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Citations for Imported Packages

ape

@Article{,
  title = {ape 5.0: an environment for modern phylogenetics and evolutionary analyses in {R}},
  author = {Emmanuel Paradis and Klaus Schliep},
  journal = {Bioinformatics},
  year = {2019},
  volume = {35},
  pages = {526-528},
  doi = {10.1093/bioinformatics/bty633},
}

ggpubr

@Manual{,
  title = {ggpubr: 'ggplot2' Based Publication Ready Plots},
  author = {Alboukadel Kassambara},
  year = {2025},
  note = {R package version 0.6.1},
  url = {https://CRAN.R-project.org/package=ggpubr},
}

ggrepel

@Manual{,
  title = {ggrepel: Automatically Position Non-Overlapping Text Labels with
'ggplot2'},
  author = {Kamil Slowikowski},
  year = {2024},
  note = {R package version 0.9.6},
  url = {https://CRAN.R-project.org/package=ggrepel},
}

ggplot2

@Book{,
  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},
}

jsonlite

@Article{,
  title = {The jsonlite Package: A Practical and Consistent Mapping Between JSON Data and R Objects},
  author = {Jeroen Ooms},
  journal = {arXiv:1403.2805 [stat.CO]},
  year = {2014},
  url = {https://arxiv.org/abs/1403.2805},
}

jsonvalidate

@Manual{,
  title = {jsonvalidate: Validate 'JSON' Schema},
  author = {Rich FitzJohn and Rob Ashton and Mathias Buus and Evgeny Poberezkin},
  year = {2025},
  note = {R package version 1.5.0},
  url = {https://CRAN.R-project.org/package=jsonvalidate},
}

magrittr

@Manual{,
  title = {magrittr: A Forward-Pipe Operator for R},
  author = {Stefan Milton Bache and Hadley Wickham},
  year = {2022},
  note = {R package version 2.0.3},
  url = {https://CRAN.R-project.org/package=magrittr},
}

patchwork

@Manual{,
  title = {patchwork: The Composer of Plots},
  author = {Thomas Lin Pedersen},
  year = {2025},
  note = {R package version 1.3.2},
  url = {https://CRAN.R-project.org/package=patchwork},
}

RColorBrewer

@Manual{,
  title = {RColorBrewer: ColorBrewer Palettes},
  author = {Erich Neuwirth},
  year = {2022},
  note = {R package version 1.1-3},
  url = {https://CRAN.R-project.org/package=RColorBrewer},
}

rhdf5

@Manual{,
  title = {rhdf5: R Interface to HDF5},
  author = {Bernd Fischer and Mike Smith and Gregoire Pau},
  year = {2023},
  note = {R package version 2.46.1},
  url = {https://bioconductor.org/packages/rhdf5},
  doi = {10.18129/B9.bioc.rhdf5},
}

rstatix

@Manual{,
  title = {rstatix: Pipe-Friendly Framework for Basic Statistical Tests},
  author = {Alboukadel Kassambara},
  year = {2023},
  note = {R package version 0.7.2},
  url = {https://CRAN.R-project.org/package=rstatix},
}

Rcpp

@Manual{,
  title = {Rcpp: Seamless R and C++ Integration},
  author = {Dirk Eddelbuettel and Romain Francois and JJ Allaire and Kevin Ushey and Qiang Kou and Nathan Russell and Iñaki Ucar and Doug Bates and John Chambers},
  year = {2025},
  note = {R package version 1.0.14},
  url = {https://CRAN.R-project.org/package=Rcpp},
}

@Article{,
  title = {{Rcpp}: Seamless {R} and {C++} Integration},
  author = {Dirk Eddelbuettel and Romain Fran\c{c}ois},
  journal = {Journal of Statistical Software},
  year = {2011},
  volume = {40},
  number = {8},
  pages = {1--18},
  doi = {10.18637/jss.v040.i08},
}

@Book{,
  title = {Seamless {R} and {C++} Integration with {Rcpp}},
  author = {Dirk Eddelbuettel},
  publisher = {Springer},
  address = {New York},
  year = {2013},
  note = {ISBN 978-1-4614-6867-7},
  doi = {10.1007/978-1-4614-6868-4},
}

@Article{,
  title = {{Extending {R} with {C++}: A Brief Introduction to {Rcpp}}},
  author = {Dirk Eddelbuettel and James Joseph Balamuta},
  journal = {The American Statistician},
  year = {2018},
  volume = {72},
  number = {1},
  pages = {28-36},
  doi = {10.1080/00031305.2017.1375990},
}

RcppParallel

@Manual{,
  title = {RcppParallel: Parallel Programming Tools for 'Rcpp'},
  author = {JJ Allaire and Romain Francois and Kevin Ushey and Gregory Vandenbrouck and Marcus Geelnard and {Intel}},
  year = {2025},
  note = {R package version 5.1.11-1},
  url = {https://CRAN.R-project.org/package=RcppParallel},
}

stats, tools, methods, utils

@Manual{,
  title = {R: A Language and Environment for Statistical Computing},
  author = {{R Core Team}},
  organization = {R Foundation for Statistical Computing},
  address = {Vienna, Austria},
  year = {2024},
  url = {https://www.R-project.org/},
}

vegan

@Manual{,
  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 Tuomas Borman 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 Cameron Martino 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 = {2025},
  note = {R package version 2.7-1},
  url = {https://CRAN.R-project.org/package=vegan},
}

yyjsonr

@Manual{,
  title = {yyjsonr: Fast 'JSON', 'NDJSON' and 'GeoJSON' Parser and Generator},
  author = {Mike Cheng and Yao Yuan},
  year = {2025},
  note = {R package version 0.1.21},
  url = {https://CRAN.R-project.org/package=yyjsonr},
}