In the beginning was R Markdown

In this talk I will give a brief review of teaching statistics and data analysis through the lens of reproducibility with R Markdown, and how to use this tool effectively in teaching to maintain reproducibility as the scope of your students' projects and their experience grow.

Transcript

1. 🔗 bit.ly/begin-rmd
   

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2. setting the stage
   

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3. replicability reproducibility
   same research question same research question
   same results same results
   new data same data
   

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5. a little bit of history…
   

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6. useR! 2012
   

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7. #1:
   
   
   Convince
   researchers to adopt
   a reproducible
   research workflow
   #2:
   
   
   Train new
   researchers who
   don’t have any
   other workflow
   

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8. reproducibility
   
   
   

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14. data
    
    
    analysis
    - descriptive stats
    
    
    - plots & tables
    
    
    - model output
    write-up
    - research question
    
    
    & context
    
    
    - interpretations
    
    
    - conclusions
    lab
    
    
    report
    copy-paste copy-paste
    text block
    data analysis
    text block
    data analysis
    text block
    + code & output tightly connected
    
    
    + easy to reproduce, update, collaborate
    
    
    + standardised format
    
    
    - unfamiliar format, must learn syntax
    Word, Google Docs, etc. R Markdown
    

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16. fast forward to the present
    

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19. growing out of r markdown
    with
    

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20. r markdown
    
    
    rstudio
    
    
    projects
    

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21. r markdown
    
    
    external
    
    
    data
    

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22. r markdown
    
    
    external
    
    
    data
    
    
    in other
    
    
    folders with
    
    
    here
    : :
    here()
    

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23. r markdown
    
    
    version
    
    
    control
    

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24. version control
    
    
    with Git and GitHub
    for students for educators
    + learn a best practice
    for reproducibility
    
    
    + get familiar with
    systems that are widely
    used in industry and
    academia
    
    
    + facilitate collaboration
    and sharing
    + teach a best practice
    for reproducibility
    
    
    + centralise the
    distribution and
    collection of
    assignments
    
    
    + enable students to
    work collaboratively
    (even when working
    remotely!)
    

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25. a simple assignment…
    

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26. …that is straightforward to assess
    

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27. a more complex project…
    

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28. …with automated checks
    
    
    leveraging GitHub actions
    

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29. allowed
    -
    f
    i
    les.yaml
    project
    -
    allowed
    -
    f
    i
    les.R
    

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30. knit
    -
    readme.yaml
    

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31. r markdown
    
    
    other
    
    
    formats
    …
    

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34. r markdown
    
    
    you,
    
    
    the
    
    
    educator
    

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35. putting it altogether
    

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37. references & acknowledgements
    - Baumer, B., Çetinkaya-Rundel, M., Bray, A., Loi, L., & Horton, N. J. (2014). "R Markdown: Integrating A Reproducible
    Analysis Tool into Introductory Statistics." Technology Innovations in Statistics Education, 8(1). https://
    escholarship.org/uc/item/90b2f5xh.
    
    
    - Beckman, M. D., Çetinkaya-Rundel, M., Horton, N. J., Rundel, C. W., Sullivan, A. J., & Tackett, M. (2020).
    Implementing version control with Git and GitHub as a learning objective in statistics and data science courses.
    Journal of Statistics Education, 1-35.
    
    
    - Carver, R., et al. (2016) "Guidelines for assessment and instruction in statistics education (GAISE) college report
    2016." http://www.amstat.org/education/gaise/GaiseCollege_full.pdf.
    
    
    - Çetinkaya-Rundel, M. (2012) "Planting seeds of reproducibility with knitr and markdown" Citizen Statistician. http://
    www.citizen-statistician.org/2012/10/planting-seeds-of-reproducibility-with-knitr-and-markdown.
    
    
    - Horst A.M., Hill A.P., Gorman K.B. (2020). palmerpenguins: Palmer Archipelago (Antarctica) penguin data. R
    package version 0.1.0. https://allisonhorst.github.io/palmerpenguins. doi: 10.5281/zenodo.3960218.
    
    
    - Sharla Gelfand (2021). ggkeyboard: Plot a Keyboard Using "ggplot2". R package version 0.0.0.9012, https://
    github.com/sharlagelfand/ggkeyboard.
    
    
    - Background image credit: Tighe Flanagan, https://www.instagram.com/p/CFcKz89nWE0.
    

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38. and R Markdown continues to facilitate reproducibility,
    
    
    no matter your scope and experience…
    🔗 bit.ly/begin-rmd
    

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