% put bibtex entries here!
@Manual{autoharp,
  title = {autoharp: Semi-Automatic Grading of R and Rmd Scripts},
  author = {Gopal, Vikneswaran and Naman, Agrawal and Huang, Yuting},
  year = {2026},
  note = {R package version 0.3.2},
  url = {https://CRAN.R-project.org/package=autoharp},
  doi = {10.32614/CRAN.package.autoharp},
}

@Book{plotly,
    author = {Carson Sievert},
    title = {{Interactive Web-Based Data Visualizatio}n with R, plotly, and shiny},
    publisher = {Chapman and Hall/CRC},
    year = {2020},
    isbn = {9781138331457},
    url = {https://plotly-r.com},
  }

@Book{st2137,
    author = {Vik Gopal and Daisy Pham},
    title = {Statistical Computing and Programming},
    publisher = {Zenodo},
    year = {2025},
    doi = {https://doi.org/10.5281/zenodo.17969651}
 }

@Manual{crosstalk,
  title = {{crosstalk}: Inter-Widget Interactivity for HTML Widgets},
  author = {Joe Cheng and Carson Sievert},
  year = {2021},
  note = {R package version 1.1.1},
  url = {https://CRAN.R-project.org/package=crosstalk},
}

@Article{lintr, 
  doi = {10.21105/joss.07240}, 
  year = {2025}, 
  publisher = {{Open Journals}}, 
  volume = {10}, 
  number = {108}, 
  pages = {7240}, 
  author = {Jim Hester and Florent Angly and Michael Chirico and Russ Hyde and Ren Kun and Indrajeet Patil and Alexander Rosenstock}, 
  title = {Static Code Analysis for R}, 
  journal = {{Journal of Open Source Software}}, 
}

@article{RJ-2021-050,
  author = {Earo Wang and Dianne Cook},
  title = {Conversations in time: interactive visualisation to explore
          structured temporal data},
  year = {2021},
  journal = {The R Journal},
  doi = {10.32614/RJ-2021-050},
  url = {https://journal.r-project.org/archive/2021/RJ-2021-050/index.html}
}

@Manual{palmerpenguins,
  title = {{palmerpenguins}: Palmer Archipelago (Antarctica) penguin data},
  author = {Allison Marie Horst and Alison Presmanes Hill and Kristen B Gorman},
  year = {2020},
  note = {R package version 0.1.0},
  url = {https://allisonhorst.github.io/palmerpenguins/},
}

@Manual{shiny,
  title = {shiny: Web Application Framework for R},
  author = {Winston Chang and Joe Cheng and JJ Allaire and Carson Sievert and Barret Schloerke and Yihui Xie and Jeff Allen and Jonathan McPherson and Alan Dipert and Barbara Borges},
  year = {2024},
  note = {R package version 1.10.0},
  url = {https://CRAN.R-project.org/package=shiny},
  doi = {10.32614/CRAN.package.shiny},
}

@Manual{shinymanager,
  title = {shinymanager: Authentication Management for 'Shiny' Applications},
  author = {Benoit Thieurmel and Victor Perrier},
  year = {2022},
  note = {R package version 1.0.410},
  url = {https://CRAN.R-project.org/package=shinymanager},
  doi = {10.32614/CRAN.package.shinymanager},
}

@Article{igraph1,
  title = {The igraph software package for complex network research}, 
  author = {Gábor Csárdi and Tamás Nepusz}, 
  journal = {InterJournal}, 
  volume = {Complex Systems}, 
  pages = {1695}, 
  year = {2006}, 
  url = {https://igraph.org}, 
}

@Article{igraph2, 
  title = {igraph enables fast and robust network analysis across programming languages}, 
  author = {Michael Antonov and Gábor Csárdi and Szabolcs Horvát and Kirill Müller and Tamás Nepusz and Daniel Noom and Maëlle Salmon and Vincent Traag and Brooke Foucault Welles and Fabio Zanini}, 
  journal = {arXiv preprint arXiv:2311.10260}, 
  year = {2023}, 
  doi = {10.48550/arXiv.2311.10260}, 
}

@Manual{igraph3, 
  title = {{igraph}: Network Analysis and Visualization in R}, 
  author = {Gábor Csárdi and Tamás Nepusz and Vincent Traag and Szabolcs Horvát and Fabio Zanini and Daniel Noom and Kirill Müller and David Schoch and Maëlle Salmon}, 
  year = {2026}, 
  note = {R package version 2.2.1}, 
  doi = {10.5281/zenodo.7682609}, 
  url = {https://CRAN.R-project.org/package=igraph}, 
}

@Manual{rlang,
  title = {rlang: Functions for Base Types and Core R and 'Tidyverse' Features},
  author = {Lionel Henry and Hadley Wickham},
  year = {2025},
  note = {R package version 1.1.6},
  url = {https://CRAN.R-project.org/package=rlang},
  doi = {10.32614/CRAN.package.rlang},
}

@Article{ruskey1981listing,
  title={Listing and counting subtrees of a tree},
  author={Ruskey, Frank},
  journal={SIAM Journal on Computing},
  volume={10},
  number={1},
  pages={141--150},
  year={1981},
  publisher={SIAM}
}

@Manual{rmarkdown1,
  title = {rmarkdown: Dynamic Documents for R},
  author = {JJ Allaire and Yihui Xie and Christophe Dervieux and Jonathan McPherson and Javier Luraschi and Kevin Ushey and Aron Atkins and Hadley Wickham and Joe Cheng and Winston Chang and Richard Iannone},
  year = {2025},
  note = {R package version 2.30},
  url = {https://github.com/rstudio/rmarkdown},
}

@Book{xie2018rmarkdown,
  title = {R Markdown: The Definitive Guide},
  author = {Yihui Xie and J.J. Allaire and Garrett Grolemund},
  publisher = {Chapman and Hall/CRC},
  address = {Boca Raton, Florida},
  year = {2018},
  isbn = {9781138359338},
  url = {https://yihui.org/rmarkdown/},
}

@Book{rmarkdown3,
  title = {R Markdown Cookbook},
  author = {Yihui Xie and Christophe Dervieux and Emily Riederer},
  publisher = {Chapman and Hall/CRC},
  address = {Boca Raton, Florida},
  year = {2020},
  isbn = {9780367563837},
  url = {https://yihui.org/rmarkdown-cookbook/},
}

@Book{wickham2019advanced,
  title={Advanced r},
  author={Wickham, Hadley},
  year={2019},
  publisher={chapman and hall/CRC},
  url = {https://adv-r.hadley.nz}
}

@Manual{baseR,
    title = {R: A Language and Environment for Statistical Computing},
    author = {{R Core Team}},
    organization = {R Foundation for Statistical Computing},
    address = {Vienna, Austria},
    year = {2025},
    url = {https://www.R-project.org/},
}

@Manual{gradeR,
    title = {gradeR: Helps Grade Assignment Submissions in Common R
      Formats},
    author = {Taylor Brown and Pete Benbow},
    year = {2026},
    note = {R package version 2.0.1},
    url = {https://github.com/tbrown122387/gradeR},
  }

@Manual{gradethis,
  title = {gradethis: Automated Feedback for Student Exercises in 'learnr' Tutorials},
  author = {Garrick Aden-Buie and Daniel Chen and Garrett Grolemund and Alexander {Rossell Hayes} and Barret Schloerke},
  year = {2023},
  note = {https://pkgs.rstudio.com/gradethis/, https://rstudio.github.io/learnr/, https://github.com/rstudio/gradethis},
}

@Manual{ottr,
  title = {{ottr}: An R Autograding Extension for Otter-Grader},
  author = {Christopher Pyles and UC Berkeley Data Science Education Program},
  year = {2025},
  note = {R package version 1.5.3},
  url = {https://CRAN.R-project.org/package=ottr},
}

@Manual{learnr,
  title = {{learnr}: Interactive Tutorials for R},
  author = {Garrick Aden-Buie and Barret Schloerke and JJ Allaire and Alexander Rossell Hayes},
  year = {2025},
  note = {R package version 0.11.6},
  url = {https://CRAN.R-project.org/package=learnr},
}


@Article{testthat,
    author = {Hadley Wickham},
    title = {testthat: Get Started with Testing},
    journal = {The R Journal},
    year = {2011},
    volume = {3},
    pages = {5--10},
    url = {https://journal.r-project.org/articles/RJ-2011-002/},
  }

@Manual{testwhat,
  title = {{testwhat}: Submission Correctness Tests for DataCamp},
  author = {{DataCamp}},
  year = {2017},
  url = {https://github.com/datacamp/testwhat},
}
@article{nbgrader, 
  doi = {10.21105/jose.00032}, 
  url = {https://doi.org/10.21105/jose.00032}, 
  year = {2019}, 
  publisher = {The Open Journal}, 
  volume = {2}, 
  number = {16}, 
  pages = {32}, 
  author = {Project Jupyter and Douglas Blank and David Bourgin and Alexander Brown and Matthias Bussonnier and Jonathan Frederic and Brian Granger and Thomas Griffiths and Jessica Hamrick and Kyle Kelley and M Pacer and Logan Page and Fernando Pérez and Benjamin Ragan-Kelley and Jordan Suchow and Carol Willing}, 
  title = {nbgrader: A Tool for Creating and Grading Assignments in the Jupyter Notebook}, 
  journal = {Journal of Open Source Education} 
}

@Manual{Rtsne,
    title = {{Rtsne}: T-Distributed Stochastic Neighbor Embedding using
      Barnes-Hut Implementation},
    author = {Jesse H. Krijthe},
    year = {2015},
    note = {R package version 0.17},
    url = {https://github.com/jkrijthe/Rtsne},
}

@Manual{DT,
  title = {{DT}: A Wrapper of the JavaScript Library 'DataTables'},
  author = {Yihui Xie and Joe Cheng and Xianying Tan and Garrick Aden-Buie},
  year = {2025},
  note = {R package version 0.34},
  url = {https://CRAN.R-project.org/package=DT},
}

@Article{baumer2014rmarkdown,
  title = {R Markdown: Integrating a reproducible analysis tool into introductory statistics},
  author = {Benjamin Baumer and Mine Çetinkaya-Rundel and Andrew Bray and Lisa Loi and Nicholas J. Horton},
  journal = {Technology Innovations in Statistics Education},
  year = {2014},
  volume = {8},
  number = {1},
}

@Misc{bryan2017workflow,
  title = {Project-oriented workflow},
  author = {Jenny Bryan},
  year = {2017},
  url = {https://tidyverse.org/blog/2017/12/workflow-vs-script/},
  note = {Tidyverse Blog},
}

@Manual{knitr1,
  title = {knitr: A General-Purpose Package for Dynamic Report Generation in {R}},
  author = {Yihui Xie},
  year = {2025},
  note = {R package version 1.50},
  url = {https://yihui.org/knitr/},
}

@Book{knitr2,
  title = {Dynamic Documents with {R} and knitr},
  author = {Yihui Xie},
  publisher = {Chapman and Hall/CRC},
  address = {Boca Raton, Florida},
  year = {2015},
  edition = {2nd},
  note = {ISBN 978-1498716963},
  url = {https://yihui.org/knitr/},
}

@InCollection{knitr3,
  booktitle = {Implementing Reproducible Computational Research},
  editor = {Victoria Stodden and Friedrich Leisch and Roger D. Peng},
  title = {knitr: A Comprehensive Tool for Reproducible Research in {R}},
  author = {Yihui Xie},
  publisher = {Chapman and Hall/CRC},
  year = {2014},
  note = {ISBN 978-1466561595},
}

@Book{r4ds,
  title = {R for Data Science (2e)},
  author = {Hadley Wickham, Mine Cetinkaya-Rundel and Garrett Grolemund},
  year={2026},
  publisher={O'Reilly},
  url = {https://r4ds.hadley.nz/}
}
