IDEAS home Printed from https://ideas.repec.org/a/eee/infome/v12y2018i1p87-100.html
   My bibliography  Save this article

Co-mention network of R packages: Scientific impact and clustering structure

Author

Listed:
  • Li, Kai
  • Yan, Erjia

Abstract

Despite its rising position as a first-class research object, scientific software remains a marginal object in studies of scholarly communication. This study aims to fill the gap by examining the co-mention network of R packages across all Public Library of Science (PLoS) journals. To that end, we developed a software entity extraction method and identified 14,310 instances of R packages across the 13,684 PLoS journal papers mentioning or citing R. A paper-level co-mention network of these packages was visualized and analyzed using three major centrality measures: degree centrality, betweenness centrality, and PageRank. We analyzed the distributive patterns of R packages in all PLoS papers, identified the top packages mentioned in these papers, and examined the clustering structure of the network. Specifically, we found that the discipline and function of the packages can partly explain the largest clusters. The present study offers the first large-scale analysis of R packages’ extensive use in scientific research. As such, it lays the foundation for future explorations of various roles played by software packages in the scientific enterprise.

Suggested Citation

  • Li, Kai & Yan, Erjia, 2018. "Co-mention network of R packages: Scientific impact and clustering structure," Journal of Informetrics, Elsevier, vol. 12(1), pages 87-100.
  • Handle: RePEc:eee:infome:v:12:y:2018:i:1:p:87-100
    DOI: 10.1016/j.joi.2017.12.001
    as

    Download full text from publisher

    File URL: http://www.sciencedirect.com/science/article/pii/S1751157717304108
    Download Restriction: Full text for ScienceDirect subscribers only

    File URL: https://libkey.io/10.1016/j.joi.2017.12.001?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
    ---><---

    As the access to this document is restricted, you may want to search for a different version of it.

    References listed on IDEAS

    as
    1. Chang-Ping Hu & Ji-Ming Hu & Yan Gao & Yao-Kun Zhang, 2011. "A journal co-citation analysis of library and information science in China," Scientometrics, Springer;Akadémiai Kiadó, vol. 86(3), pages 657-670, March.
    2. Henry Small, 1973. "Co‐citation in the scientific literature: A new measure of the relationship between two documents," Journal of the American Society for Information Science, Association for Information Science & Technology, vol. 24(4), pages 265-269, July.
    3. Pan, Xuelian & Yan, Erjia & Wang, Qianqian & Hua, Weina, 2015. "Assessing the impact of software on science: A bootstrapped learning of software entities in full-text papers," Journal of Informetrics, Elsevier, vol. 9(4), pages 860-871.
    4. Erjia Yan & Ying Ding, 2009. "Applying centrality measures to impact analysis: A coauthorship network analysis," Journal of the American Society for Information Science and Technology, Association for Information Science & Technology, vol. 60(10), pages 2107-2118, October.
    5. Ming-yueh Tsay & Hong Xu & Chia-wen Wu, 2003. "Journal co-citation analysis of semiconductor literature," Scientometrics, Springer;Akadémiai Kiadó, vol. 57(1), pages 7-25, May.
    6. Per Ahlgren & Bo Jarneving & Ronald Rousseau, 2003. "Requirements for a cocitation similarity measure, with special reference to Pearson's correlation coefficient," Journal of the American Society for Information Science and Technology, Association for Information Science & Technology, vol. 54(6), pages 550-560, April.
    7. Rongying Zhao & Mingkun Wei, 2017. "Impact evaluation of open source software: an Altmetrics perspective," Scientometrics, Springer;Akadémiai Kiadó, vol. 110(2), pages 1017-1033, February.
    8. Ying Ding & Gobinda G. Chowdhury & Schubert Foo, 2000. "Journal as Markers of Intellectual Space: Journal Co-Citation Analysis of Information Retrieval Area, 1987–1997," Scientometrics, Springer;Akadémiai Kiadó, vol. 47(1), pages 55-73, January.
    9. Li, Kai & Yan, Erjia & Feng, Yuanyuan, 2017. "How is R cited in research outputs? Structure, impacts, and citation standard," Journal of Informetrics, Elsevier, vol. 11(4), pages 989-1002.
    10. Darrel C. Ince & Leslie Hatton & John Graham-Cumming, 2012. "The case for open computer programs," Nature, Nature, vol. 482(7386), pages 485-488, February.
    11. Nees Jan Eck & Ludo Waltman, 2010. "Software survey: VOSviewer, a computer program for bibliometric mapping," Scientometrics, Springer;Akadémiai Kiadó, vol. 84(2), pages 523-538, August.
    12. Katherine W. McCain, 1990. "Mapping authors in intellectual space: A technical overview," Journal of the American Society for Information Science, Association for Information Science & Technology, vol. 41(6), pages 433-443, September.
    13. Zao Liu, 2005. "Visualizing the intellectual structure in urban studies: A journal co-citation analysis (1992-2002)," Scientometrics, Springer;Akadémiai Kiadó, vol. 62(3), pages 385-402, March.
    14. Howard D. White & Belver C. Griffith, 1981. "Author cocitation: A literature measure of intellectual structure," Journal of the American Society for Information Science, Association for Information Science & Technology, vol. 32(3), pages 163-171, May.
    15. Xuelian Pan & Erjia Yan & Weina Hua, 2016. "Disciplinary differences of software use and impact in scientific literature," Scientometrics, Springer;Akadémiai Kiadó, vol. 109(3), pages 1593-1610, December.
    16. Howard D. White & Katherine W. McCain, 1998. "Visualizing a discipline: An author co‐citation analysis of information science, 1972–1995," Journal of the American Society for Information Science, Association for Information Science & Technology, vol. 49(4), pages 327-355.
    Full references (including those not matched with items on IDEAS)

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Li, Kai & Chen, Pei-Ying & Yan, Erjia, 2019. "Challenges of measuring software impact through citations: An examination of the lme4 R package," Journal of Informetrics, Elsevier, vol. 13(1), pages 449-461.
    2. Wang, Yuzhuo & Zhang, Chengzhi, 2020. "Using the full-text content of academic articles to identify and evaluate algorithm entities in the domain of natural language processing," Journal of Informetrics, Elsevier, vol. 14(4).
    3. Yuzhuo Wang & Chengzhi Zhang & Kai Li, 2022. "A review on method entities in the academic literature: extraction, evaluation, and application," Scientometrics, Springer;Akadémiai Kiadó, vol. 127(5), pages 2479-2520, May.
    4. Esther Prieto-Jiménez & Luis López-Catalán & Blanca López-Catalán & Guillermo Domínguez-Fernández, 2021. "Sustainable Development Goals and Education: A Bibliometric Mapping Analysis," Sustainability, MDPI, vol. 13(4), pages 1-20, February.
    5. Enrique Orduña-Malea & Rodrigo Costas, 2021. "Link-based approach to study scientific software usage: the case of VOSviewer," Scientometrics, Springer;Akadémiai Kiadó, vol. 126(9), pages 8153-8186, September.
    6. Alsudais, Abdulkareem, 2021. "In-code citation practices in open research software libraries," Journal of Informetrics, Elsevier, vol. 15(2).
    7. Xiao Han & Chu Wei, 2021. "Household energy consumption: state of the art, research gaps, and future prospects," Environment, Development and Sustainability: A Multidisciplinary Approach to the Theory and Practice of Sustainable Development, Springer, vol. 23(8), pages 12479-12504, August.

    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. Jun-Ping Qiu & Ke Dong & Hou-Qiang Yu, 2014. "Comparative study on structure and correlation among author co-occurrence networks in bibliometrics," Scientometrics, Springer;Akadémiai Kiadó, vol. 101(2), pages 1345-1360, November.
    2. Ying Huang & Wolfgang Glänzel & Lin Zhang, 2021. "Tracing the development of mapping knowledge domains," Scientometrics, Springer;Akadémiai Kiadó, vol. 126(7), pages 6201-6224, July.
    3. Zhigao Liu & Yimei Yin & Weidong Liu & Michael Dunford, 2015. "Visualizing the intellectual structure and evolution of innovation systems research: a bibliometric analysis," Scientometrics, Springer;Akadémiai Kiadó, vol. 103(1), pages 135-158, April.
    4. Perianes-Rodriguez, Antonio & Waltman, Ludo & van Eck, Nees Jan, 2016. "Constructing bibliometric networks: A comparison between full and fractional counting," Journal of Informetrics, Elsevier, vol. 10(4), pages 1178-1195.
    5. Yun, Jinhyuk & Ahn, Sejung & Lee, June Young, 2020. "Return to basics: Clustering of scientific literature using structural information," Journal of Informetrics, Elsevier, vol. 14(4).
    6. Francisco García-Lillo & Enrique Claver-Cortés & Bartolomé Marco-Lajara & Mercedes Úbeda-García, 2017. "Mapping the Intellectual Structure of Research on ‘Born Global’ Firms and INVs: A Citation/Co-citation Analysis," Management International Review, Springer, vol. 57(4), pages 631-652, August.
    7. Kraker, Peter & Schlögl, Christian & Jack, Kris & Lindstaedt, Stefanie, 2015. "Visualization of co-readership patterns from an online reference management system," Journal of Informetrics, Elsevier, vol. 9(1), pages 169-182.
    8. Hsiao, Chun Hua & Yang, Chyan, 2011. "The intellectual development of the technology acceptance model: A co-citation analysis," International Journal of Information Management, Elsevier, vol. 31(2), pages 128-136.
    9. Worapan Kusakunniran & Amit Singh Dahal & Wantanee Viriyasitavat, 2018. "Journal Co-Citation Analysis for Identifying Trends of Inter-Disciplinary Research: An Exploratory Case Study in a University," Journal of Information & Knowledge Management (JIKM), World Scientific Publishing Co. Pte. Ltd., vol. 17(04), pages 1-22, December.
    10. Mora, Luca & Deakin, Mark & Reid, Alasdair, 2019. "Combining co-citation clustering and text-based analysis to reveal the main development paths of smart cities," Technological Forecasting and Social Change, Elsevier, vol. 142(C), pages 56-69.
    11. Chang-Ping Hu & Ji-Ming Hu & Yan Gao & Yao-Kun Zhang, 2011. "A journal co-citation analysis of library and information science in China," Scientometrics, Springer;Akadémiai Kiadó, vol. 86(3), pages 657-670, March.
    12. Shiau, Wen-Lung & Dwivedi, Yogesh K. & Yang, Han Suan, 2017. "Co-citation and cluster analyses of extant literature on social networks," International Journal of Information Management, Elsevier, vol. 37(5), pages 390-399.
    13. Pan, Xuelian & Yan, Erjia & Cui, Ming & Hua, Weina, 2018. "Examining the usage, citation, and diffusion patterns of bibliometric mapping software: A comparative study of three tools," Journal of Informetrics, Elsevier, vol. 12(2), pages 481-493.
    14. Enrique Orduña-Malea & Rodrigo Costas, 2021. "Link-based approach to study scientific software usage: the case of VOSviewer," Scientometrics, Springer;Akadémiai Kiadó, vol. 126(9), pages 8153-8186, September.
    15. Bruno Miranda Henrique & Vinicius Amorim Sobreiro & Herbert Kimura, 2018. "Building direct citation networks," Scientometrics, Springer;Akadémiai Kiadó, vol. 115(2), pages 817-832, May.
    16. Zhao, Dangzhi & Strotmann, Andreas, 2008. "Comparing all-author and first-author co-citation analyses of information science," Journal of Informetrics, Elsevier, vol. 2(3), pages 229-239.
    17. Dzikowski, Piotr, 2018. "A bibliometric analysis of born global firms," Journal of Business Research, Elsevier, vol. 85(C), pages 281-294.
    18. Chaoqun Ni & Cassidy R. Sugimoto & Jiepu Jiang, 2013. "Venue-author-coupling: A measure for identifying disciplines through author communities," Journal of the Association for Information Science & Technology, Association for Information Science & Technology, vol. 64(2), pages 265-279, February.
    19. Markus Gmür, 2003. "Co-citation analysis and the search for invisible colleges: A methodological evaluation," Scientometrics, Springer;Akadémiai Kiadó, vol. 57(1), pages 27-57, January.
    20. Koseoglu, Mehmet Ali & Rahimi, Roya & Okumus, Fevzi & Liu, Jingyan, 2016. "Bibliometric studies in tourism," Annals of Tourism Research, Elsevier, vol. 61(C), pages 180-198.

    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:eee:infome:v:12:y:2018:i:1:p:87-100. 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: Catherine Liu (email available below). General contact details of provider: http://www.elsevier.com/locate/joi .

    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.