packages.bib

@Manual{R-ape,
  title = {ape: Analyses of Phylogenetics and Evolution},
  author = {Emmanuel Paradis and Simon Blomberg and Ben Bolker and Joseph Brown and Santiago Claramunt and Julien Claude and Hoa Sien Cuong and Richard Desper and Gilles Didier and Benoit Durand and Julien Dutheil and RJ Ewing and Olivier Gascuel and Thomas Guillerme and Christoph Heibl and Anthony Ives and Bradley Jones and Franz Krah and Daniel Lawson and Vincent Lefort and Pierre Legendre and Jim Lemon and Guillaume Louvel and Eric Marcon and Rosemary McCloskey and Johan Nylander and Rainer Opgen-Rhein and Andrei-Alin Popescu and Manuela Royer-Carenzi and Klaus Schliep and Korbinian Strimmer and Damien {de Vienne}},
  year = {2022},
  note = {R package version 5.6-2},
  url = {http://ape-package.ird.fr/},
}

@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 = {2021},
  url = {https://www.R-project.org/},
}

@Manual{R-bookdown,
  title = {bookdown: Authoring Books and Technical Documents with R Markdown},
  author = {Yihui Xie},
  year = {2021},
  note = {R package version 0.24},
  url = {https://CRAN.R-project.org/package=bookdown},
}

@Manual{R-cowplot,
  title = {cowplot: Streamlined Plot Theme and Plot Annotations for ggplot2},
  author = {Claus O. Wilke},
  year = {2020},
  note = {R package version 1.1.1},
  url = {https://wilkelab.org/cowplot/},
}

@Manual{R-DiagrammeR,
  title = {DiagrammeR: Graph/Network Visualization},
  author = {Richard Iannone},
  year = {2022},
  note = {R package version 1.0.9},
  url = {https://github.com/rich-iannone/DiagrammeR},
}

@Manual{R-dotwhisker,
  title = {dotwhisker: Dot-and-Whisker Plots of Regression Results},
  author = {Frederick Solt and Yue Hu},
  year = {2021},
  note = {R package version 0.7.4},
  url = {https://CRAN.R-project.org/package=dotwhisker},
}

@Manual{R-dplyr,
  title = {dplyr: A Grammar of Data Manipulation},
  author = {Hadley Wickham and Romain François and Lionel Henry and Kirill Müller},
  year = {2022},
  note = {R package version 1.0.8},
  url = {https://CRAN.R-project.org/package=dplyr},
}

@Manual{R-forcats,
  title = {forcats: Tools for Working with Categorical Variables (Factors)},
  author = {Hadley Wickham},
  year = {2021},
  note = {R package version 0.5.1},
  url = {https://CRAN.R-project.org/package=forcats},
}

@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 = {2021},
  note = {R package version 3.3.5},
  url = {https://CRAN.R-project.org/package=ggplot2},
}

@Manual{R-ggpubr,
  title = {ggpubr: ggplot2 Based Publication Ready Plots},
  author = {Alboukadel Kassambara},
  year = {2020},
  note = {R package version 0.4.0},
  url = {https://rpkgs.datanovia.com/ggpubr/},
}

@Manual{R-ggspatial,
  title = {ggspatial: Spatial Data Framework for ggplot2},
  author = {Dewey Dunnington},
  year = {2021},
  note = {R package version 1.1.5},
  url = {https://CRAN.R-project.org/package=ggspatial},
}

@Manual{R-knitr,
  title = {knitr: A General-Purpose Package for Dynamic Report Generation in R},
  author = {Yihui Xie},
  year = {2021},
  note = {R package version 1.37},
  url = {https://yihui.org/knitr/},
}

@Manual{R-lattice,
  title = {lattice: Trellis Graphics for R},
  author = {Deepayan Sarkar},
  year = {2021},
  note = {R package version 0.20-45},
  url = {http://lattice.r-forge.r-project.org/},
}

@Manual{R-permute,
  title = {permute: Functions for Generating Restricted Permutations of Data},
  author = {Gavin L. Simpson},
  year = {2022},
  note = {R package version 0.9-7},
  url = {https://github.com/gavinsimpson/permute},
}

@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-RAM,
  title = {RAM: R for Amplicon-Sequencing-Based Microbial-Ecology},
  author = {Wen Chen and Joshua Simpson and C. Andre Levesque},
  year = {2015},
  note = {R package version 1.2.1},
  url = {http://cran.r-project.org/web/packages/RAM/index.html},
}

@Manual{R-readr,
  title = {readr: Read Rectangular Text Data},
  author = {Hadley Wickham and Jim Hester and Jennifer Bryan},
  year = {2022},
  note = {R package version 2.1.2},
  url = {https://CRAN.R-project.org/package=readr},
}

@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 = {2022},
  note = {R package version 2.12},
  url = {https://CRAN.R-project.org/package=rmarkdown},
}

@Manual{R-scales,
  title = {scales: Scale Functions for Visualization},
  author = {Hadley Wickham and Dana Seidel},
  year = {2022},
  note = {R package version 1.2.0},
  url = {https://CRAN.R-project.org/package=scales},
}

@Manual{R-sf,
  title = {sf: Simple Features for R},
  author = {Edzer Pebesma},
  year = {2022},
  note = {R package version 1.0-7},
  url = {https://CRAN.R-project.org/package=sf},
}

@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 = {2021},
  note = {R package version 3.1.6},
  url = {https://CRAN.R-project.org/package=tibble},
}

@Manual{R-tidyr,
  title = {tidyr: Tidy Messy Data},
  author = {Hadley Wickham and Maximilian Girlich},
  year = {2022},
  note = {R package version 1.2.0},
  url = {https://CRAN.R-project.org/package=tidyr},
}

@Manual{R-tidyverse,
  title = {tidyverse: Easily Install and Load the Tidyverse},
  author = {Hadley Wickham},
  year = {2021},
  note = {R package version 1.3.1},
  url = {https://CRAN.R-project.org/package=tidyverse},
}

@Manual{R-tufte,
  title = {tufte: Tufte's Styles for R Markdown Documents},
  author = {Yihui Xie and JJ Allaire},
  year = {2022},
  note = {R package version 0.12},
  url = {https://github.com/rstudio/tufte},
}

@Manual{R-vegan,
  title = {vegan: Community Ecology Package},
  author = {Jari Oksanen and Gavin L. Simpson and F. Guillaume Blanchet and Roeland Kindt and Pierre Legendre and Peter R. Minchin and R.B. O'Hara and Peter Solymos and M. Henry H. Stevens and Eduard Szoecs and Helene Wagner and Matt Barbour and Michael Bedward and Ben Bolker and Daniel Borcard and Gustavo Carvalho and Michael Chirico and Miquel {De Caceres} and Sebastien Durand and Heloisa Beatriz Antoniazi Evangelista and Rich FitzJohn and Michael Friendly and Brendan Furneaux and Geoffrey Hannigan and Mark O. Hill and Leo Lahti and Dan McGlinn and Marie-Helene Ouellette and Eduardo {Ribeiro Cunha} and Tyler Smith and Adrian Stier and Cajo J.F. {Ter Braak} and James Weedon},
  year = {2022},
  note = {R package version 2.6-2},
  url = {https://github.com/vegandevs/vegan},
}

@Article{ape2019,
  title = {ape 5.0: an environment for modern phylogenetics and evolutionary analyses in {R}},
  author = {E. Paradis and K. Schliep},
  journal = {Bioinformatics},
  year = {2019},
  volume = {35},
  pages = {526-528},
}

@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://bookdown.org/yihui/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},
}

@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},
}

@Book{lattice2008,
  title = {Lattice: Multivariate Data Visualization with R},
  author = {Deepayan Sarkar},
  publisher = {Springer},
  address = {New York},
  year = {2008},
  note = {ISBN 978-0-387-75968-5},
  url = {http://lmdvr.r-forge.r-project.org},
}

@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{sf2018,
  author = {Edzer Pebesma},
  title = {{Simple Features for R: Standardized Support for Spatial Vector Data}},
  year = {2018},
  journal = {{The R Journal}},
  doi = {10.32614/RJ-2018-009},
  url = {https://doi.org/10.32614/RJ-2018-009},
  pages = {439--446},
  volume = {10},
  number = {1},
}

@Article{tidyverse2019,
  title = {Welcome to the {tidyverse}},
  author = {Hadley Wickham and Mara Averick and Jennifer Bryan and Winston Chang and Lucy D'Agostino McGowan and Romain François and Garrett Grolemund and Alex Hayes and Lionel Henry and Jim Hester and Max Kuhn and Thomas Lin Pedersen and Evan Miller and Stephan Milton Bache and Kirill Müller and Jeroen Ooms and David Robinson and Dana Paige Seidel and Vitalie Spinu and Kohske Takahashi and Davis Vaughan and Claus Wilke and Kara Woo and Hiroaki Yutani},
  year = {2019},
  journal = {Journal of Open Source Software},
  volume = {4},
  number = {43},
  pages = {1686},
  doi = {10.21105/joss.01686},
}