packages.bib

@Manual{R-classifly,
  title = {classifly: Explore Classification Models in High Dimensions},
  author = {Hadley Wickham},
  year = {2022},
  note = {R package version 0.4.1},
  url = {http://had.co.nz/classifly},
}

@Manual{R-colorspace,
  title = {colorspace: A Toolbox for Manipulating and Assessing Colors and Palettes},
  author = {Ross Ihaka and Paul Murrell and Kurt Hornik and Jason C. Fisher and Reto Stauffer and Claus O. Wilke and Claire D. McWhite and Achim Zeileis},
  year = {2023},
  note = {R package version 2.1-0},
  url = {https://colorspace.R-Forge.R-project.org/},
}

@Manual{R-crosstalk,
  title = {crosstalk: Inter-Widget Interactivity for HTML Widgets},
  author = {Joe Cheng and Carson Sievert},
  year = {2023},
  note = {R package version 1.2.1, 
https://github.com/rstudio/crosstalk},
  url = {https://rstudio.github.io/crosstalk/},
}

@Manual{R-cxhull,
  title = {cxhull: Convex Hull},
  author = {Stéphane Laurent},
  year = {2023},
  note = {R package version 0.7.3},
  url = {https://github.com/stla/cxhull},
}

@Manual{R-detourr,
  title = {detourr: Portable and Performant Tour Animations},
  author = {Casper Hart and Earo Wang},
  year = {2022},
  note = {R package version 0.1.0},
  url = {https://casperhart.github.io/detourr/},
}

@Manual{R-dplyr,
  title = {dplyr: A Grammar of Data Manipulation},
  author = {Hadley Wickham and Romain François and Lionel Henry and Kirill Müller and Davis Vaughan},
  year = {2023},
  note = {R package version 1.1.4},
  url = {https://dplyr.tidyverse.org},
}


@Manual{R-ferrn,
  title = {ferrn: Facilitate Exploration of touRR optimisatioN},
  author = {H. Sherry Zhang and Dianne Cook and Ursula Laa and Nicolas Langrené and Patricia Menéndez},
  year = {2022},
  note = {R package version 0.0.2},
  url = {https://github.com/huizezhang-sherry/ferrn/},
}

@Manual{R-geozoo,
  title = {geozoo: Zoo of Geometric Objects},
  author = {Barret Schloerke},
  year = {2016},
  note = {R package version 0.5.1},
  url = {http://schloerke.github.io/geozoo/},
}

@Manual{R-GGally,
  title = {GGally: Extension to ggplot2},
  author = {Barret Schloerke and Di Cook and Joseph Larmarange and Francois Briatte and Moritz Marbach and Edwin Thoen and Amos Elberg and Jason Crowley},
  year = {2024},
  note = {R package version 2.2.1},
  url = {https://ggobi.github.io/ggally/},
}

@Manual{R-ggdendro,
  title = {ggdendro: Create Dendrograms and Tree Diagrams Using ggplot2},
  author = {Andrie {de Vries} and Brian D. Ripley},
  year = {2022},
  note = {R package version 0.1.23},
  url = {https://github.com/andrie/ggdendro},
}

@Manual{R-ggfortify,
  title = {ggfortify: Data Visualization Tools for Statistical Analysis Results},
  author = {Masaaki Horikoshi and Yuan Tang},
  year = {2023},
  note = {R package version 0.4.16},
  url = {https://github.com/sinhrks/ggfortify},
}

@Manual{R-ggplot2,
  title = {ggplot2: Create Elegant Data Visualisations Using the Grammar of Graphics},
  author = {Hadley Wickham and Winston Chang and Lionel Henry and Thomas Lin Pedersen and Kohske Takahashi and Claus Wilke and Kara Woo and Hiroaki Yutani and Dewey Dunnington and Teun {van den Brand}},
  year = {2024},
  note = {R package version 3.5.0, 
https://github.com/tidyverse/ggplot2},
  url = {https://ggplot2.tidyverse.org},
}

@Manual{R-ggpubr,
  title = {ggpubr: ggplot2 Based Publication Ready Plots},
  author = {Alboukadel Kassambara},
  year = {2023},
  note = {R package version 0.6.0},
  url = {https://rpkgs.datanovia.com/ggpubr/},
}

@Manual{R-ggrepel,
  title = {ggrepel: Automatically Position Non-Overlapping Text Labels with
ggplot2},
  author = {Kamil Slowikowski},
  year = {2023},
  note = {R package version 0.9.3},
  url = {https://github.com/slowkow/ggrepel},
}

@Manual{R-ggthemes,
  title = {ggthemes: Extra Themes, Scales and Geoms for ggplot2},
  author = {Jeffrey B. Arnold},
  year = {2021},
  note = {R package version 4.2.4},
  url = {https://github.com/jrnold/ggthemes},
}


@Manual{R-gt,
  title = {gt: Easily Create Presentation-Ready Display Tables},
  author = {Richard Iannone and Joe Cheng and Barret Schloerke and Ellis Hughes and Alexandra Lauer and JooYoung Seo},
  year = {2023},
  note = {R package version 0.9.0},
  url = {https://gt.rstudio.com/},
}

@Manual{R-gtExtras,
  title = {gtExtras: Extending gt for Beautiful HTML Tables},
  author = {Thomas Mock},
  year = {2022},
  note = {R package version 0.4.5, 
https://jthomasmock.github.io/gtExtras/},
  url = {https://github.com/jthomasmock/gtExtras},
}

@Manual{R-gtsummary,
  title = {gtsummary: Presentation-Ready Data Summary and Analytic Result Tables},
  author = {Daniel D. Sjoberg and Joseph Larmarange and Michael Curry and Jessica Lavery and Karissa Whiting and Emily C. Zabor},
  year = {2023},
  note = {R package version 1.7.1, 
https://www.danieldsjoberg.com/gtsummary/},
  url = {https://github.com/ddsjoberg/gtsummary},
}

@Manual{R-htmlwidgets,
  title = {htmlwidgets: HTML Widgets for R},
  author = {Ramnath Vaidyanathan and Yihui Xie and JJ Allaire and Joe Cheng and Carson Sievert and Kenton Russell},
  year = {2023},
  note = {R package version 1.6.4},
  url = {https://github.com/ramnathv/htmlwidgets},
}

@Manual{R-kableExtra,
  title = {kableExtra: Construct Complex Table with kable and Pipe Syntax},
  author = {Hao Zhu},
  year = {2021},
  note = {R package version 1.3.4, 
https://github.com/haozhu233/kableExtra},
  url = {http://haozhu233.github.io/kableExtra/},
}


@Manual{R-langevitour,
  title = {langevitour: Langevin Tour},
  author = {Paul Harrison},
  year = {2023},
  note = {R package version 0.6},
  url = {https://logarithmic.net/langevitour/},
}

@Manual{R-liminal,
  title = {liminal: Multivariate Data Visualization with Tours and Embeddings},
  author = {Stuart Lee},
  year = {2021},
  note = {R package version 0.1.2, 
https://sa-lee.github.io/liminal/},
  url = {https://github.com/sa-lee/liminal/},
}

@Manual{R-MASS,
  title = {MASS: Support Functions and Datasets for Venables and Ripley's MASS},
  author = {Brian Ripley},
  year = {2024},
  note = {R package version 7.3-60.0.1},
  url = {http://www.stats.ox.ac.uk/pub/MASS4/},
}

@Manual{R-mclust,
  title = {mclust: Gaussian Mixture Modelling for Model-Based Clustering,
Classification, and Density Estimation},
  author = {Chris Fraley and Adrian E. Raftery and Luca Scrucca},
  year = {2024},
  note = {R package version 6.1},
  url = {https://mclust-org.github.io/mclust/},
}


@Manual{R-mulgar,
  title = {mulgar: Functions for Pre-Processing Data for Multivariate Data
Visualisation using Tours},
  author = {Dianne Cook and Ursula Laa},
  year = {2023},
  note = {R package version 1.0.2},
  url = {https://dicook.github.io/mulgar/},
}

@Manual{R-naniar,
  title = {naniar: Data Structures, Summaries, and Visualisations for Missing Data},
  author = {Nicholas Tierney and Di Cook and Miles McBain and Colin Fay},
  year = {2023},
  note = {R package version 1.0.0},
  url = {https://github.com/njtierney/naniar},
}

@Manual{R-nnet,
  title = {nnet: Feed-Forward Neural Networks and Multinomial Log-Linear Models},
  author = {Brian Ripley},
  year = {2023},
  note = {R package version 7.3-19},
  url = {http://www.stats.ox.ac.uk/pub/MASS4/},
}

@Manual{R-palmerpenguins,
  title = {palmerpenguins: Palmer Archipelago (Antarctica) Penguin Data},
  author = {Allison Horst and Alison Hill and Kristen Gorman},
  year = {2022},
  note = {R package version 0.1.1, 
https://github.com/allisonhorst/palmerpenguins},
  url = {https://allisonhorst.github.io/palmerpenguins/},
}

@Manual{R-patchwork,
  title = {patchwork: The Composer of Plots},
  author = {Thomas Lin Pedersen},
  year = {2024},
  note = {R package version 1.2.0, 
https://github.com/thomasp85/patchwork},
  url = {https://patchwork.data-imaginist.com},
}

@Manual{R-plotly,
  title = {plotly: Create Interactive Web Graphics via plotly.js},
  author = {Carson Sievert and Chris Parmer and Toby Hocking and Scott Chamberlain and Karthik Ram and Marianne Corvellec and Pedro Despouy},
  year = {2024},
  note = {R package version 4.10.4},
  url = {https://plotly-r.com},
}

@Manual{R-randomForest,
  title = {randomForest: Breiman and Cutler's Random Forests for Classification and
Regression},
  author = {Leo Breiman and Adele Cutler and Andy Liaw and Matthew Wiener},
  year = {2022},
  note = {R package version 4.7-1.1},
  url = {https://www.stat.berkeley.edu/~breiman/RandomForests/},
}

@Manual{R-readr,
  title = {readr: Read Rectangular Text Data},
  author = {Hadley Wickham and Jim Hester and Jennifer Bryan},
  year = {2024},
  note = {R package version 2.1.5},
  url = {https://readr.tidyverse.org},
}

@Manual{R-rpart,
  title = {rpart: Recursive Partitioning and Regression Trees},
  author = {Terry Therneau and Beth Atkinson},
  year = {2023},
  note = {R package version 4.1.21, 
https://cran.r-project.org/package=rpart},
  url = {https://github.com/bethatkinson/rpart},
}

@Manual{R-rpart.plot,
  title = {rpart.plot: Plot rpart Models: An Enhanced Version of plot.rpart},
  author = {Stephen Milborrow},
  year = {2022},
  note = {R package version 3.1.1},
  url = {http://www.milbo.org/rpart-plot/index.html},
}

@Manual{R-Rtsne,
  title = {Rtsne: T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut
Implementation},
  author = {Jesse Krijthe},
  year = {2022},
  note = {R package version 0.16},
  url = {https://github.com/jkrijthe/Rtsne},
}

@Manual{R-tidymodels,
  title = {tidymodels: Easily Install and Load the Tidymodels Packages},
  author = {Max Kuhn and Hadley Wickham},
  year = {2023},
  note = {R package version 1.1.0, 
https://github.com/tidymodels/tidymodels},
  url = {https://tidymodels.tidymodels.org},
}

@Manual{R-tourr,
  title = {tourr: Tour Methods for Multivariate Data Visualisation},
  author = {Hadley Wickham and Dianne Cook},
  year = {2023},
  note = {R package version 1.1.0},
  url = {https://github.com/ggobi/tourr},
}

@Article{colorspace2020a,
  title = {{colorspace}: A Toolbox for Manipulating and Assessing Colors and Palettes},
  author = {Achim Zeileis and Jason C. Fisher and Kurt Hornik and Ross Ihaka and Claire D. McWhite and Paul Murrell and Reto Stauffer and Claus O. Wilke},
  journal = {Journal of Statistical Software},
  year = {2020},
  volume = {96},
  number = {1},
  pages = {1--49},
  doi = {10.18637/jss.v096.i01},
}

@Article{colorspace2009a,
  title = {Escaping {RGB}land: Selecting Colors for Statistical Graphics},
  author = {Achim Zeileis and Kurt Hornik and Paul Murrell},
  journal = {Computational Statistics \& Data Analysis},
  year = {2009},
  volume = {53},
  number = {9},
  pages = {3259--3270},
  doi = {10.1016/j.csda.2008.11.033},
}

@Article{colorspace2009b,
  title = {Somewhere over the Rainbow: How to Make Effective Use of Colors in Meteorological Visualizations},
  author = {Reto Stauffer and Georg J. Mayr and Markus Dabernig and Achim Zeileis},
  journal = {Bulletin of the American Meteorological Society},
  year = {2009},
  volume = {96},
  number = {2},
  pages = {203--216},
  doi = {10.1175/BAMS-D-13-00155.1},
}

@Article{ferrn2021,
  title = {Visual Diagnostics for Constrained Optimisation with Application to Guided Tours},
  author = {H. Sherry Zhang and Dianne Cook and Ursula Laa and Nicolas Langren{é} and Patricia Men{é}ndez},
  journal = {The R Journal},
  year = {2021},
  volume = {13},
  number = {2},
  pages = {624-641},
  url = {https://doi.org/10.32614/RJ-2021-105},
  doi = {10.32614/RJ-2021-105},
}

@Article{ggfortify2016,
  author = {Yuan Tang and Masaaki Horikoshi and Wenxuan Li},
  title = {ggfortify: Unified Interface to Visualize Statistical Result of Popular R Packages},
  journal = {The R Journal},
  year = {2016},
  number = {2},
  volume = {8},
  pages = {474--485},
  url = {https://doi.org/10.32614/RJ-2016-060},
  doi = {10.32614/RJ-2016-060},
}

@Manual{ggfortify2018,
  author = {Masaaki Horikoshi and Yuan Tang},
  title = {ggfortify: Data Visualization Tools for Statistical Analysis Results},
  year = {2018},
  url = {https://CRAN.R-project.org/package=ggfortify},
}

@Book{ggplot22016,
  author = {Hadley Wickham},
  title = {ggplot2: Elegant Graphics for Data Analysis},
  publisher = {Springer-Verlag New York},
  year = {2016},
  isbn = {978-3-319-24277-4},
  url = {https://ggplot2.tidyverse.org},
}

@Article{gtsummary,
  author = {Daniel D. Sjoberg and Karissa Whiting and Michael Curry and Jessica A. Lavery and Joseph Larmarange},
  title = {Reproducible Summary Tables with the gtsummary Package},
  journal = {{The R Journal}},
  year = {2021},
  url = {https://doi.org/10.32614/RJ-2021-053},
  doi = {10.32614/RJ-2021-053},
  volume = {13},
  issue = {1},
  pages = {570-580},
}

@Article{kohonen2018,
  title = {Flexible Self-Organizing Maps in {kohonen} 3.0},
  author = {Ron Wehrens and Johannes Kruisselbrink},
  journal = {Journal of Statistical Software},
  year = {2018},
  volume = {87},
  number = {7},
  pages = {1--18},
  doi = {10.18637/jss.v087.i07},
}

@Article{kohonen2007,
  title = {Self- and Super-Organizing Maps in {R}: The {kohonen} Package},
  author = {Ron Wehrens and Lutgarde M. C. Buydens},
  journal = {Journal of Statistical Software},
  year = {2007},
  volume = {21},
  number = {5},
  pages = {1--19},
  doi = {10.18637/jss.v021.i05},
}

@Article{langevitour2023,
  title = {langevitour: Smooth Interactive Touring of High Dimensions, Demonstrated with scRNA-Seq Data},
  author = {Paul Harrison},
  journal = {The R Journal},
  year = {2023},
  volume = {15},
  number = {2},
  pages = {206-219},
  doi = {10.32614/RJ-2023-046},
}

@Book{MASS2002,
  title = {Modern Applied Statistics with S},
  author = {W. N. Venables and B. D. Ripley},
  publisher = {Springer},
  edition = {Fourth},
  address = {New York},
  year = {2002},
  note = {ISBN 0-387-95457-0},
  url = {https://www.stats.ox.ac.uk/pub/MASS4/},
}

@Book{mclust2023,
  title = {Model-Based Clustering, Classification, and Density Estimation Using {mclust} in {R}},
  author = {Luca Scrucca and Chris Fraley and T. Brendan Murphy and Adrian E. Raftery},
  publisher = {Chapman and Hall/CRC},
  isbn = {978-1032234953},
  doi = {10.1201/9781003277965},
  year = {2023},
  url = {https://mclust-org.github.io/book/},
}

@Article{naniar2023,
  title = {Expanding Tidy Data Principles to Facilitate Missing Data Exploration, Visualization and Assessment of Imputations},
  author = {Nicholas Tierney and Dianne Cook},
  journal = {Journal of Statistical Software},
  year = {2023},
  volume = {105},
  number = {7},
  pages = {1--31},
  doi = {10.18637/jss.v105.i07},
}

@Book{nnet2002,
  title = {Modern Applied Statistics with S},
  author = {W. N. Venables and B. D. Ripley},
  publisher = {Springer},
  edition = {Fourth},
  address = {New York},
  year = {2002},
  note = {ISBN 0-387-95457-0},
  url = {https://www.stats.ox.ac.uk/pub/MASS4/},
}

@Book{plotly2020,
  author = {Carson Sievert},
  title = {Interactive Web-Based Data Visualization with R, plotly, and shiny},
  publisher = {Chapman and Hall/CRC},
  year = {2020},
  isbn = {9781138331457},
  url = {https://plotly-r.com},
}

@Article{randomForest2002,
  title = {Classification and Regression by randomForest},
  author = {Andy Liaw and Matthew Wiener},
  journal = {R News},
  year = {2002},
  volume = {2},
  number = {3},
  pages = {18-22},
  url = {https://CRAN.R-project.org/doc/Rnews/},
}

@Article{Rtsne2008,
  title = {Visualizing High-Dimensional Data Using t-SNE},
  volume = {9},
  pages = {2579-2605},
  year = {2008},
  author = {L.J.P. {van der Maaten} and G.E. Hinton},
  journal = {Journal of Machine Learning Research},
}

@Article{Rtsne2014,
  title = {Accelerating t-SNE using Tree-Based Algorithms},
  volume = {15},
  pages = {3221-3245},
  year = {2014},
  author = {L.J.P. {van der Maaten}},
  journal = {Journal of Machine Learning Research},
}

@Manual{tidymodels2020,
  title = {Tidymodels: a collection of packages for modeling and machine learning using tidyverse principles.},
  author = {Max Kuhn and Hadley Wickham},
  url = {https://www.tidymodels.org},
  year = {2020},
}

@Article{tourr2011,
  title = {{tourr}: An {R} Package for Exploring Multivariate Data with Projections},
  author = {Hadley Wickham and Dianne Cook and Heike Hofmann and Andreas Buja},
  journal = {Journal of Statistical Software},
  year = {2011},
  volume = {40},
  number = {2},
  pages = {1--18},
  url = {https://doi.org/10.18637/jss.v040.i02},
}

@Article{tourr2020,
  title = {A slice tour for finding hollowness in high-dimensional data},
  author = {Ursula Laa and Dianne Cook and German Valencia},
  journal = {Journal of Computational and Graphical Statistics},
  year = {2020},
  volume = {29},
  number = {3},
  pages = {681--687},
  url = {https://doi.org/10.1080/10618600.2020.1777140},
}