Interactive RShiny Reports – Independence and Autonomy in Medical Data Visualization
DOI:
https://doi.org/10.31261/IJREL.2024.10.1.03Keywords:
RShiny, R, data visualization, interactive report, statistics, medical teachingAbstract
The article discusses the use of the R language, especially the RShiny tool, to create interactive reports in the field of medical data analysis. The authors emphasize the need for an interdisciplinary approach to teaching statistics among medical students. An alternative to traditional static reports was presented, proposing the creation of interactive web applications that enable exploration, analysis and visualization of medical data changing in real time. The use of the R language as an open source tool allows for the development of medical students' competences in the field of data analysis and the adaptation of research tools to individual needs. A draft lesson plan using sample medical data on cervical cancer was also presented, along with a proposal for specific analyzes of these data and their visualization using interactive RShiny reports. The article ends with a discussion on the role of learning the R language in the education of students of Polish medical universities and the need to expand the educational offer for them with courses in data analysis in an open source environment.
References
ABM, Creation and development of Regional Digital Medicine Centers–2023–Medical Research Agency, konkurs ABM. https://www.abm.gov.pl/pl/konkursy/archiwalne-nabory-1/2023/1918, Tworzenie-i-rozwoj-Regionalnych-Centrow-Medycyny-Cyfrowej.html.
Biecek, P. (2013). Data analysis with R program. https://ksiegarnia.pwn.pl/Analiza-dani-z-programem-R,68467550,p.html.
Biecek, P. (2017). Guide to the R package – Publishing House of the Warsaw University of Technology.
http://www.wydawnictwopw.pl/index.php?s=karta&id=3217.
Central Statistical Office / Thematic areas / Health. (n.d.). Retrieved 7 January 2024, from https://stat.gov.pl/obszary-tematyczne/zdrowie/.
CRAN:Manuals. (n.d.). Retrieved December 28, 2023, from https://cran.r-project.org/manuals.html
Daniel Adrian | IntroStat Shiny Apps. (n.d.). Retrieved 28 December 2023, from https://facweb.gvsu.edu/adriand1/215apps.html.
Farrel, A., Li, P., Veenbergen, S., Patel, K., Maris, J. M., & Leonard, W. J. (2023). ROGUE: an R Shiny app for RNA sequencing analysis and biomarker discovery. BMC Bioinformatics, 24 (1), 303. https://doi.org/10.1186/s12859-023-05420-y.
Fawcett, L. (2018). Using Interactive Shiny Applications to Facilitate Research-Informed Learning and Teaching. Journal of Statistics Education, 26 (1), 2–16. https://doi.org/10.1080/10691898.2018.1436999.
Fernandes, Kelwin, Cardoso, Jaime, & Fernandes, J. (2017). Cervical cancer (Risk Factors).
Published: UCI Machine Learning Repository. https://archive.ics.uci.edu/dataset/383/cervical+cancer+risk+factors.
Garfield, J. & Ben-Zvi, D. (2007). How Students Learn Statistics Revisited: A Current Review of Research on Teaching and Learning Statistics. International Statistical Review, 75 (3), 372–396. https://doi.org/10.1111/j.1751-5823.2007.00029.x.
Gov.pl: How to get access to SRP - Ministry of Digitization–Gov.pl portal. (n.d.). Retrieved 7 January 2024, from https://www.gov.pl/web/cyfryzacji/jak-uzyskac-dostep-do-srp.
Grześkowiak, M., Chudzicka-Strugała, I., Zwoździak, B., Swora-Cwynar, E., Nijakowski, K., Jokiel, M., & Roszak, M. (2020). E-learning During the Coronavirus Pandemic – Creating Educational Resources for Teaching Medical Students. Studies in Logic, Grammar and Rhetoric, 64 (1), 77–97. https://doi.org/doi:10.2478/slgr-2020-0041.
Guzik, P. & Więckowska, B. (2023). Data distribution analysis – a preliminary approach to quantitative data in biomedical research. Journal of Medical Science, 92(2):e869. https://doi.org/10.20883/medical.e869.
Hegarty, M. (2004). Dynamic visualizations and learning: Getting to the difficult questions. Learn Instr, 14. https://doi.org/10.1016/j.learninstruc.2004.06.007.
Discover! Disclose! Explain! A collection of essays on the art of presenting data – PDF, (2014). https://www.wuw.pl/product-pol-6322-Odkryc-Ujawniac-Objasniac-Zbior-esejow-o-sztuce-prezentowania-anych-PDF.html.
Jamie, D. M. (2002). Using Computer Simulation Methods to Teach Statistics: A Review of the Literature. Journal of Statistics Education, 10 (1), null-null. https://doi.org/10.1080/10691898.2002.11910548.
Jiang, Z., Cao, W., Chu, H., Bazerbachi, F., & Siegel, L. (2023). RIMeta: An R shiny tool for estimating the reference interval from a meta-analysis. Research Synthesis Methods, 14 (3), 468–478. https://doi.org/10.1002/jrsm.1626.
Kumar, A., Kumar, P., Palvia, S. C. J., & Verma, S. (2017). Online education worldwide: Current status and emerging trends. Journal of Information Technology Case and Application Research, 19. https://doi.org/10.1080/15228053.2017.1294867.
Laureaci_szp_2023_2.pdf. (n.d.). Retrieved 22 December 2023, from https://www.umb.edu.pl/photo/pliki/aktualnosci/2023/laureaci_szp_2023_2.pdf.
Liebig, P., Pröhl, H., Sudhaus-Jörn, N., Hankel, J., Visscher, C., & Jung, K. (2022). Interactive, Browser-Based Graphics to Visualize Complex Data in Education of Biomedical Sciences for Veterinary Students. Medical Science Educator, 32 (6), 1323–1335. https://doi.org/10.1007/s40670-022-01613-x.
Liu, L., Xie, Y., Yang, H., Lin, A., Dong, M., Wang, H., Zhang, C., Liu, Z., Cheng, Q., Zhang, J., Yuan, S., & Luo, P. (2023). HPVTIMER: A shiny web application for tumor immune estimation in human papillomavirus-associated cancers. IMeta, 2 (3), e130. https://doi.org/10.1002/imt2.130.
Milewski, R. & Roszak, M. (2023). The Issue of Selection of Appropriate Methodology and Methods of Graphical Representation of Data in Biomedical Research. Studies in Logic, Grammar and Rhetoric, 68 (1), 123–131. https://doi.org/10.2478/slgr-2023-0006.
Murray, S. (2014). Interactive data visualization (1–1 online resource). Helion; WorldCat. http://www.myilibrary.com?id=610946.
Pfannkuch, M. (2011). The Role of Context in Developing Informal Statistical Inferential Reasoning: A Classroom Study. Mathematical Thinking and Learning, 13 (1–2), 27–46. https://doi.org/10.1080/10986065.2011.538302.
The Polish Mbaza AI application is one of the best in the world according to UNESCO. (2023, December 28). MamStartup. https://mamstartup.pl/polska-aplikacja-mbaza-ai-chodzi-z-najlepszych-na-swiecie-wg-unesco/.
Roszak, M., Leszczyński, P., Starowicz, K., Wiktorzak, P., Torres, K., Świniarski, P., & Kononowicz, A. (2020). E-learning in medical education. Warsaw: Warsaw University of Technology. https://ruj.uj.edu.pl/xmlui/handle/item/266266.
Jagiellonian University Medical College syllabus. Retrieved 28 December 2023, from https://sylabus.cm-uj.krakow.pl/pl/6/1/7/1/1?masterElement.
Wang, C., Govindarajan, H., Katsonis, P., & Lichtarge, O. (2023). ShinyBioHEAT: an interactive shiny app to identify phenotype driver genes in E.coli and B.subtilis. Bioinformatics, 39 (8), btad467. https://doi.org/10.1093/bioinformatics/btad467.
Wang, S. L., Zhang, A. Y., Messer, S., Wiesner, A., & Pearl, D. K. (2021). Student-Developed Shiny Applications for Teaching Statistics. Journal of Statistics and Data Science Education, 29 (3), 218–227. https://doi.org/10.1080/26939169.2021.1995545.
Wickham, H. (2021). Welcome | Mastering Shiny (2021st ed.). https://mastering-shiny.org/.
Wickham, H. (2023). R for Data Science, 2nd Edition [Book]. https://www.oreilly.com/library/view/r-for-data/9781492097396/.
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