Connecting RStudio and Github

Author

Robert W. Walker

Published

November 12, 2023

obertwwalker.github.io

Last updated: 2023-11-17 12:10:57.394047

Timezone: America/Los_Angeles

Connecting RStudio and Github

There are a number of useful references for doing this. I merely document this here for my own reference as the process of updating OS’s and moving drives has necessitated that I do this a few times over the last few days. Here are the steps.

The key thing is a personal access token (PAT). You can use keys and such, though this way is the easiest. We will generate the PAT via Github and then make the system aware of it. Here is the process; the first step can be done in either of two ways. Before starting, there are two packages we may need. We also need to have git installed and RStudio needs to know our Github account in the abstract.

# install the necessary packages
install.packages(c("usethis","credentials"))
# Let our R session know about our github account
usethis::use_git_config(user.name = "YourName", user.email = "your@mail.com")
  1. Generate the PAT using

    • either usethis::create_github_token()

    • or on the Github website, Settings > Developer Settings > Personal Access Tokens and clicking Generate new token

    Github PAT

In either case, this will create a token that can allow RStudio and Github to communicate. In either case, a collection of letters and numbers will emerge and it should be copied to the clipboard.

  1. We now need to make RStudio aware of the token.
credentials::set_github_pat("YourPAT")

To make future R sessions aware of the token, we need to make it a part of our environment.

usethis::edit_r_environ()

will need a line [without quotes or whatever]

GITHUB_PAT=YourPAT

Next time R starts, this linkage to Github is known. Or should be.

How’s that done? 
knitr::write_bib(names(sessionInfo()$otherPkgs), file="bibliography.bib")

References

Arnold, Jeffrey B. 2021. Ggthemes: Extra Themes, Scales and Geoms for Ggplot2. https://github.com/jrnold/ggthemes.
Bache, Stefan Milton, and Hadley Wickham. 2022. Magrittr: A Forward-Pipe Operator for r. https://CRAN.R-project.org/package=magrittr.
Cheng, Joe. 2023. D3scatter: Demo of D3 Scatter Plot; Testbed for Crosstalk Library.
Cheng, Joe, and Carson Sievert. 2021. Crosstalk: Inter-Widget Interactivity for HTML Widgets. https://rstudio.github.io/crosstalk/.
Cheng, Joe, Carson Sievert, Barret Schloerke, Winston Chang, Yihui Xie, and Jeff Allen. 2022. Htmltools: Tools for HTML. https://CRAN.R-project.org/package=htmltools.
Dancho, Matt, and Davis Vaughan. 2022. Tidyquant: Tidy Quantitative Financial Analysis. https://github.com/business-science/tidyquant.
Gohel, David, and Panagiotis Skintzos. 2023. Ggiraph: Make Ggplot2 Graphics Interactive. https://davidgohel.github.io/ggiraph/.
Grolemund, Garrett, and Hadley Wickham. 2011. “Dates and Times Made Easy with lubridate.” Journal of Statistical Software 40 (3): 1–25. https://www.jstatsoft.org/v40/i03/.
Müller, Kirill, and Hadley Wickham. 2022. Tibble: Simple Data Frames. https://CRAN.R-project.org/package=tibble.
Pedersen, Thomas Lin. 2022. Patchwork: The Composer of Plots. https://CRAN.R-project.org/package=patchwork.
Peterson, Brian G., and Peter Carl. 2020. PerformanceAnalytics: Econometric Tools for Performance and Risk Analysis. https://github.com/braverock/PerformanceAnalytics.
Ryan, Jeffrey A., and Joshua M. Ulrich. 2022a. Quantmod: Quantitative Financial Modelling Framework. https://CRAN.R-project.org/package=quantmod.
———. 2022b. Xts: eXtensible Time Series. https://github.com/joshuaulrich/xts.
Sievert, Carson. 2020. Interactive Web-Based Data Visualization with r, Plotly, and Shiny. Chapman; Hall/CRC. https://plotly-r.com.
Sievert, Carson, Chris Parmer, Toby Hocking, Scott Chamberlain, Karthik Ram, Marianne Corvellec, and Pedro Despouy. 2022. Plotly: Create Interactive Web Graphics via Plotly.js. https://CRAN.R-project.org/package=plotly.
Slowikowski, Kamil. 2023. Ggrepel: Automatically Position Non-Overlapping Text Labels with Ggplot2. https://github.com/slowkow/ggrepel.
Spinu, Vitalie, Garrett Grolemund, and Hadley Wickham. 2023. Lubridate: Make Dealing with Dates a Little Easier. https://CRAN.R-project.org/package=lubridate.
Ulrich, Joshua. 2021. TTR: Technical Trading Rules. https://github.com/joshuaulrich/TTR.
Wickham, Hadley. 2016. Ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York. https://ggplot2.tidyverse.org.
———. 2022a. Stringr: Simple, Consistent Wrappers for Common String Operations. https://CRAN.R-project.org/package=stringr.
———. 2022b. Tidyverse: Easily Install and Load the Tidyverse. https://CRAN.R-project.org/package=tidyverse.
———. 2023. Forcats: Tools for Working with Categorical Variables (Factors). https://CRAN.R-project.org/package=forcats.
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, Winston Chang, Lionel Henry, Thomas Lin Pedersen, Kohske Takahashi, Claus Wilke, Kara Woo, Hiroaki Yutani, and Dewey Dunnington. 2023. Ggplot2: Create Elegant Data Visualisations Using the Grammar of Graphics. https://CRAN.R-project.org/package=ggplot2.
Wickham, Hadley, Romain François, Lionel Henry, Kirill Müller, and Davis Vaughan. 2023. Dplyr: A Grammar of Data Manipulation. https://CRAN.R-project.org/package=dplyr.
Wickham, Hadley, and Lionel Henry. 2023. Purrr: Functional Programming Tools. https://CRAN.R-project.org/package=purrr.
Wickham, Hadley, Jim Hester, and Jennifer Bryan. 2023. Readr: Read Rectangular Text Data. https://CRAN.R-project.org/package=readr.
Wickham, Hadley, Davis Vaughan, and Maximilian Girlich. 2023. Tidyr: Tidy Messy Data. https://CRAN.R-project.org/package=tidyr.
Xie, Yihui, Joe Cheng, and Xianying Tan. 2023. DT: A Wrapper of the JavaScript Library DataTables. https://github.com/rstudio/DT.
Zeileis, Achim, and Gabor Grothendieck. 2005. “Zoo: S3 Infrastructure for Regular and Irregular Time Series.” Journal of Statistical Software 14 (6): 1–27. https://doi.org/10.18637/jss.v014.i06.
Zeileis, Achim, Gabor Grothendieck, and Jeffrey A. Ryan. 2022. Zoo: S3 Infrastructure for Regular and Irregular Time Series (z’s Ordered Observations). https://zoo.R-Forge.R-project.org/.