pkg-bib.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 Federico Marotta 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 = {2024},
  note = {R package version 5.8-1},
  url = {https://github.com/emmanuelparadis/ape},
}

@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 = {2025},
  url = {https://www.R-project.org/},
}

@Manual{R-bookdown,
  title = {bookdown: Authoring Books and Technical Documents with R Markdown},
  author = {Yihui Xie},
  note = {R package version 0.42.1},
  url = {https://github.com/rstudio/bookdown},
  year = {2025},
}

@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-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 3.5.1},
  url = {https://ggplot2.tidyverse.org},
}

@Manual{R-kableExtra,
  title = {kableExtra: Construct Complex Table with kable and Pipe Syntax},
  author = {Hao Zhu},
  year = {2024},
  note = {R package version 1.4.0},
  url = {http://haozhu233.github.io/kableExtra/},
}

@Manual{R-knitr,
  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/},
}

@Manual{R-labdsv,
  title = {labdsv: Ordination and Multivariate Analysis for Ecology},
  author = {David W. Roberts},
  year = {2023},
  note = {R package version 2.1-0},
}

@Manual{R-lattice,
  title = {lattice: Trellis Graphics for R},
  author = {Deepayan Sarkar},
  year = {2024},
  note = {R package version 0.22-6},
  url = {https://lattice.r-forge.r-project.org/},
}

@Manual{R-magrittr,
  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://magrittr.tidyverse.org},
}

@Manual{R-maps,
  title = {maps: Draw Geographical Maps},
  author = {Alex Deckmyn},
  year = {2024},
  note = {R package version 3.4.2.1},
}

@Manual{R-mgcv,
  title = {mgcv: Mixed GAM Computation Vehicle with Automatic Smoothness
Estimation},
  author = {Simon Wood},
  year = {2023},
  note = {R package version 1.9-1},
  url = {https://CRAN.R-project.org/package=mgcv},
}

@Manual{R-nlme,
  title = {nlme: Linear and Nonlinear Mixed Effects Models},
  author = {José Pinheiro and Douglas Bates and {R Core Team}},
  year = {2025},
  note = {R package version 3.1-167},
  url = {https://svn.r-project.org/R-packages/trunk/nlme/},
}

@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-printr,
  title = {printr: Automatically Print R Objects to Appropriate Formats According
to the knitr Output Format},
  author = {Yihui Xie},
  year = {2023},
  note = {R package version 0.3},
  url = {https://yihui.org/printr/},
}

@Manual{R-purrr,
  title = {purrr: Functional Programming Tools},
  author = {Hadley Wickham and Lionel Henry},
  year = {2025},
  note = {R package version 1.0.4},
  url = {https://purrr.tidyverse.org/},
}

@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-rmarkdown,
  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 = {2024},
  note = {R package version 2.29},
  url = {https://github.com/rstudio/rmarkdown},
}

@Manual{R-TeachingDemos,
  title = {TeachingDemos: Demonstrations for Teaching and Learning},
  author = {Greg Snow},
  year = {2024},
  note = {R package version 2.13},
}

@Manual{R-tibble,
  title = {tibble: Simple Data Frames},
  author = {Kirill Müller and Hadley Wickham},
  year = {2023},
  note = {R package version 3.2.1},
  url = {https://tibble.tidyverse.org/},
}

@Manual{R-tidyr,
  title = {tidyr: Tidy Messy Data},
  author = {Hadley Wickham and Davis Vaughan and Maximilian Girlich},
  year = {2024},
  note = {R package version 1.3.1},
  url = {https://tidyr.tidyverse.org},
}

@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 and Tuomas Borman},
  year = {2025},
  note = {R package version 2.6-10},
  url = {https://github.com/vegandevs/vegan},
}

@Article{ape2019,
  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},
}

@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},
  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},
}

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

@Article{mgcv2011,
  title = {Fast stable restricted maximum likelihood and marginal 
likelihood estimation of semiparametric generalized linear models},
  journal = {Journal of the Royal Statistical Society (B)},
  volume = {73},
  number = {1},
  pages = {3-36},
  year = {2011},
  author = {S. N. Wood},
}

@Article{mgcv2016,
  title = {Smoothing parameter and model selection for general smooth models (with discussion)},
  author = {S.N. Wood and {N.} and {Pya} and B. S{"a}fken},
  journal = {Journal of the American Statistical Association},
  year = {2016},
  pages = {1548-1575},
  volume = {111},
}

@Article{mgcv2004,
  title = {Stable and efficient multiple smoothing parameter estimation for 
         generalized additive models},
  journal = {Journal of the American Statistical Association},
  volume = {99},
  number = {467},
  pages = {673-686},
  year = {2004},
  author = {S. N. Wood},
}

@Book{mgcv2017,
  title = {Generalized Additive Models: An Introduction with R},
  year = {2017},
  author = {S.N Wood},
  edition = {2},
  publisher = {Chapman and Hall/CRC},
}

@Article{mgcv2003,
  title = {Thin-plate regression splines},
  journal = {Journal of the Royal Statistical Society (B)},
  volume = {65},
  number = {1},
  pages = {95-114},
  year = {2003},
  author = {S. N. Wood},
}

@Book{nlme2000,
  title = {Mixed-Effects Models in S and S-PLUS},
  author = {José C. Pinheiro and Douglas M. Bates},
  year = {2000},
  publisher = {Springer},
  address = {New York},
  doi = {10.1007/b98882},
}

@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},
  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},
  isbn = {9780367563837},
  url = {https://bookdown.org/yihui/rmarkdown-cookbook},
}