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packages.bib
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@Manual{R-ade4,
title = {ade4: Analysis of Ecological Data: Exploratory and Euclidean Methods
in Environmental Sciences},
author = {Stéphane Dray and Anne-Béatrice Dufour and Jean Thioulouse and Thibaut Jombart and Sandrine Pavoine and Jean R. Lobry and Sébastien Ollier and Aurélie Siberchicot and Daniel Chessel},
year = {2023},
note = {R package version 1.7-22},
url = {http://pbil.univ-lyon1.fr/ADE-4/},
}
@Manual{R-adegenet,
title = {adegenet: Exploratory Analysis of Genetic and Genomic Data},
author = {Thibaut Jombart and Zhian N. Kamvar},
year = {2023},
note = {R package version 2.1.10},
url = {https://github.com/thibautjombart/adegenet},
}
@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 = {2024},
note = {R package version 5.8},
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 = {2024},
url = {https://www.R-project.org/},
}
@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-forcats,
title = {forcats: Tools for Working with Categorical Variables (Factors)},
author = {Hadley Wickham},
year = {2023},
note = {R package version 1.0.0,
https://github.com/tidyverse/forcats},
url = {https://forcats.tidyverse.org/},
}
@Manual{R-ggdendro,
title = {ggdendro: Create Dendrograms and Tree Diagrams Using ggplot2},
author = {Andrie {de Vries} and Brian D. Ripley},
year = {2024},
note = {R package version 0.2.0},
url = {https://andrie.github.io/ggdendro/},
}
@Manual{R-ggnewscale,
title = {ggnewscale: Multiple Fill and Colour Scales in ggplot2},
author = {Elio Campitelli},
year = {2024},
note = {R package version 0.4.10,
https://github.com/eliocamp/ggnewscale},
url = {https://eliocamp.github.io/ggnewscale/},
}
@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,
https://github.com/tidyverse/ggplot2},
url = {https://ggplot2.tidyverse.org},
}
@Manual{R-ggtree,
title = {ggtree: an R package for visualization of tree and annotation data},
author = {Guangchuang Yu and Tommy Tsan-Yuk Lam and Shuangbin Xu},
year = {2024},
note = {R package version 3.12.0},
url = {https://bioconductor.org/packages/ggtree},
doi = {10.18129/B9.bioc.ggtree},
}
@Manual{R-heatmaply,
title = {heatmaply: Interactive Cluster Heat Maps Using plotly and ggplot2},
author = {Tal Galili and Alan O'Callaghan},
year = {2023},
note = {R package version 1.5.0,
https://cran.r-project.org/package=heatmaply,
https://github.com/talgalili/heatmaply/},
url = {https://talgalili.github.io/heatmaply/},
}
@Manual{R-igraph,
title = {igraph: Network Analysis and Visualization},
author = {Gábor Csárdi and Tamás Nepusz and Vincent Traag and Szabolcs Horvát and Fabio Zanini and Daniel Noom and Kirill Müller},
year = {2024},
note = {R package version 2.0.3},
url = {https://r.igraph.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,
https://github.com/haozhu233/kableExtra},
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 = {2024},
note = {R package version 1.46},
url = {https://yihui.org/knitr/},
}
@Manual{R-lubridate,
title = {lubridate: Make Dealing with Dates a Little Easier},
author = {Vitalie Spinu and Garrett Grolemund and Hadley Wickham},
year = {2023},
note = {R package version 1.9.3,
https://github.com/tidyverse/lubridate},
url = {https://lubridate.tidyverse.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,
https://github.com/tidyverse/magrittr},
url = {https://magrittr.tidyverse.org},
}
@Manual{R-metacoder,
title = {metacoder: Tools for Parsing, Manipulating, and Graphing Taxonomic
Abundance Data},
author = {Zachary Foster},
year = {2024},
note = {R package version 0.3.7},
url = {https://grunwaldlab.github.io/metacoder_documentation/},
}
@Manual{R-palmerpenguins,
title = {palmerpenguins: Palmer Archipelago (Antarctica) Penguin Data},
author = {Allison Horst and Alison Hill and Kristen Gorman},
year = {2022},
note = {R package version 0.1.1,
https://github.com/allisonhorst/palmerpenguins},
url = {https://allisonhorst.github.io/palmerpenguins/},
}
@Manual{R-phangorn,
title = {phangorn: Phylogenetic Reconstruction and Analysis},
author = {Klaus Schliep and Emmanuel Paradis and Leonardo {de Oliveira Martins} and Alastair Potts and Iris Bardel-Kahr},
year = {2023},
note = {R package version 2.11.1,
https://klausvigo.github.io/phangorn/},
url = {https://github.com/KlausVigo/phangorn},
}
@Manual{R-pheatmap,
title = {pheatmap: Pretty Heatmaps},
author = {Raivo Kolde},
year = {2019},
note = {R package version 1.0.12},
url = {https://CRAN.R-project.org/package=pheatmap},
}
@Manual{R-phylocanvas,
title = {phylocanvas: Interactive Phylogenetic Trees Using the Phylocanvas
JavaScript Library},
author = {zachary charlop-powers},
year = {2017},
note = {R package version 0.1.3},
url = {https://github.com/zachcp/phylocanvas},
}
@Manual{R-plotly,
title = {plotly: Create Interactive Web Graphics via plotly.js},
author = {Carson Sievert and Chris Parmer and Toby Hocking and Scott Chamberlain and Karthik Ram and Marianne Corvellec and Pedro Despouy},
year = {2024},
note = {R package version 4.10.4},
url = {https://plotly-r.com},
}
@Manual{R-poppr,
title = {poppr: Genetic Analysis of Populations with Mixed Reproduction},
author = {Zhian N. Kamvar and Javier F. Tabima and Jonah C. Brooks and David Folarin},
year = {2024},
note = {R package version 2.9.6,
https://github.com/grunwaldlab/poppr/},
url = {https://grunwaldlab.github.io/poppr/},
}
@Manual{R-psminer,
title = {psminer: What the Package Does (Title Case)},
author = {Who wrote it},
note = {R package version 0.1.0},
year = {2024},
}
@Manual{R-purrr,
title = {purrr: Functional Programming Tools},
author = {Hadley Wickham and Lionel Henry},
year = {2023},
note = {R package version 1.0.2},
url = {https://purrr.tidyverse.org/},
}
@Manual{R-rcrossref,
title = {rcrossref: Client for Various CrossRef 'APIs'},
author = {Scott Chamberlain and Hao Zhu and Najko Jahn and Carl Boettiger and Karthik Ram},
year = {2022},
note = {R package version 1.2.0,
https://github.com/ropensci/rcrossref},
url = {https://docs.ropensci.org/rcrossref/},
}
@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 2.26,
https://pkgs.rstudio.com/rmarkdown/},
url = {https://github.com/rstudio/rmarkdown},
}
@Manual{R-stringr,
title = {stringr: Simple, Consistent Wrappers for Common String Operations},
author = {Hadley Wickham},
year = {2023},
note = {R package version 1.5.1,
https://github.com/tidyverse/stringr},
url = {https://stringr.tidyverse.org},
}
@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-tidyverse,
title = {tidyverse: Easily Install and Load the Tidyverse},
author = {Hadley Wickham},
year = {2023},
note = {R package version 2.0.0,
https://github.com/tidyverse/tidyverse},
url = {https://tidyverse.tidyverse.org},
}
@Manual{R-viridis,
title = {viridis: Colorblind-Friendly Color Maps for R},
author = {Simon Garnier},
year = {2024},
note = {R package version 0.6.5,
https://github.com/sjmgarnier/viridis/},
url = {https://sjmgarnier.github.io/viridis/},
}
@Manual{R-viridisLite,
title = {viridisLite: Colorblind-Friendly Color Maps (Lite Version)},
author = {Simon Garnier},
year = {2023},
note = {R package version 0.4.2,
https://github.com/sjmgarnier/viridisLite/},
url = {https://sjmgarnier.github.io/viridisLite/},
}
@Manual{R-visNetwork,
title = {visNetwork: Network Visualization using vis.js Library},
author = {{Almende B.V. and Contributors} and Benoit Thieurmel},
year = {2022},
note = {R package version 2.1.2},
url = {https://datastorm-open.github.io/visNetwork/},
}
@Manual{R-webshot2,
title = {webshot2: Take Screenshots of Web Pages},
author = {Winston Chang},
year = {2023},
note = {R package version 0.1.1,
https://github.com/rstudio/webshot2},
url = {https://rstudio.github.io/webshot2/},
}
@Manual{R-yaml,
title = {yaml: Methods to Convert R Data to YAML and Back},
author = {Shawn P Garbett and Jeremy Stephens and Kirill Simonov and Yihui Xie and Zhuoer Dong and Hadley Wickham and Jeffrey Horner and {reikoch} and Will Beasley and Brendan O'Connor and Gregory R. Warnes and Michael Quinn and Zhian N. Kamvar},
year = {2023},
note = {R package version 2.3.8},
url = {https://github.com/vubiostat/r-yaml/},
}
@Article{ade42007a,
title = {The {ade4} Package: Implementing the Duality Diagram for Ecologists},
author = {St\'ephane Dray and Anne--B\'eatrice Dufour},
journal = {Journal of Statistical Software},
year = {2007},
volume = {22},
number = {4},
pages = {1--20},
doi = {10.18637/jss.v022.i04},
}
@Article{ade42018a,
title = {Supervised Multiblock Analysis in {R} with the {ade4} Package},
author = {St\'ephanie Bougeard and St\'ephane Dray},
journal = {Journal of Statistical Software},
year = {2018},
volume = {86},
number = {1},
pages = {1--17},
doi = {10.18637/jss.v086.i01},
}
@Article{ade42004a,
title = {The {ade4} Package -- {I}: One-Table Methods},
author = {Daniel Chessel and Anne-B\'eatrice Dufour and Jean Thioulouse},
journal = {R News},
year = {2004},
volume = {4},
number = {1},
pages = {5--10},
url = {https://cran.r-project.org/doc/Rnews/},
}
@Article{ade42007b,
title = {The {ade4} Package -- {II}: Two-Table and {K}-Table Methods},
author = {St\'ephane Dray and Anne-B\'eatrice Dufour and Daniel Chessel},
journal = {R News},
year = {2007},
volume = {7},
number = {2},
pages = {47--52},
url = {https://cran.r-project.org/doc/Rnews/},
}
@Book{ade42018b,
title = {Multivariate Analysis of Ecological Data with {ade4}},
author = {Jean Thioulouse and St\'ephane Dray and Anne--B\'eatrice Dufour and Aur\'elie Siberchicot and Thibaut Jombart and Sandrine Pavoine},
year = {2018},
publisher = {Springer},
doi = {10.1007/978-1-4939-8850-1},
}
@Article{adegenet2008,
title = {adegenet: a R package for the multivariate analysis of genetic markers},
journal = {Bioinformatics},
year = {2008},
author = {T. Jombart},
volume = {24},
pages = {1403-1405},
doi = {10.1093/bioinformatics/btn129},
}
@Article{adegenet2011,
title = {adegenet 1.3-1: new tools for the analysis of genome-wide SNP data},
journal = {Bioinformatics},
year = {2011},
author = {T. Jombart and I. Ahmed},
doi = {10.1093/bioinformatics/btr521},
}
@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{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{ggtree2022a,
title = {Data Integration, Manipulation and Visualization of Phylogenetic Treess},
author = {Guangchuang Yu},
publisher = {Chapman and Hall/{CRC}},
year = {2022},
edition = {1st edition},
doi = {10.1201/9781003279242},
url = {https://www.amazon.com/Integration-Manipulation-Visualization-Phylogenetic-Computational-ebook/dp/B0B5NLZR1Z/},
}
@Article{ggtree2022b,
title = {Ggtree: A serialized data object for visualization of a phylogenetic tree and annotation data},
author = {Shuangbin Xu and Lin Li and Xiao Luo and Meijun Chen and Wenli Tang and Li Zhan and Zehan Dai and {Tommy T. Lam} and Yi Guan and Guangchuang Yu},
year = {2022},
journal = {iMeta},
volume = {1},
number = {4},
pages = {e56},
doi = {10.1002/imt2.56},
url = {https://onlinelibrary.wiley.com/doi/full/10.1002/imt2.56},
}
@Article{ggtree2020a,
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{ggtree2018a,
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{ggtree2017a,
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},
}
@Article{heatmaply2017,
author = {{Galili} and {Tal} and {O'Callaghan} and {Alan} and {Sidi} and {Jonathan} and {Sievert} and {Carson}},
title = {heatmaply: an R package for creating interactive cluster heatmaps for online publishing},
journal = {Bioinformatics},
year = {2017},
doi = {10.1093/bioinformatics/btx657},
url = {https://academic.oup.com/bioinformatics/article-pdf/doi/10.1093/bioinformatics/btx657/21358327/btx657.pdf},
}
@Article{igraph2006,
title = {The igraph software package for complex network research},
author = {Gabor Csardi and Tamas Nepusz},
journal = {InterJournal},
volume = {Complex Systems},
pages = {1695},
year = {2006},
url = {https://igraph.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},
}
@Article{lubridate2011,
title = {Dates and Times Made Easy with {lubridate}},
author = {Garrett Grolemund and Hadley Wickham},
journal = {Journal of Statistical Software},
year = {2011},
volume = {40},
number = {3},
pages = {1--25},
url = {https://www.jstatsoft.org/v40/i03/},
}
@Article{metacoder2017,
title = {Metacoder: An R package for visualization and manipulation of community taxonomic diversity data.},
author = {Zachary Foster and Thomas Sharpton and Niklaus Grünwald},
journal = {PLOS Computational Biology},
publisher = {Public Library of Science},
year = {2017},
month = {02},
volume = {13},
pages = {1-15},
number = {2},
doi = {10.1371/journal.pcbi.1005404},
url = {https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005404},
}
@Article{phangorn2011,
title = {phangorn: phylogenetic analysis in R},
author = {K.P. Schliep},
journal = {Bioinformatics},
year = {2011},
volume = {27},
number = {4},
pages = {592--593},
doi = {10.1093/bioinformatics/btq706},
}
@Article{phangorn2017,
author = {{Schliep} and {Klaus} and {Potts} and Alastair J. and {Morrison} and David A. and {Grimm} and Guido W.},
title = {Intertwining phylogenetic trees and networks},
journal = {Methods in Ecology and Evolution},
volume = {8},
number = {10},
pages = {1212--1220},
keywords = {exploratory data analysis, networks, phangorn, R, trees},
year = {2017},
}
@Book{plotly2020,
author = {Carson Sievert},
title = {Interactive Web-Based Data Visualization with R, plotly, and shiny},
publisher = {Chapman and Hall/CRC},
year = {2020},
isbn = {9781138331457},
url = {https://plotly-r.com},
}
@Article{kamvar2014poppr,
title = {\textit{Poppr}: an {R} package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction.},
author = {Zhian N. Kamvar and Javier F. Tabima and Niklaus J. Grünwald},
year = {2014},
month = {3},
volume = {2},
pages = {e281},
keywords = {population genetics, clonality, genotypic diversity, index of association, Bruvo's distance, clone correction, minimum spanning networks, hierarchy, bootstrap, permutation},
issn = {2167-8359},
url = {https://doi.org/10.7717/peerj.281},
doi = {10.7717/peerj.281},
journal = {PeerJ},
}
@Article{kamvar2015novel,
title = {{Novel R tools for analysis of genome-wide population genetic data with emphasis on clonality}},
author = {Zhian N. Kamvar and Jonah C. Brooks and Niklaus J. Grünwald},
year = {2015},
month = {6},
volume = {6},
pages = {208},
keywords = {clonality, population genomics, bootstrap, index of association, hierarchical analysis, sliding window},
url = {https://doi.org/10.3389/fgene.2015.00208},
doi = {10.3389/fgene.2015.00208},
journal = {Front. Genet.},
}
@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},
}
@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},
}
@Manual{viridis2024,
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},
}
@Manual{viridisLite2023,
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 = {2023},
note = {viridisLite package version 0.4.2},
url = {https://sjmgarnier.github.io/viridis/},
doi = {10.5281/zenodo.4678327},
}