# 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},
}
```


## data.table

```
@Manual{,
  title = {data.table: Extension of `data.frame`},
  author = {Tyson Barrett and Matt Dowle and Arun Srinivasan and Jan Gorecki and Michael Chirico and Toby Hocking and Benjamin Schwendinger and Ivan Krylov},
  year = {2025},
  note = {R package version 1.17.0},
  url = {https://CRAN.R-project.org/package=data.table},
}
```


## gghalves

```
@Manual{,
  title = {gghalves: Compose Half-Half Plots Using Your Favourite Geoms},
  author = {Frederik Tiedemann},
  year = {2022},
  note = {R package version 0.1.4},
  url = {https://CRAN.R-project.org/package=gghalves},
}
```


## 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},
}
```


## 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},
}
```


## Matrix

```
@Manual{,
  title = {Matrix: Sparse and Dense Matrix Classes and Methods},
  author = {Douglas Bates and Martin Maechler and Mikael Jagan},
  year = {2024},
  note = {R package version 1.6-5},
  url = {https://CRAN.R-project.org/package=Matrix},
}
```


## patchwork

```
@Manual{,
  title = {patchwork: The Composer of Plots},
  author = {Thomas Lin Pedersen},
  year = {2025},
  note = {R package version 1.3.1},
  url = {https://CRAN.R-project.org/package=patchwork},
}
```


## purrr

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


## R6

```
@Manual{,
  title = {R6: Encapsulated Classes with Reference Semantics},
  author = {Winston Chang},
  year = {2025},
  note = {R package version 2.6.1},
  url = {https://CRAN.R-project.org/package=R6},
}
```


## rbiom

```
@Manual{,
  title = {rbiom: Read/Write, Analyze, and Visualize 'BIOM' Data},
  author = {Daniel P. Smith},
  year = {2025},
  note = {R package version 2.2.1},
  url = {https://CRAN.R-project.org/package=rbiom},
}
```


## 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},
}
```


## rmarkdown

```
@Manual{,
  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},
}

@Book{,
  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{,
  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},
}
```


## 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},
}
```


## slam

```
@Manual{,
  title = {slam: Sparse Lightweight Arrays and Matrices},
  author = {Kurt Hornik and David Meyer and Christian Buchta},
  year = {2024},
  note = {R package version 0.1-55},
  url = {https://CRAN.R-project.org/package=slam},
}
```


## stats

```
@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/},
}
```


## tools

```
@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/},
}
```


## 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},
}
```


## viridis

```
@Manual{,
  title = {{viridis(Lite)} - Colorblind-Friendly Color Maps for R},
  author = {{Garnier} and {Simon} and {Ross} and {Noam} and {Rudis} and {Robert} and {Camargo} and Antônio Pedro and {Sciaini} and {Marco} and {Scherer} and {Cédric}},
  year = {2024},
  note = {viridis package version 0.6.5},
  url = {https://sjmgarnier.github.io/viridis/},
  doi = {10.5281/zenodo.4679423},
}
```


## 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},
}
```


## downloadthis

```
@Manual{,
  title = {downloadthis: Implement Download Buttons in 'rmarkdown'},
  author = {Felipe {Mattioni Maturana}},
  year = {2025},
  note = {R package version 0.5.0},
  url = {https://CRAN.R-project.org/package=downloadthis},
}
```


## DT

```
@Manual{,
  title = {DT: A Wrapper of the JavaScript Library 'DataTables'},
  author = {Yihui Xie and Joe Cheng and Xianying Tan},
  year = {2024},
  note = {R package version 0.33},
  url = {https://CRAN.R-project.org/package=DT},
}
```