packages.bib

@Manual{R-aplot,
  title = {aplot: Decorate a ggplot with Associated Information},
  author = {Guangchuang Yu},
  year = {2020},
  note = {R package version 0.0.6},
  url = {https://github.com/YuLab-SMU/aplot},
}

@Manual{R-base,
  title = {R: A Language and Environment for Statistical Computing},
  author = {{R Core Team}},
  organization = {R Foundation for Statistical Computing},
  address = {Vienna, Austria},
  year = {2020},
  url = {https://www.R-project.org/},
}

@Manual{R-bibliometrix,
  title = {bibliometrix: Comprehensive Science Mapping Analysis},
  author = {Massimo Aria and Corrado Cuccurullo},
  year = {2020},
  note = {R package version 3.0.3},
  url = {https://CRAN.R-project.org/package=bibliometrix},
}

@Manual{R-bookdown,
  title = {bookdown: Authoring Books and Technical Documents with R Markdown},
  author = {Yihui Xie},
  year = {2020},
  note = {R package version 0.21},
  url = {https://github.com/rstudio/bookdown},
}

@Manual{R-cowplot,
  title = {cowplot: Streamlined Plot Theme and Plot Annotations for ggplot2},
  author = {Claus O. Wilke},
  year = {2020},
  note = {R package version 1.1.0},
  url = {https://wilkelab.org/cowplot/},
}

@Manual{R-dplyr,
  title = {dplyr: A Grammar of Data Manipulation},
  author = {Hadley Wickham and Romain Fran?ois and Lionel {
             Henry} and Kirill Müller},
  year = {2020},
  note = {R package version 1.0.2},
  url = {https://CRAN.R-project.org/package=dplyr},
}

@Manual{R-DT,
  title = {DT: A Wrapper of the JavaScript Library DataTables},
  author = {Yihui Xie and Joe Cheng and Xianying Tan},
  year = {2020},
  note = {R package version 0.16},
  url = {https://github.com/rstudio/DT},
}

@Manual{R-export,
  title = {export: Streamlined Export of Graphs and Data Tables},
  author = {Tom Wenseleers and Christophe Vanderaa},
  year = {2020},
  note = {R package version 0.3.0},
}

@Manual{R-forcats,
  title = {forcats: Tools for Working with Categorical Variables (Factors)},
  author = {Hadley Wickham},
  year = {2020},
  note = {R package version 0.5.0},
  url = {https://CRAN.R-project.org/package=forcats},
}

@Manual{R-gganimate,
  title = {gganimate: A Grammar of Animated Graphics},
  author = {Thomas Lin Pedersen and David Robinson},
  year = {2020},
  note = {R package version 1.0.7},
  url = {https://CRAN.R-project.org/package=gganimate},
}

@Manual{R-ggflags,
  title = {ggflags: What the Package Does (Title Case)},
  author = {Baptiste Auguie},
  year = {2020},
  note = {R package version 0.0.1},
}

@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},
  year = {2020},
  note = {R package version 3.3.2},
  url = {https://CRAN.R-project.org/package=ggplot2},
}

@Manual{R-ggraph,
  title = {ggraph: An Implementation of Grammar of Graphics for Graphs and Networks},
  author = {Thomas Lin Pedersen},
  year = {2020},
  note = {R package version 2.0.3},
  url = {https://CRAN.R-project.org/package=ggraph},
}

@Manual{R-igraph,
  title = {igraph: Network Analysis and Visualization},
  author = {See AUTHORS file.},
  year = {2020},
  note = {R package version 1.2.6},
  url = {https://igraph.org},
}

@Manual{R-knitr,
  title = {knitr: A General-Purpose Package for Dynamic Report Generation in R},
  author = {Yihui Xie},
  year = {2020},
  note = {R package version 1.30},
  url = {https://yihui.org/knitr/},
}

@Manual{R-lubridate,
  title = {lubridate: Make Dealing with Dates a Little Easier},
  author = {Vitalie Spinu and Garrett Grolemund and Hadley Wickham},
  year = {2020},
  note = {R package version 1.7.9},
  url = {https://CRAN.R-project.org/package=lubridate},
}

@Manual{R-magrittr,
  title = {magrittr: A Forward-Pipe Operator for R},
  author = {Stefan Milton Bache and Hadley Wickham},
  year = {2014},
  note = {R package version 1.5},
  url = {https://CRAN.R-project.org/package=magrittr},
}

@Manual{R-mrgut,
  title = {mrgut: What the Package Does (Title Case)},
  author = {Who wrote it},
  note = {R package version 0.2.0},
  year = {2020},
}

@Manual{R-networkD3,
  title = {networkD3: D3 JavaScript Network Graphs from R},
  author = {J.J. Allaire and Christopher Gandrud and Kenton Russell and CJ Yetman},
  year = {2017},
  note = {R package version 0.4},
  url = {https://CRAN.R-project.org/package=networkD3},
}

@Manual{R-patchwork,
  title = {patchwork: The Composer of Plots},
  author = {Thomas Lin Pedersen},
  year = {2020},
  note = {R package version 1.1.0},
  url = {https://CRAN.R-project.org/package=patchwork},
}

@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 = {2020},
  note = {R package version 4.9.2.1},
  url = {https://CRAN.R-project.org/package=plotly},
}

@Manual{R-purrr,
  title = {purrr: Functional Programming Tools},
  author = {Lionel Henry and Hadley Wickham},
  year = {2020},
  note = {R package version 0.3.4},
  url = {https://CRAN.R-project.org/package=purrr},
}

@Manual{R-RColorBrewer,
  title = {RColorBrewer: ColorBrewer Palettes},
  author = {Erich Neuwirth},
  year = {2014},
  note = {R package version 1.1-2},
  url = {https://CRAN.R-project.org/package=RColorBrewer},
}

@Manual{R-rmarkdown,
  title = {rmarkdown: Dynamic Documents for R},
  author = {JJ Allaire and Yihui Xie 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 = {2020},
  note = {R package version 2.5},
  url = {https://github.com/rstudio/rmarkdown},
}

@Manual{R-rvest,
  title = {rvest: Easily Harvest (Scrape) Web Pages},
  author = {Hadley Wickham},
  year = {2020},
  note = {R package version 0.3.6},
  url = {https://CRAN.R-project.org/package=rvest},
}

@Manual{R-stringr,
  title = {stringr: Simple, Consistent Wrappers for Common String Operations},
  author = {Hadley Wickham},
  year = {2019},
  note = {R package version 1.4.0},
  url = {https://CRAN.R-project.org/package=stringr},
}

@Manual{R-tibble,
  title = {tibble: Simple Data Frames},
  author = {Kirill Müller and Hadley Wickham},
  year = {2020},
  note = {R package version 3.0.4},
  url = {https://CRAN.R-project.org/package=tibble},
}

@Manual{R-tidyr,
  title = {tidyr: Tidy Messy Data},
  author = {Hadley Wickham},
  year = {2020},
  note = {R package version 1.1.2},
  url = {https://CRAN.R-project.org/package=tidyr},
}

@Manual{R-tidytext,
  title = {tidytext: Text Mining using dplyr, ggplot2, and Other Tidy Tools},
  author = {David Robinson and Julia Silge},
  year = {2020},
  note = {R package version 0.2.6},
  url = {https://github.com/juliasilge/tidytext},
}

@Manual{R-treemap,
  title = {treemap: Treemap Visualization},
  author = {Martijn Tennekes},
  year = {2017},
  note = {R package version 2.4-2},
  url = {https://CRAN.R-project.org/package=treemap},
}

@Manual{R-UpSetR,
  title = {UpSetR: A More Scalable Alternative to Venn and Euler Diagrams for
Visualizing Intersecting Sets},
  author = {Nils Gehlenborg},
  year = {2019},
  note = {R package version 1.4.0},
  url = {http://github.com/hms-dbmi/UpSetR},
}

@Manual{R-visNetwork,
  title = {visNetwork: Network Visualization using vis.js Library},
  author = {{Almende B.V.} and Benoit Thieurmel and Titouan Robert},
  year = {2019},
  note = {R package version 2.0.9},
  url = {http://datastorm-open.github.io/visNetwork/},
}

@Manual{R-wordcloud2,
  title = {wordcloud2: Create Word Cloud by htmlwidget},
  author = {Dawei Lang and Guan-tin Chien},
  year = {2018},
  note = {R package version 0.2.1},
  url = {https://github.com/lchiffon/wordcloud2},
}

@Manual{R-xml2,
  title = {xml2: Parse XML},
  author = {Hadley Wickham and Jim Hester and Jeroen Ooms},
  year = {2020},
  note = {R package version 1.3.2},
  url = {https://CRAN.R-project.org/package=xml2},
}

@Article{bibliometrix2017,
  author = {Massimo Aria and Corrado Cuccurullo},
  title = {bibliometrix: An R-tool for comprehensive science mapping analysis},
  journal = {Journal of Informetrics},
  volume = {11},
  number = {4},
  pages = {959-975},
  publisher = {Elsevier},
  year = {2017},
  url = {https://doi.org/10.1016/j.joi.2017.08.007},
}

@Book{bookdown2016,
  title = {bookdown: Authoring Books and Technical Documents with {R} Markdown},
  author = {Yihui Xie},
  publisher = {Chapman and Hall/CRC},
  address = {Boca Raton, Florida},
  year = {2016},
  note = {ISBN 978-1138700109},
  url = {https://github.com/rstudio/bookdown},
}

@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{igraph2006,
  title = {The igraph software package for complex network research},
  author = {Gabor Csardi and Tamas Nepusz},
  journal = {InterJournal},
  volume = {Complex Systems},
  pages = {1695},
  year = {2006},
  url = {https://igraph.org},
}

@Book{knitr2015,
  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{knitr2014,
  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},
  url = {http://www.crcpress.com/product/isbn/9781466561595},
}

@Article{lubridate2011,
  title = {Dates and Times Made Easy with {lubridate}},
  author = {Garrett Grolemund and Hadley Wickham},
  journal = {Journal of Statistical Software},
  year = {2011},
  volume = {40},
  number = {3},
  pages = {1--25},
  url = {http://www.jstatsoft.org/v40/i03/},
}

@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},
}

@Book{rmarkdown2018,
  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},
  note = {ISBN 9781138359338},
  url = {https://bookdown.org/yihui/rmarkdown},
}

@Book{rmarkdown2020,
  title = {R Markdown Cookbook},
  author = {Yihui Xie and Christophe Dervieux and Emily Riederer},
  publisher = {Chapman and Hall/CRC},
  address = {Boca Raton, Florida},
  year = {2020},
  note = {ISBN 9780367563837},
  url = {https://bookdown.org/yihui/rmarkdown-cookbook},
}

@Article{tidytext2016,
  title = {tidytext: Text Mining and Analysis Using Tidy Data Principles in R},
  author = {Julia Silge and David Robinson},
  doi = {10.21105/joss.00037},
  url = {http://dx.doi.org/10.21105/joss.00037},
  year = {2016},
  publisher = {The Open Journal},
  volume = {1},
  number = {3},
  journal = {JOSS},
}