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@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 = {2020},
note = {R package version 5.4},
url = {https://CRAN.R-project.org/package=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 = {2020},
url = {https://www.R-project.org/},
}
@Manual{R-bookdown,
title = {bookdown: Authoring Books and Technical Documents with R Markdown},
author = {Yihui Xie},
year = {2020},
note = {R package version 0.20},
url = {https://CRAN.R-project.org/package=bookdown},
}
@Manual{R-dplyr,
title = {dplyr: A Grammar of Data Manipulation},
author = {Hadley Wickham and Romain François and Lionel Henry and Kirill Müller},
year = {2020},
note = {R package version 1.0.0},
url = {https://CRAN.R-project.org/package=dplyr},
}
@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-geiger,
title = {geiger: Analysis of Evolutionary Diversification},
author = {Luke Harmon and Matthew Pennell and Chad Brock and Joseph Brown and Wendell Challenger and Jon Eastman and Rich FitzJohn and Rich Glor and Gene Hunt and Liam Revell and Graham Slater and Josef Uyeda and Jason Weir},
year = {2020},
note = {R package version 2.0.7},
url = {https://CRAN.R-project.org/package=geiger},
}
@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-ggtree,
title = {ggtree: an R package for visualization of tree and annotation data},
author = {Guangchuang Yu and Tommy Tsan-Yuk Lam},
year = {2020},
note = {R package version 2.2.3},
url = {https://yulab-smu.github.io/treedata-book/},
}
@Manual{R-gridExtra,
title = {gridExtra: Miscellaneous Functions for "Grid" Graphics},
author = {Baptiste Auguie},
year = {2017},
note = {R package version 2.3},
url = {https://CRAN.R-project.org/package=gridExtra},
}
@Manual{R-knitr,
title = {knitr: A General-Purpose Package for Dynamic Report Generation in R},
author = {Yihui Xie},
year = {2020},
note = {R package version 1.29},
url = {https://CRAN.R-project.org/package=knitr},
}
@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-maps,
title = {maps: Draw Geographical Maps},
author = {Ray Brownrigg},
year = {2018},
note = {R package version 3.3.0},
url = {https://CRAN.R-project.org/package=maps},
}
@Manual{R-Matrix,
title = {Matrix: Sparse and Dense Matrix Classes and Methods},
author = {Douglas Bates and Martin Maechler},
year = {2019},
note = {R package version 1.2-18},
url = {https://CRAN.R-project.org/package=Matrix},
}
@Manual{R-phytools,
title = {phytools: Phylogenetic Tools for Comparative Biology (and Other Things)},
author = {Liam J. Revell},
year = {2020},
note = {R package version 0.7-47},
url = {https://CRAN.R-project.org/package=phytools},
}
@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-readr,
title = {readr: Read Rectangular Text Data},
author = {Hadley Wickham and Jim Hester and Romain Francois},
year = {2018},
note = {R package version 1.3.1},
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 = {2020},
note = {R package version 2.3},
url = {https://CRAN.R-project.org/package=rmarkdown},
}
@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 3.0.3},
url = {https://CRAN.R-project.org/package=tibble},
}
@Manual{R-tidyr,
title = {tidyr: Tidy Messy Data},
author = {Hadley Wickham and Lionel Henry},
year = {2020},
note = {R package version 1.1.0},
url = {https://CRAN.R-project.org/package=tidyr},
}
@Manual{R-tidyverse,
title = {tidyverse: Easily Install and Load the 'Tidyverse'},
author = {Hadley Wickham},
year = {2019},
note = {R package version 1.3.0},
url = {https://CRAN.R-project.org/package=tidyverse},
}
@Manual{R-treeio,
title = {treeio: Base Classes and Functions for Phylogenetic Tree Input and
Output},
author = {Guangchuang Yu},
year = {2020},
note = {https://github.com/YuLab-SMU/treeio (devel),
https://docs.ropensci.org/treeio/ (docs),
https://yulab-smu.github.io/treedata-book/ (book)},
}
@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://github.com/rstudio/bookdown},
}
@Article{geiger2009,
title = {Nine exceptional radiations plus high turnover explain species diversity in jawed vertebrates},
author = {ME Alfaro and F Santini and C Brock and H Alamillo and A Dornburg and DL Rabosky and G Carnevale and LJ Harmon},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
year = {2009},
volume = {106},
pages = {13410-13414},
}
@Article{geiger2011,
title = {A novel comparative method for identifying shifts in the rate of character evolution on trees},
author = {JM Eastman and ME Alfaro and P Joyce and AL Hipp and LJ Harmon},
journal = {Evolution},
year = {2011},
volume = {65},
pages = {3578-3589},
}
@Article{geiger2012,
title = {Fitting models of continuous trait evolution to incompletely sampled comparative data using approximate Bayesian computation},
author = {GJ Slater and LJ Harmon and D Wegmann and P Joyce and LJ Revell and ME Alfaro},
journal = {Evolution},
year = {2012},
volume = {66},
pages = {752-762},
}
@Article{geiger2008,
title = {GEIGER: investigating evolutionary radiations},
author = {LJ Harmon and JT Weir and CD Brock and RE Glor and W Challenger},
journal = {Bioinformatics},
year = {2008},
volume = {24},
pages = {129-131},
}
@Article{geiger2014,
title = {geiger v2.0: an expanded suite of methods for fitting macroevolutionary models to phylogenetic trees},
author = {MW Pennell and JM Eastman and GJ Slater and JW Brown and JC Uyeda and RG Fitzjohn and ME Alfaro and LJ Harmon},
journal = {Bioinformatics},
year = {2014},
volume = {30},
pages = {2216-2218},
}
@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{ggtree2020,
title = {Using ggtree to Visualize Data on Tree-Like Structures},
author = {Guangchuang Yu},
year = {2020},
journal = {Current Protocols in Bioinformatics},
volume = {69},
pages = {e96},
number = {1},
url = {https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/cpbi.96},
doi = {10.1002/cpbi.96},
}
@Article{ggtree2018,
title = {Two methods for mapping and visualizing associated data on phylogeny using ggtree.},
author = {Guangchuang Yu and Tommy Tsan-Yuk Lam and Huachen Zhu and Yi Guan},
year = {2018},
journal = {Molecular Biology and Evolution},
volume = {35},
issue = {2},
pages = {3041-3043},
doi = {10.1093/molbev/msy194},
url = {https://academic.oup.com/mbe/article/35/12/3041/5142656},
}
@Article{ggtree2017,
title = {ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data.},
author = {Guangchuang Yu and David Smith and Huachen Zhu and Yi Guan and Tommy Tsan-Yuk Lam},
year = {2017},
journal = {Methods in Ecology and Evolution},
volume = {8},
issue = {1},
pages = {28-36},
doi = {10.1111/2041-210X.12628},
url = {http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12628/abstract},
}
@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{phytools2012,
title = {phytools: An R package for phylogenetic comparative biology (and other things).},
author = {Liam J. Revell},
journal = {Methods in Ecology and Evolution},
year = {2012},
volume = {3},
pages = {217-223},
}
@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},
}
@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},
}
@Article{treeio2020,
title = {treeio: an R package for phylogenetic tree input and output with richly annotated and associated data.},
author = {Li-Gen Wang and Tommy Tsan-Yuk Lam and Shuangbin Xu and Zehan Dai and Lang Zhou and Tingze Feng and Pingfan Guo and Casey W. Dunn and Bradley R. Jones and Tyler Bradley and Huachen Zhu and Yi Guan and Yong Jiang and Guangchuang Yu},
year = {2020},
journal = {Molecular Biology and Evolution},
volume = {37},
issue = {2},
pages = {599-603},
doi = {10.1093/molbev/msz240},
}