Appendix H — Statistical computing in R

There are an overwhelming number of great resources for learning R; here are some recommendations:

• Introduction to modern R: Wickham, Çetinkaya-Rundel, and Grolemund (2023)
• Advanced R programming: Wickham (2019)
• Examples of graphics: Chang (2024)
• Building R packages: Wickham and Bryan (2023)
• Translations from SAS: Kleinman and Horton (2009)

H.1 Functions

• Read this ASAP: https://r4ds.hadley.nz/functions.html
• Use this as a reference: https://adv-r.hadley.nz/functions.html

H.1.1 Methods versus functions

See https://adv-r.hadley.nz/oo.html#oop-systems

H.1.2 Debugging R and C code

See https://www.maths.ed.ac.uk/~swood34/RCdebug/RCdebug.html

H.2 data.frames and tibbles

H.2.1 Displaying tibbles

See vignette("digits", package = "tibble")

H.3 The tidyverse

The tidyverse is an opinionated collection of R packages designed for data science. All packages share an underlying design philosophy, grammar, and data structures.

• https://www.tidyverse.org/

These packages are being actively developed by Hadley Wickham and his colleagues at posit¹.

Details:

• Wickham et al. (2019)
• Wickham, Çetinkaya-Rundel, and Grolemund (2023)
• Kuhn and Silge (2022)

H.4 Piping

See Wickham, Çetinkaya-Rundel, and Grolemund (2023) for details.

There are currently (2024) two commonly-used pipe operators in R:

• %>%: the “magrittr pipe”, from the magrittr package (Bache and Wickham (2022); re-exported by dplyr and others) .

• |>: the “native pipe”, from base R (≥4.1.0)

H.4.1 Which pipe should I use?

Wickham, Çetinkaya-Rundel, and Grolemund (2023) recommends the native pipe:

For simple cases, |> and %>% behave identically. So why do we recommend the base pipe? Firstly, because it’s part of base R, it’s always available for you to use, even when you’re not using the tidyverse. Secondly, |> is quite a bit simpler than %>%: in the time between the invention of %>% in 2014 and the inclusion of |> in R 4.1.0 in 2021, we gained a better understanding of the pipe. This allowed the base implementation to jettison infrequently used and less important features.

H.4.2 Why doesn’t ggplot2 use piping?

Here’s tidyverse creator Hadley Wickham’s answer (from 2018):

I think it’s worth unpacking this question into a few smaller pieces:

• Should ggplot2 use the pipe? IMO, yes.
• Could ggplot2 support both the pipe and plus? No
• Would it be worth it to create a ggplot3 that uses the pipe? No.

https://forum.posit.co/t/why-cant-ggplot2-use/4372/7

H.5 Quarto

Quarto is a system for writing documents with embedded R code and/or results:

• Read this ASAP: https://r4ds.hadley.nz/communicate
• Then use this for reference: https://quarto.org/docs/reference/

H.6 Packages

This book espouses our philosophy of package development: anything that can be automated, should be automated. Do as little as possible by hand. Do as much as possible with functions. The goal is to spend your time thinking about what you want your package to do rather than thinking about the minutiae of package structure.

• https://r-pkgs.org/introduction.html#:~:text=This%20book%20espouses,of%20package%20structure.

• Read this ASAP: https://r-pkgs.org/whole-game.html

• Use the rest of Wickham and Bryan (2023) as a reference

H.7 Git

94% of respondents to a 2022 Stack Overflow survey reported using git for version control link

More details

• https://happygitwithr.com/

• https://usethis.r-lib.org/articles/pr-functions.html

H.8 Spatial data science

• Pebesma and Bivand (2023)

H.9 Shiny apps

• Read this first: Wickham (2021)
• Use this as a reference: Fay et al. (2021)

Bache, Stefan Milton, and Hadley Wickham. 2022. Magrittr: A Forward-Pipe Operator for r. https://CRAN.R-project.org/package=magrittr.

Chang, Winston. 2024. R Graphics Cookbook: Practical Recipes for Visualizing Data. O’Reilly Media. https://r-graphics.org/.

Fay, Colin, Sébastien Rochette, Vincent Guyader, and Cervan Girard. 2021. Engineering Production-Grade Shiny Apps. Chapman; Hall/CRC. https://engineering-shiny.org/.

Kleinman, Ken, and Nicholas J Horton. 2009. SAS and r: Data Management, Statistical Analysis, and Graphics. Chapman; Hall/CRC. https://www.routledge.com/SAS-and-R-Data-Management-Statistical-Analysis-and-Graphics-Second-Edition/Kleinman-Horton/p/book/9781466584495.

Kuhn, Max, and Julia Silge. 2022. Tidy Modeling with r. " O’Reilly Media, Inc.". https://www.tmwr.org/.

Pebesma, Edzer, and Roger Bivand. 2023. Spatial Data Science: With Applications in R. Boca Raton: Chapman; Hall/CRC. https://doi.org/10.1201/9780429459016.

Wickham, Hadley. 2019. Advanced r. Chapman; Hall/CRC. https://adv-r.hadley.nz/index.html.

———. 2021. Mastering Shiny. " O’Reilly Media, Inc.". https://mastering-shiny.org/.

Wickham, Hadley, Mara Averick, Jennifer Bryan, Winston Chang, Lucy D’Agostino McGowan, Romain François, Garrett Grolemund, et al. 2019. “Welcome to the tidyverse.” Journal of Open Source Software 4 (43): 1686. https://doi.org/10.21105/joss.01686.

Wickham, Hadley, and Jennifer Bryan. 2023. R Packages. " O’Reilly Media, Inc.". https://r-pkgs.org/.

Wickham, Hadley, Mine Çetinkaya-Rundel, and Garrett Grolemund. 2023. R for Data Science. " O’Reilly Media, Inc.". https://r4ds.hadley.nz/.

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