IDEAS home Printed from https://ideas.repec.org/a/plo/pbio00/3000763.html
   My bibliography  Save this article

Low availability of code in ecology: A call for urgent action

Author

Listed:
  • Antica Culina
  • Ilona van den Berg
  • Simon Evans
  • Alfredo Sánchez-Tójar

Abstract

Access to analytical code is essential for transparent and reproducible research. We review the state of code availability in ecology using a random sample of 346 nonmolecular articles published between 2015 and 2019 under mandatory or encouraged code-sharing policies. Our results call for urgent action to increase code availability: only 27% of eligible articles were accompanied by code. In contrast, data were available for 79% of eligible articles, highlighting that code availability is an important limiting factor for computational reproducibility in ecology. Although the percentage of ecological journals with mandatory or encouraged code-sharing policies has increased considerably, from 15% in 2015 to 75% in 2020, our results show that code-sharing policies are not adhered to by most authors. We hope these results will encourage journals, institutions, funding agencies, and researchers to address this alarming situation.Publication of the analytical code underlying a scientific study is increasingly expected or even mandated by journals, allowing others to reproduce the results. However, a survey of more than 300 recently published ecology papers finds the majority have no code publicly available, handicapping efforts to improve scientific transparency.

Suggested Citation

  • Antica Culina & Ilona van den Berg & Simon Evans & Alfredo Sánchez-Tójar, 2020. "Low availability of code in ecology: A call for urgent action," PLOS Biology, Public Library of Science, vol. 18(7), pages 1-9, July.
    • Handle: RePEc:plo:pbio00:3000763
    DOI: 10.1371/journal.pbio.3000763
    as

    Download full text from publisher

    File URL: https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3000763
    Download Restriction: no
    File URL: https://journals.plos.org/plosbiology/article/file?id=10.1371/journal.pbio.3000763&type=printable
    Download Restriction: no
    File URL: https://libkey.io/10.1371/journal.pbio.3000763?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Leonard P Freedman & Iain M Cockburn & Timothy S Simcoe, 2015. "The Economics of Reproducibility in Preclinical Research," PLOS Biology, Public Library of Science, vol. 13(6), pages 1-9, June.
    2. Christopher Allen & David M A Mehler, 2019. "Open science challenges, benefits and tips in early career and beyond," PLOS Biology, Public Library of Science, vol. 17(5), pages 1-14, May.
    3. Christopher Allen & David M A Mehler, 2019. "Correction: Open science challenges, benefits and tips in early career and beyond," PLOS Biology, Public Library of Science, vol. 17(12), pages 1-1, December.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Akshay Gurdita & Heather Vovko & Mark Ungrin, 2016. "A Simple and Low-Cost Monitoring System to Investigate Environmental Conditions in a Biological Research Laboratory," PLOS ONE, Public Library of Science, vol. 11(1), pages 1-10, January.
    2. Dean A Fergusson & Marc T Avey & Carly C Barron & Mathew Bocock & Kristen E Biefer & Sylvain Boet & Stephane L Bourque & Isidora Conic & Kai Chen & Yuan Yi Dong & Grace M Fox & Ronald B George & Neil , 2019. "Reporting preclinical anesthesia study (REPEAT): Evaluating the quality of reporting in the preclinical anesthesiology literature," PLOS ONE, Public Library of Science, vol. 14(5), pages 1-15, May.
    3. Seibold, Heidi & Charlton, Alethea & Boulesteix, Anne-Laure & Hoffmann, Sabine, 2020. "Statisticians roll up your sleeves! There’s a crisis to be solved," MetaArXiv frta7, Center for Open Science.
    4. Watzinger, Martin & Schnitzer, Monika, 2019. "Standing on the Shoulders of Science," Rationality and Competition Discussion Paper Series 215, CRC TRR 190 Rationality and Competition.
    5. Colin F. Camerer & Anna Dreber & Felix Holzmeister & Teck-Hua Ho & Jürgen Huber & Magnus Johannesson & Michael Kirchler & Gideon Nave & Brian A. Nosek & Thomas Pfeiffer & Adam Altmejd & Nick Buttrick , 2018. "Evaluating the replicability of social science experiments in Nature and Science between 2010 and 2015," Nature Human Behaviour, Nature, vol. 2(9), pages 637-644, September.
    6. Tang, Xuli & Li, Xin & Ding, Ying & Song, Min & Bu, Yi, 2020. "The pace of artificial intelligence innovations: Speed, talent, and trial-and-error," Journal of Informetrics, Elsevier, vol. 14(4).
    7. Vivian Leung & Frédérik Rousseau-Blass & Guy Beauchamp & Daniel S J Pang, 2018. "ARRIVE has not ARRIVEd: Support for the ARRIVE (Animal Research: Reporting of in vivo Experiments) guidelines does not improve the reporting quality of papers in animal welfare, analgesia or anesthesi," PLOS ONE, Public Library of Science, vol. 13(5), pages 1-13, May.
    8. Muradchanian, Jasmine & Hoekstra, Rink & Kiers, Henk & van Ravenzwaaij, Don, 2020. "How Best to Quantify Replication Success? A Simulation Study on the Comparison of Replication Success Metrics," MetaArXiv wvdjf_v1, Center for Open Science.
    9. Shuaijun Guo & Xiaoming Yu & Orkan Okan, 2020. "Moving Health Literacy Research and Practice towards a Vision of Equity, Precision and Transparency," IJERPH, MDPI, vol. 17(20), pages 1-14, October.
    10. Rosa Virginia Encinas Quille & Felipe Valencia de Almeida & Mauro Yuji Ohara & Pedro Luiz Pizzigatti Corrêa & Leandro Gomes de Freitas & Solange Nice Alves-Souza & Jorge Rady de Almeida & Maggie Davis, 2023. "Architecture of a Data Portal for Publishing and Delivering Open Data for Atmospheric Measurement," IJERPH, MDPI, vol. 20(7), pages 1-20, April.
    11. Kiri, Bralind & Lacetera, Nicola & Zirulia, Lorenzo, 2018. "Above a swamp: A theory of high-quality scientific production," Research Policy, Elsevier, vol. 47(5), pages 827-839.
    12. Mueller-Langer, Frank & Fecher, Benedikt & Harhoff, Dietmar & Wagner, Gert G., 2019. "Replication studies in economics—How many and which papers are chosen for replication, and why?," Research Policy, Elsevier, vol. 48(1), pages 62-83.
    13. Julia Koehler Leman & Sergey Lyskov & Steven M. Lewis & Jared Adolf-Bryfogle & Rebecca F. Alford & Kyle Barlow & Ziv Ben-Aharon & Daniel Farrell & Jason Fell & William A. Hansen & Ameya Harmalkar & Je, 2021. "Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks," Nature Communications, Nature, vol. 12(1), pages 1-15, December.
    14. Malika Ihle & Isabel S. Winney & Anna Krystalli & Michael Croucher, 2017. "Striving for transparent and credible research: practical guidelines for behavioral ecologists," Behavioral Ecology, International Society for Behavioral Ecology, vol. 28(2), pages 348-354.
    15. Jens Rommel & Meike Weltin, 2021. "Is There a Cult of Statistical Significance in Agricultural Economics?," Applied Economic Perspectives and Policy, John Wiley & Sons, vol. 43(3), pages 1176-1191, September.
    16. Bernhard Voelkl & Lucile Vogt & Emily S Sena & Hanno Würbel, 2018. "Reproducibility of preclinical animal research improves with heterogeneity of study samples," PLOS Biology, Public Library of Science, vol. 16(2), pages 1-13, February.
    17. Muradchanian, Jasmine & Hoekstra, Rink & Kiers, Henk & van Ravenzwaaij, Don, 2020. "How Best to Quantify Replication Success? A Simulation Study on the Comparison of Replication Success Metrics," MetaArXiv wvdjf, Center for Open Science.
    18. Wang, Xuefeng & Zhang, Shuo & Liu, Yuqin & Du, Jian & Huang, Heng, 2021. "How pharmaceutical innovation evolves: The path from science to technological development to marketable drugs," Technological Forecasting and Social Change, Elsevier, vol. 167(C).
    19. Martin Backfisch, 2018. "The Development of Firm Size and Innovativeness in the Pharmaceutical industry between 1989 and 2010," MAGKS Papers on Economics 201813, Philipps-Universität Marburg, Faculty of Business Administration and Economics, Department of Economics (Volkswirtschaftliche Abteilung).
    20. Matthias Steinfath & Silvia Vogl & Norman Violet & Franziska Schwarz & Hans Mielke & Thomas Selhorst & Matthias Greiner & Gilbert Schönfelder, 2018. "Simple changes of individual studies can improve the reproducibility of the biomedical scientific process as a whole," PLOS ONE, Public Library of Science, vol. 13(9), pages 1-20, September.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:plo:pbio00:3000763. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: plosbiology (email available below). General contact details of provider: https://journals.plos.org/plosbiology/ .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.