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đź”— bit.ly/begin-rmd
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setting the stage
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replicability reproducibility
same research question same research question
same results same results
new data same data
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a little bit of history…
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useR! 2012
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#1:
Convince
researchers to adopt
a reproducible
research workflow
#2:
Train new
researchers who
don’t have any
other workflow
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reproducibility
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data
analysis
- descriptive stats
- plots & tables
- model output
write-up
- research question
& context
- interpretations
- conclusions
lab
report
copy-paste copy-paste
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data analysis
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data analysis
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+ 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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fast forward to the present
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growing out of r markdown
with
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r markdown
rstudio
projects
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r markdown
external
data
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r markdown
external
data
in other
folders with
here
: :
here()
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r markdown
version
control
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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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a simple assignment…
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…that is straightforward to assess
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a more complex project…
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…with automated checks
leveraging GitHub actions
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allowed
-
f
i
les.yaml
project
-
allowed
-
f
i
les.R
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knit
-
readme.yaml
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r markdown
other
formats
…
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r markdown
you,
the
educator
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putting it altogether
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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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and R Markdown continues to facilitate reproducibility,
no matter your scope and experience…
đź”— bit.ly/begin-rmd