{stodden2014,
  title={Best Practices for Computational Science: Software Infrastructure and Environments for Reproducible and Extensible Research},
  author={Stodden, V and Miguez, SB},
  journal={Journal of Open Research Software},
  volume={2},
  number={1},
  pages={e21},
  year={2014},
  url={https://doi.org/10.5334/jors.ay}
}


@article{tenopir2011,
  author = {Tenopir, C and Allard, S and Douglass, K and Aydinoglu, AU and Wu, L and Read, E and Manoff, M and Frame, M},
  title = {Data Sharing by Scientists: Practices and Perceptions},
  journal = {PLoS ONE},
  number = {6},
  pages = {e21101},
  pmid = {21738610},
  url = {https://doi.org/10.1371/journal.pone.0021101},
  volume = {6},
  year = {2011},
  doi = {10.1371/journal.pone.0021101}
}


@article{tenopir2015,
  author = {Tenopir, C and Dalton, ED and Allard, S and Frame, M and Pjesivac, I and Birch, B and Pollock, D and Dorsett, K},
  doi = {10.1371/journal.pone.0134826},
  journal = {PLoS ONE},
  number = {8},
  pages = {e0134826},
  title = {Changes in data sharing and data reuse practices and perceptions among scientists worldwide},
  url = {https://doi.org/10.1371/journal.pone.0134826},
  volume = {10},
  year = {2015}
}


@article{tenopir2020,
  title={Data sharing, management, use, and reuse: Practices and perceptions of scientists worldwide},
  author={Tenopir, C and Rice, NM and Allard, S and Baird, L and Borycz, J and Christian, L and Grant, B and Olendorf, R and Sandusky, RJ},
  journal={PLoS ONE},
  volume={15},
  number={3},
  pages={e0229003},
  year={2020},
  publisher={Public Library of Science San Francisco, CA USA},
  url={https://doi.org/10.1371/journal.pone.0229003}
}

@article{turingway2019,
  title={The Turing Way: A Handbook for Reproducible Data Science},
  doi={10.5281/zenodo.3233986},
  url={https://the-turing-way.netlify.app/welcome.html},
  publisher={Zenodo},
  author={{The Turing Way Community} and Becky Arnold and Louise Bowler and Sarah Gibson and Patricia Herterich and Rosie Higman and Anna Krystalli and Alexander Morley and Martin O\'Reilly and Kirstie Whitaker and et al.},
  year={2019},
  month={Mar},
  note={This work was supported by The UKRI Strategic Priorities Fund under the EPSRC Grant EP/T001569/, particularly the "Tools, Practices and Systems" theme within that grant, and by The Alan Turing Institute under the EPSRC grant EP/N510129/1.}
}

@article{vasilevsky2017,
  title={Reproducible and reusable research: are journal data sharing policies meeting the mark?},
  author={NA Vasilevsky and J Minnier and MA Haendel and RE Champieux},
  journal={PeerJ},
  volume={5},
  pages={e3208},
  year={2017},
  url={https://doi.org/10.7717/peerj.3208}
}

@article{wilson2017,
  title={Good enough practices in scientific computing},
  author={G Wilson and J Bryan and K Cranston and J Kitzes and L Nederbragt and TK Teal},
  journal={PLoS Computacional Biology},
  volume={13},
  number={6},
  pages={e1005510},
  year={2017},
  url={https://dx.doi.org/10.1371/journal.pcbi.1005510}
}


@book{wilson2019,
  author={Greg Wilson},
  title={Teaching Tech Together: How to make lessons that work and build a teaching community around it},
  isbn={978-0-367-35328-5},
  url={https://teachtogether.tech/},
  year={2019},
  publisher={Taylor & Francis}
}


@book{xie2018,
  title={R markdown: The definitive guide},
  author={Xie, Y and Allaire, JJ and Grolemund, G},
  year={2018},
  publisher={CRC Press},
  url={https://bookdown.org/yihui/rmarkdown/}
}


@book{xie2019,
  title={bookdown: Authoring Books and Technical Documents with R Markdown},
  author={Xie, Y},
  year={2019},
  publisher={CRC Press},
  url={https://bookdown.org/yihui/bookdown/}
}