Rpackages.bib

@Manual{broom,
  title = {broom: Convert Statistical Objects into Tidy Tibbles},
  author = {David Robinson and Alex Hayes and Simon Couch},
  year = {2020},
  note = {R package version 0.7.3},
  url = {https://CRAN.R-project.org/package=broom},
}

@Manual{caret,
  title = {caret: Classification and Regression Training},
  author = {Max Kuhn},
  year = {2020},
  note = {R package version 6.0-86},
  url = {https://github.com/topepo/caret/},
}

@Manual{ComplexHeatmap,
  title = {ComplexHeatmap: Make Complex Heatmaps},
  author = {Zuguang Gu},
  year = {2020},
  note = {https://github.com/jokergoo/ComplexHeatmap,
https://jokergoo.github.io/ComplexHeatmap-reference/book/},
}

@Manual{crosstalk,
  title = {crosstalk: Inter-Widget Interactivity for HTML Widgets},
  author = {Joe Cheng},
  year = {2020},
  note = {R package version 1.1.0.1},
  url = {https://rstudio.github.io/crosstalk/},
}

@Manual{faraway,
  title = {faraway: Functions and Datasets for Books by Julian Faraway},
  author = {Julian Faraway},
  year = {2016},
  note = {R package version 1.0.7},
  url = {http://people.bath.ac.uk/jjf23/},
}

@Manual{furrr,
  title = {furrr: Apply Mapping Functions in Parallel using Futures},
  author = {Davis Vaughan and Matt Dancho},
  year = {2020},
  note = {R package version 0.2.1},
  url = {https://github.com/DavisVaughan/furrr},
}

@Manual{future,
  title = {future: Unified Parallel and Distributed Processing in R for Everyone},
  author = {Henrik Bengtsson},
  year = {2020},
  note = {R package version 1.21.0},
  url = {https://github.com/HenrikBengtsson/future},
}

@Manual{geoR,
  title = {geoR: Analysis of Geostatistical Data},
  author = {Paulo J. {Ribeiro Jr} and Peter J. Diggle and Martin Schlather and Roger Bivand and Brian Ripley},
  year = {2020},
  note = {R package version 1.8-1},
  url = {http://www.leg.ufpr.br/geoR},
}

@Manual{ggpmisc,
  title = {ggpmisc: Miscellaneous Extensions to ggplot2},
  author = {Pedro J. Aphalo},
  year = {2020},
  note = {R package version 0.3.7},
  url = {https://CRAN.R-project.org/package=ggpmisc},
}

@Manual{ggraph,
  title = {ggraph: An Implementation of Grammar of Graphics for Graphs and Networks},
  author = {Thomas Lin Pedersen},
  year = {2020},
  note = {R package version 2.0.4},
  url = {https://CRAN.R-project.org/package=ggraph},
}

@Manual{ggridges,
  title = {ggridges: Ridgeline Plots in ggplot2},
  author = {Claus O. Wilke},
  year = {2020},
  note = {R package version 0.5.2},
  url = {https://wilkelab.org/ggridges},
}

@Manual{ggthemes,
  title = {ggthemes: Extra Themes, Scales and Geoms for ggplot2},
  author = {Jeffrey B. Arnold},
  year = {2019},
  note = {R package version 4.2.0},
  url = {http://github.com/jrnold/ggthemes},
}

@Manual{glue,
  title = {glue: Interpreted String Literals},
  author = {Jim Hester},
  year = {2020},
  note = {R package version 1.4.2},
  url = {https://CRAN.R-project.org/package=glue},
}

@Manual{gstat,
  title = {gstat: Spatial and Spatio-Temporal Geostatistical Modelling, Prediction
and Simulation},
  author = {Edzer Pebesma and Benedikt Graeler},
  year = {2020},
  note = {R package version 2.0-6},
  url = {https://github.com/r-spatial/gstat/},
}

@Manual{igraph,
  title = {igraph: Network Analysis and Visualization},
  author = {See AUTHORS file.},
  year = {2020},
  note = {R package version 1.2.6},
  url = {https://igraph.org},
}

@Manual{INLA,
  title = {INLA: Full Bayesian Analysis of Latent Gaussian Models using
Integrated Nested Laplace Approximations},
  author = {Havard Rue and Finn Lindgren and Daniel Simpson and Sara Martino and Elias {Teixeira Krainski} and Haakon Bakka and Andrea Riebler and Geir-Arne Fuglstad},
  year = {2021},
  note = {R package version 21.01.18},
}

@Manual{inlabru,
  title = {inlabru: Spatial Inference using Integrated Nested Laplace Approximation},
  author = {Fabian E. Bachl and Finn Lindgren},
  year = {2020},
  note = {R package version 2.1.13},
  url = {https://CRAN.R-project.org/package=inlabru},
}

@Manual{kableExtra,
  title = {kableExtra: Construct Complex Table with kable and Pipe Syntax},
  author = {Hao Zhu},
  year = {2020},
  note = {R package version 1.3.1},
  url = {https://CRAN.R-project.org/package=kableExtra},
}

@Manual{knitr,
  title = {knitr: A General-Purpose Package for Dynamic Report Generation in R},
  author = {Yihui Xie},
  year = {2021},
  note = {R package version 1.32},
  url = {https://yihui.org/knitr/},
}

@Manual{latex2exp,
  title = {latex2exp: Use LaTeX Expressions in Plots},
  author = {Stefano Meschiari},
  year = {2015},
  note = {R package version 0.4.0},
  url = {http://github.com/stefano-meschiari/latex2exp},
}

@Manual{leaflet,
  title = {leaflet: Create Interactive Web Maps with the JavaScript Leaflet
Library},
  author = {Joe Cheng and Bhaskar Karambelkar and Yihui Xie},
  year = {2019},
  note = {R package version 2.0.3},
  url = {http://rstudio.github.io/leaflet/},
}

@Manual{magrittr,
  title = {magrittr: A Forward-Pipe Operator for R},
  author = {Stefan Milton Bache and Hadley Wickham},
  year = {2020},
  note = {R package version 2.0.1},
  url = {https://CRAN.R-project.org/package=magrittr},
}

@Manual{memoise,
  title = {memoise: Memoisation of Functions},
  author = {Hadley Wickham and Jim Hester and Kirill Müller and Daniel Cook},
  year = {2017},
  note = {R package version 1.1.0},
  url = {https://github.com/hadley/memoise},
}

@Manual{naniar,
  title = {naniar: Data Structures, Summaries, and Visualisations for Missing Data},
  author = {Nicholas Tierney and Di Cook and Miles McBain and Colin Fay},
  year = {2020},
  note = {R package version 0.6.0},
  url = {https://github.com/njtierney/naniar},
}

@Manual{patchwork,
  title = {patchwork: The Composer of Plots},
  author = {Thomas Lin Pedersen},
  year = {2020},
  note = {R package version 1.1.1},
  url = {https://CRAN.R-project.org/package=patchwork},
}

@Manual{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{raster,
  title = {raster: Geographic Data Analysis and Modeling},
  author = {Robert J. Hijmans},
  year = {2020},
  note = {R package version 3.4-5},
  url = {https://rspatial.org/raster},
}

@Manual{reactable,
  title = {reactable: Interactive Data Tables Based on React Table},
  author = {Greg Lin},
  year = {2020},
  note = {R package version 0.2.3},
  url = {https://CRAN.R-project.org/package=reactable},
}

@Manual{rgdal,
  title = {rgdal: Bindings for the Geospatial Data Abstraction Library},
  author = {Roger Bivand and Tim Keitt and Barry Rowlingson},
  year = {2020},
  note = {R package version 1.5-18},
  url = {https://CRAN.R-project.org/package=rgdal},
}

@Manual{robotstxt,
  title = {robotstxt: A robots.txt Parser and Webbot/'Spider'/Crawler
Permissions Checker},
  author = {Peter Meissner and Kun Ren},
  year = {2020},
  note = {R package version 0.7.13},
  url = {https://CRAN.R-project.org/package=robotstxt},
}

@Manual{rvest,
  title = {rvest: Easily Harvest (Scrape) Web Pages},
  author = {Hadley Wickham},
  year = {2021},
  note = {R package version 1.0.0},
  url = {https://CRAN.R-project.org/package=rvest},
}

@Manual{scales,
  title = {scales: Scale Functions for Visualization},
  author = {Hadley Wickham and Dana Seidel},
  year = {2020},
  note = {R package version 1.1.1},
  url = {https://CRAN.R-project.org/package=scales},
}

@Manual{sf,
  title = {sf: Simple Features for R},
  author = {Edzer Pebesma},
  year = {2020},
  note = {R package version 0.9-6},
  url = {https://CRAN.R-project.org/package=sf},
}

@Manual{sp,
  title = {sp: Classes and Methods for Spatial Data},
  author = {Edzer Pebesma and Roger Bivand},
  year = {2020},
  note = {R package version 1.4-4},
  url = {https://CRAN.R-project.org/package=sp},
}

@Manual{stopwords,
  title = {stopwords: Multilingual Stopword Lists},
  author = {Kenneth Benoit and David Muhr and Kohei Watanabe},
  year = {2020},
  note = {R package version 2.1},
  url = {https://github.com/quanteda/stopwords},
}

@Manual{stringi,
  title = {stringi: Character String Processing Facilities},
  author = {Marek Gagolewski and Bartek Tartanus and and other contributors; IBM and {Unicode} and {Inc.} and other contributors; Unicode and {Inc.}},
  year = {2020},
  note = {R package version 1.5.3},
  url = {https://CRAN.R-project.org/package=stringi},
}

@Manual{tidytext,
  title = {tidytext: Text Mining using dplyr, ggplot2, and Other Tidy Tools},
  author = {David Robinson and Julia Silge},
  year = {2020},
  note = {R package version 0.2.6},
  url = {https://github.com/juliasilge/tidytext},
}

@Manual{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{viridis,
  title = {viridis: Default Color Maps from matplotlib},
  author = {Simon Garnier},
  year = {2018},
  note = {R package version 0.5.1},
  url = {https://github.com/sjmgarnier/viridis},
}

@Manual{visdat,
  title = {visdat: Preliminary Visualisation of Data},
  author = {Nicholas Tierney},
  year = {2019},
  note = {R package version 0.5.3},
  url = {https://CRAN.R-project.org/package=visdat},
}

@Manual{widyr,
  title = {widyr: Widen, Process, then Re-Tidy Data},
  author = {David Robinson},
  year = {2020},
  note = {R package version 0.1.3},
  url = {http://github.com/dgrtwo/widyr},
}

@Article{ComplexHeatmap2016,
  title = {Complex heatmaps reveal patterns and correlations in multidimensional genomic data},
  author = {Zuguang Gu and Roland Eils and Matthias Schlesner},
  journal = {Bioinformatics},
  year = {2016},
}

@Misc{future2020,
  author = {Henrik Bengtsson},
  title = {A Unifying Framework for Parallel and Distributed Processing in R using Futures},
  year = {2020},
  month = {aug},
  eprint = {2008.00553},
  archiveprefix = {arXiv},
  primaryclass = {cs.DC},
  url = {https://arxiv.org/abs/2008.00553},
}

@Article{gstat2004,
  title = {Multivariable geostatistics in {S}: the gstat package},
  author = {Edzer J. Pebesma},
  journal = {Computers & Geosciences},
  year = {2004},
  volume = {30},
  pages = {683-691},
}

@Article{gstat2016,
  title = {Spatio-Temporal Interpolation using gstat},
  author = {Benedikt Gräler and Edzer Pebesma and Gerard Heuvelink},
  year = {2016},
  journal = {The R Journal},
  volume = {8},
  issue = {1},
  pages = {204-218},
  url = {https://journal.r-project.org/archive/2016/RJ-2016-014/index.html},
}

@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},
}

@Article{INLA2009a,
  author = {H{\aa}vard Rue and Sara Martino and Nicholas Chopin},
  title = {Approximate {Bayesian} Inference for Latent {Gaussian} Models Using Integrated Nested {Laplace} Approximations (with discussion).},
  journal = {Journal of the Royal Statistical Society B},
  year = {2009},
  volume = {71},
  pages = {319--392},
}

@Article{INLA2013a,
  title = {Bayesian computing with {INLA}: {N}ew features.},
  author = {Thiago G. Martins and Daniel Simpson and Finn Lindgren and H{\aa}vard Rue},
  year = {2013},
  volume = {67},
  pages = {68--83},
  journal = {Computational Statistics and Data Analysis},
}

@Article{INLA2011a,
  title = {An Explicit Link between {Gaussian} Fields and {Gaussian} {Markov} Random Fields: The Stochastic Partial Differential Equation Approach (with discussion).},
  author = {Finn Lindgren and H{\aa}vard Rue and Johan Lindstr{\"o}m},
  year = {2011},
  volume = {73},
  number = {4},
  pages = {423--498},
  journal = {Journal of the Royal Statistical Society B},
}

@Article{INLA2015a,
  title = {Bayesian Spatial Modelling with {R}-{INLA}},
  author = {Finn Lindgren and H{\aa}vard Rue},
  journal = {Journal of Statistical Software},
  year = {2015},
  volume = {63},
  number = {19},
  pages = {1--25},
  url = {http://www.jstatsoft.org/v63/i19/},
}

@Article{INLA2017a,
  title = {Bayesian computing with {INLA}: {A} review},
  author = {H{\aa}vard Rue and Andrea I. Riebler and Sigrunn H. S{\o}rbye and Janine B. Illian and Daniel P. Simpson and Finn K. Lindgren},
  journal = {Annual Reviews of Statistics and Its Applications},
  year = {2017},
  volume = {4},
  number = {March},
  pages = {395--421},
  url = {http://arxiv.org/abs/1604.00860},
}

@Article{INLA2018a,
  title = {Spatial modelling with {INLA}: {A} review},
  author = {Haakon Bakka and H{\aa}vard Rue and Geir-Arne Fuglstad and Andrea I. Riebler and David Bolin and Janine Illian and Elias Krainski and Daniel P. Simpson and Finn K. Lindgren},
  journal = {WIRES (Invited extended review)},
  year = {2018},
  volume = {xx},
  number = {Feb},
  pages = {xx--xx},
  url = {http://arxiv.org/abs/1802.06350},
}

@Article{INLA2016a,
  title = {Needles: Toward Large-Scale Genomic Prediction with Marker-by-Environment Interaction},
  author = {Arne {De Coninck} and Bernard {De Baets} and Drosos Kourounis and Fabio Verbosio and Olaf Schenk and Steven Maenhout and Jan Fostier},
  volume = {203},
  number = {1},
  pages = {543--555},
  year = {2016},
  doi = {10.1534/genetics.115.179887},
  journal = {Genetics},
  url = {http://dx.doi.org/10.1534/genetics.115.179887},
  eprint = {http://www.genetics.org/content/203/1/543.full.pdf},
}

@Article{INLA2017b,
  title = {Enhancing the scalability of selected inversion factorization algorithms in genomic prediction},
  author = {Fabio Verbosio and Arne {De Coninck} and Drosos Kourounis and Olaf Schenk},
  journal = {Journal of Computational Science},
  volume = {22},
  number = {Supplement C},
  pages = {99-108},
  year = {2017},
  issn = {1877-7503},
  url = {https://doi.org/10.1016/j.jocs.2017.08.013},
}

@Article{INLA2018b,
  title = {Towards the Next Generation of Multiperiod Optimal Power Flow Solvers},
  author = {D. Kourounis and A. Fuchs and O. Schenk},
  journal = {IEEE Transactions on Power Systems},
  year = {2018},
  volume = {PP},
  number = {99},
  pages = {1-10},
  url = {https://doi.org/10.1109/TPWRS.2017.2789187},
}

@Article{inlabru2019,
  title = {{inlabru}: an {R} package for Bayesian spatial modelling from ecological survey data},
  author = {Fabian E. Bachl and Finn Lindgren and David L. Borchers and Janine B. Illian},
  year = {2019},
  journal = {Methods in Ecology and Evolution},
  volume = {10},
  pages = {760--766},
  doi = {10.1111/2041-210X.13168},
  publisher = {British Ecological Society},
}

@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{sf2018,
  author = {Edzer Pebesma},
  title = {{Simple Features for R: Standardized Support for Spatial Vector Data}},
  year = {2018},
  journal = {{The R Journal}},
  doi = {10.32614/RJ-2018-009},
  url = {https://doi.org/10.32614/RJ-2018-009},
  pages = {439--446},
  volume = {10},
  number = {1},
}

@Article{sp2005,
  author = {Edzer J. Pebesma and Roger S. Bivand},
  title = {Classes and methods for spatial data in {R}},
  journal = {R News},
  year = {2005},
  volume = {5},
  number = {2},
  pages = {9--13},
  month = {November},
  url = {https://CRAN.R-project.org/doc/Rnews/},
}

@Book{sp2013,
  author = {Roger S. Bivand and Edzer Pebesma and Virgilio Gomez-Rubio},
  title = {Applied spatial data analysis with {R}, Second edition},
  year = {2013},
  publisher = {Springer, NY},
  url = {https://asdar-book.org/},
}

@Manual{stringi2020,
  title = {R package stringi: Character string processing facilities},
  author = {Marek Gagolewski},
  year = {2020},
  url = {http://www.gagolewski.com/software/stringi/},
}

@Article{tidytext2016,
  title = {tidytext: Text Mining and Analysis Using Tidy Data Principles in R},
  author = {Julia Silge and David Robinson},
  doi = {10.21105/joss.00037},
  url = {http://dx.doi.org/10.21105/joss.00037},
  year = {2016},
  publisher = {The Open Journal},
  volume = {1},
  number = {3},
  journal = {JOSS},
}

@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{visdat2017,
  title = {visdat: Visualising Whole Data Frames},
  author = {Nicholas Tierney},
  doi = {10.21105/joss.00355},
  url = {http://dx.doi.org/10.21105/joss.00355},
  year = {2017},
  publisher = {Journal of Open Source Software},
  volume = {2},
  number = {16},
  pages = {355},
  journal = {JOSS},
}

@Manual{brinla,
  title = {brinla: Bayesian Regression with INLA},
  author = {Julian Faraway and Ryan Yue and Xiaofeng Wang},
  year = {2021},
  note = {R package version 0.1.0},
  url = {http://github.com/julianfaraway/brinla},
}

@Manual{ggregplot,
  title = {ggregplot: What the Package Does (Title Case)},
  author = {Who wrote it},
  year = {2021},
  note = {R package version 0.1.0},
}