grateful-refs.bib

@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},
}
@Manual{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{BayesianNetworks,
title = {{BayesianNetworks}: Bayesian Modelling of Bipartite Networks},
  author = {Francisco Rodriguez-Sanchez and Jean-Gabriel Young},
  year = {2024},
  note = {R package version 0.0.7, commit 6965aa0904ca23ef532873c2adf797ed76a8a832},
  url = {https://github.com/Pakillo/BayesianNetworks},
}
@Article{bayestestR,
title = {{bayestestR}: Describing Effects and their Uncertainty, Existence and Significance within the Bayesian Framework.},
  author = {Dominique Makowski and Mattan S. Ben-Shachar and Daniel Lüdecke},
  journal = {Journal of Open Source Software},
  doi = {10.21105/joss.01541},
  year = {2019},
  number = {40},
  volume = {4},
  pages = {1541},
  url = {https://joss.theoj.org/papers/10.21105/joss.01541},
}
@Article{bipartite2009,
  title = {Indices, graphs and null models: analyzing bipartite ecological networks.},
  author = {Carsten F. Dormann and Jochen Fruend and Nico Bluethgen and Bernd Gruber},
  journal = {The Open Ecology Journal},
  volume = {2},
  pages = {7-24},
  year = {2009},
}

@Article{bipartite2008,
  title = {Introducing the bipartite Package: Analysing Ecological Networks.},
  author = {Carsten F. Dormann and Bernd Gruber and Jochen Fruend},
  journal = {R News},
  volume = {8},
  number = {2},
  pages = {8-11},
  year = {2008},
}

@Article{bipartite2011,
  title = {How to be a specialist? Quantifying specialisation in pollination networks.},
  author = {Carsten F. Dormann},
  journal = {Network Biology},
  volume = {1},
  number = {1},
  pages = {1-20},
  year = {2011},
}
@Manual{cluster,
title = {{cluster}: Cluster Analysis Basics and Extensions},
  author = {Martin Maechler and Peter Rousseeuw and Anja Struyf and Mia Hubert and Kurt Hornik},
  year = {2023},
  url = {https://CRAN.R-project.org/package=cluster},
  note = {R package version 2.1.6 --- For new features, see the 'NEWS' and the 'Changelog' file in the package source)},
}
@Manual{datatable,
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},
  year = {2024},
  note = {R package version 1.15.4},
  url = {https://CRAN.R-project.org/package=data.table},
}
@Manual{DHARMa,
title = {{DHARMa}: Residual Diagnostics for Hierarchical (Multi-Level / Mixed)
Regression Models},
  author = {Florian Hartig},
  year = {2022},
  note = {R package version 0.4.6},
  url = {https://CRAN.R-project.org/package=DHARMa},
}
@Manual{fmsb,
title = {{fmsb}: Functions for Medical Statistics Book with some Demographic Data},
  author = {Minato Nakazawa},
  year = {2024},
  note = {R package version 0.7.6},
  url = {https://CRAN.R-project.org/package=fmsb},
}
@Manual{GGally,
title = {{GGally}: Extension to `{ggplot2}'},
  author = {Barret Schloerke and Di Cook and Joseph Larmarange and Francois Briatte and Moritz Marbach and Edwin Thoen and Amos Elberg and Jason Crowley},
  year = {2024},
  note = {R package version 2.2.1},
  url = {https://CRAN.R-project.org/package=GGally},
}
@Manual{ggcorrplot,
title = {{ggcorrplot}: Visualization of a Correlation Matrix using `{ggplot2}'},
  author = {Alboukadel Kassambara},
  year = {2023},
  note = {R package version 0.1.4.1},
  url = {https://CRAN.R-project.org/package=ggcorrplot},
}
@Article{ggdist2024a,
  author = {Matthew Kay},
  title = {{ggdist}: Visualizations of Distributions and Uncertainty in the Grammar of Graphics},
  journal = {IEEE Transactions on Visualization and Computer Graphics},
  year = {2024},
  volume = {30},
  number = {1},
  pages = {414--424},
  doi = {10.1109/TVCG.2023.3327195},
}

@Manual{ggdist2024b,
  title = {{ggdist}: Visualizations of Distributions and Uncertainty},
  author = {Matthew Kay},
  year = {2024},
  note = {R package version 3.3.2},
  url = {https://mjskay.github.io/ggdist/},
  doi = {10.5281/zenodo.3879620},
}
@Article{ggfortify2016,
  author = {Yuan Tang and Masaaki Horikoshi and Wenxuan Li},
title = {{ggfortify}: Unified Interface to Visualize Statistical Result of Popular R Packages},
  journal = {The R Journal},
  year = {2016},
  number = {2},
  volume = {8},
  pages = {474--485},
  url = {https://doi.org/10.32614/RJ-2016-060},
  doi = {10.32614/RJ-2016-060},
}

@Manual{ggfortify2018,
  author = {Masaaki Horikoshi and Yuan Tang},
title = {{ggfortify}: Data Visualization Tools for Statistical Analysis Results},
  year = {2018},
  url = {https://CRAN.R-project.org/package=ggfortify},
}
@Manual{ggh4x,
  title = {ggh4x: Hacks for `{ggplot2}'},
  author = {Teun {van den Brand}},
  year = {2024},
  note = {R package version 0.2.8},
  url = {https://CRAN.R-project.org/package=ggh4x},
}
@Manual{ggrepel,
title = {{ggrepel}: Automatically Position Non-Overlapping Text Labels with
`{ggplot2}'},
  author = {Kamil Slowikowski},
  year = {2024},
  note = {R package version 0.9.5},
  url = {https://CRAN.R-project.org/package=ggrepel},
}
@Manual{ggridges,
title = {{ggridges}: Ridgeline Plots in `{ggplot2}'},
  author = {Claus O. Wilke},
  year = {2024},
  note = {R package version 0.5.6},
  url = {https://CRAN.R-project.org/package=ggridges},
}
@Article{glmmTMB,
  author = {Mollie E. Brooks and Kasper Kristensen and Koen J. {van Benthem} and Arni Magnusson and Casper W. Berg and Anders Nielsen and Hans J. Skaug and Martin Maechler and Benjamin M. Bolker},
  title = {{glmmTMB} Balances Speed and Flexibility Among Packages for Zero-inflated Generalized Linear Mixed Modeling},
  year = {2017},
  journal = {The R Journal},
  doi = {10.32614/RJ-2017-066},
  pages = {378--400},
  volume = {9},
  number = {2},
}
@Manual{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{here,
title = {{here}: A Simpler Way to Find Your Files},
  author = {Kirill Müller},
  year = {2020},
  note = {R package version 1.0.1},
  url = {https://CRAN.R-project.org/package=here},
}
@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},
}

@Manual{igraph2024,
  title = {{igraph}: Network Analysis and Visualization in R},
  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},
  doi = {10.5281/zenodo.7682609},
  url = {https://CRAN.R-project.org/package=igraph},
}
@Manual{iNEXT2024,
title = {{iNEXT}: Interpolation and Extrapolation for Species Diversity},
  author = {T. C. Hsieh and K. H. Ma and Anne Chao},
  year = {2024},
  note = {R package version 3.0.1},
  url = {http://chao.stat.nthu.edu.tw/wordpress/software_download/},
}

@Article{iNEXT2014,
  title = {Rarefaction and extrapolation with Hill numbers: a framework for sampling and estimation in species diversity studies},
  author = {Anne Chao and Nicholas J. Gotelli and T. C. Hsieh and Elizabeth L. Sander and K. H. Ma and Robert K. Colwell and Aaron M. Ellison},
  journal = {Ecological Monographs},
  year = {2014},
  volume = {84},
  pages = {45--67},
}
@Manual{knitr2024,
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/},
}

@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},
}
@Manual{MetBrewer,
title = {{MetBrewer}: Color Palettes Inspired by Works at the Metropolitan Museum of
Art},
  author = {Blake Robert Mills},
  year = {2022},
  note = {R package version 0.2.0},
  url = {https://CRAN.R-project.org/package=MetBrewer},
}
@Article{modelbased,
  title = {Estimation of Model-Based Predictions, Contrasts and Means.},
  author = {Dominique Makowski and Mattan S. Ben-Shachar and Indrajeet Patil and Daniel Lüdecke},
  journal = {CRAN},
  year = {2020},
  url = {https://github.com/easystats/modelbased},
}
@Manual{networktools,
title = {{network.tools}: Tools to Analyse and Visualise Bipartite Networks},
  author = {Francisco Rodriguez-Sanchez},
  year = {2024},
  note = {R package version 0.0.4, commit 60f8ecab55befe1fdade39d16ba603cc936a1000},
  url = {https://github.com/Pakillo/network.tools},
}
@Manual{paletteer,
title = {{paletteer}: Comprehensive Collection of Color Palettes},
  author = {Emil Hvitfeldt},
  year = {2021},
  note = {R package version 1.3.0},
  url = {https://github.com/EmilHvitfeldt/paletteer},
}
@Manual{patchwork,
title = {{patchwork}: The Composer of Plots},
  author = {Thomas Lin Pedersen},
  year = {2024},
  note = {R package version 1.2.0},
  url = {https://CRAN.R-project.org/package=patchwork},
}
@Manual{psych,
title = {{psych}: Procedures for Psychological, Psychometric, and Personality Research},
  author = {{William Revelle}},
  organization = {Northwestern University},
  address = {Evanston, Illinois},
  year = {2024},
  note = {R package version 2.4.3},
  url = {https://CRAN.R-project.org/package=psych},
}
@Manual{rcartocolor,
  author = {Jakub Nowosad},
  title = {`{CARTOColors}' Palettes},
  year = {2018},
  note = {R package version 1.0.0},
  url = {https://jakubnowosad.com/rcartocolor/},
}
@Manual{renv,
title = {{renv}: Project Environments},
  author = {Kevin Ushey and Hadley Wickham},
  year = {2024},
  note = {R package version 1.0.7},
  url = {https://CRAN.R-project.org/package=renv},
}
@Article{reshape2,
  title = {Reshaping Data with the {reshape} Package},
  author = {Hadley Wickham},
  journal = {Journal of Statistical Software},
  year = {2007},
  volume = {21},
  number = {12},
  pages = {1--20},
  url = {http://www.jstatsoft.org/v21/i12/},
}
@Manual{rmarkdown2024,
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},
  url = {https://github.com/rstudio/rmarkdown},
}

@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},
}
@Manual{scales,
title = {{scales}: Scale Functions for Visualization},
  author = {Hadley Wickham and Thomas Lin Pedersen and Dana Seidel},
  year = {2023},
  note = {R package version 1.3.0},
  url = {https://CRAN.R-project.org/package=scales},
}
@Manual{summarytools,
title = {{summarytools}: Tools to Quickly and Neatly Summarize Data},
  author = {Dominic Comtois},
  year = {2022},
  note = {R package version 1.0.1},
  url = {https://CRAN.R-project.org/package=summarytools},
}
@Manual{tidylog,
title = {{tidylog}: Logging for `{dplyr}' and `{tidyr}' Functions},
  author = {Benjamin Elbers},
  year = {2020},
  note = {R package version 1.0.2},
  url = {https://CRAN.R-project.org/package=tidylog},
}
@Book{tnet,
  title = {Structure and Evolution of Weighted Networks},
  author = {Tore Opsahl},
  year = {2009},
  publisher = {University of London (Queen Mary College), London, UK},
  pages = {104-122},
  url = {http://toreopsahl.com/publications/thesis/},
}
@Article{tidyverse,
  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},
}