packages.bib

@Manual{R-alphahull,
  title = {alphahull: Generalization of the Convex Hull of a Sample of Points in the
Plane},
  author = {Beatriz Pateiro-Lopez and Alberto Rodriguez-Casal and {.}},
  year = {2022},
  note = {R package version 2.5},
  url = {https://CRAN.R-project.org/package=alphahull},
}

@Manual{R-alphashape3d,
  title = {alphashape3d: Implementation of the 3D Alpha-Shape for the Reconstruction of
3D Sets from a Point Cloud},
  author = {Thomas Lafarge and Beatriz Pateiro-Lopez},
  year = {2023},
  note = {R package version 1.3.2},
  url = {https://CRAN.R-project.org/package=alphashape3d},
}

@Manual{R-animation,
  title = {animation: A Gallery of Animations in Statistics and Utilities to Create
Animations},
  author = {Yihui Xie},
  year = {2021},
  note = {R package version 2.7},
  url = {https://yihui.org/animation/},
}

@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-bookdown,
  title = {bookdown: Authoring Books and Technical Documents with R Markdown},
  author = {Yihui Xie},
  year = {2024},
  note = {R package version 0.39},
  url = {https://github.com/rstudio/bookdown},
}

@Manual{R-deldir,
  title = {deldir: Delaunay Triangulation and Dirichlet (Voronoi) Tessellation},
  author = {Rolf Turner},
  year = {2024},
  note = {R package version 2.0-4},
  url = {https://CRAN.R-project.org/package=deldir},
}

@Manual{R-DiagrammeR,
  title = {DiagrammeR: Graph/Network Visualization},
  author = {Richard Iannone and Olivier Roy},
  year = {2024},
  note = {R package version 1.0.11},
  url = {https://rich-iannone.github.io/DiagrammeR/},
}

@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-geojsonio,
  title = {geojsonio: Convert Data from and to GeoJSON or TopoJSON},
  author = {Scott Chamberlain and Andy Teucher and Michael Mahoney},
  year = {2023},
  note = {R package version 0.11.3},
  url = {https://github.com/ropensci/geojsonio},
}

@Manual{R-geojsonsf,
  title = {geojsonsf: GeoJSON to Simple Feature Converter},
  author = {David Cooley},
  year = {2022},
  note = {R package version 2.0.3},
  url = {https://github.com/SymbolixAU/geojsonsf},
}

@Manual{R-geometry,
  title = {geometry: Mesh Generation and Surface Tessellation},
  author = {Kai Habel and Raoul Grasman and Robert B. Gramacy and Pavlo Mozharovskyi and David C. Sterratt},
  year = {2023},
  note = {R package version 0.4.7},
  url = {https://davidcsterratt.github.io/geometry/},
}

@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},
  url = {https://ggplot2.tidyverse.org},
}

@Manual{R-htmlwidgets,
  title = {htmlwidgets: HTML Widgets for R},
  author = {Ramnath Vaidyanathan and Yihui Xie and JJ Allaire and Joe Cheng and Carson Sievert and Kenton Russell},
  year = {2023},
  note = {R package version 1.6.4},
  url = {https://github.com/ramnathv/htmlwidgets},
}

@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-knitr,
  title = {knitr: A General-Purpose Package for Dynamic Report Generation in R},
  author = {Yihui Xie},
  year = {2024},
  note = {R package version 1.47},
  url = {https://yihui.org/knitr/},
}

@Manual{R-leafem,
  title = {leafem: leaflet Extensions for mapview},
  author = {Tim Appelhans},
  year = {2023},
  note = {R package version 0.2.3},
  url = {https://github.com/r-spatial/leafem},
}

@Manual{R-leaflet,
  title = {leaflet: Create Interactive Web Maps with the JavaScript Leaflet
Library},
  author = {Joe Cheng and Barret Schloerke and Bhaskar Karambelkar and Yihui Xie},
  year = {2024},
  note = {R package version 2.2.2},
  url = {https://rstudio.github.io/leaflet/},
}

@Manual{R-lidR,
  title = {lidR: Airborne LiDAR Data Manipulation and Visualization for Forestry
Applications},
  author = {Jean-Romain Roussel and David Auty},
  year = {2024},
  note = {R package version 4.1.1},
  url = {https://github.com/r-lidar/lidR},
}

@Manual{R-mgcv,
  title = {mgcv: Mixed GAM Computation Vehicle with Automatic Smoothness
Estimation},
  author = {Simon Wood},
  year = {2023},
  note = {R package version 1.9-1},
  url = {https://CRAN.R-project.org/package=mgcv},
}

@Manual{R-networkD3,
  title = {networkD3: D3 JavaScript Network Graphs from R},
  author = {J.J. Allaire and Christopher Gandrud and Kenton Russell and CJ Yetman},
  year = {2017},
  note = {R package version 0.4},
  url = {https://CRAN.R-project.org/package=networkD3},
}

@Manual{R-nlme,
  title = {nlme: Linear and Nonlinear Mixed Effects Models},
  author = {José Pinheiro and Douglas Bates and {R Core Team}},
  year = {2023},
  note = {R package version 3.1-164},
  url = {https://svn.r-project.org/R-packages/trunk/nlme/},
}

@Manual{R-plyr,
  title = {plyr: Tools for Splitting, Applying and Combining Data},
  author = {Hadley Wickham},
  year = {2023},
  note = {R package version 1.8.9},
  url = {http://had.co.nz/plyr},
}

@Manual{R-raster,
  title = {raster: Geographic Data Analysis and Modeling},
  author = {Robert J. Hijmans},
  year = {2023},
  note = {R package version 3.6-26},
  url = {https://rspatial.org/raster},
}

@Manual{R-RColorBrewer,
  title = {RColorBrewer: ColorBrewer Palettes},
  author = {Erich Neuwirth},
  year = {2022},
  note = {R package version 1.1-3},
  url = {https://CRAN.R-project.org/package=RColorBrewer},
}

@Manual{R-rgl,
  title = {rgl: 3D Visualization Using OpenGL},
  author = {Daniel Adler and Duncan Murdoch},
  year = {2024},
  note = {R package version 1.3.1},
  url = {https://github.com/dmurdoch/rgl},
}

@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 2.27},
  url = {https://github.com/rstudio/rmarkdown},
}

@Manual{R-sf,
  title = {sf: Simple Features for R},
  author = {Edzer Pebesma},
  year = {2024},
  note = {R package version 1.0-16},
  url = {https://r-spatial.github.io/sf/},
}

@Manual{R-sp,
  title = {sp: Classes and Methods for Spatial Data},
  author = {Edzer Pebesma and Roger Bivand},
  year = {2024},
  note = {R package version 2.1-4},
  url = {https://github.com/edzer/sp/},
}

@Manual{R-topoDistance,
  title = {topoDistance: Calculating Topographic Paths and Distances},
  author = {Ian Wang},
  year = {2022},
  note = {R package version 1.0.2},
  url = {https://CRAN.R-project.org/package=topoDistance},
}

@Manual{R-tripack,
  title = {tripack: Triangulation of Irregularly Spaced Data},
  author = {Fortran code by R. J. Renka. R functions by Albrecht Gebhardt. With contributions from Stephen Eglen <stephen@anc.ed.ac.uk> and Sergei Zuyev and Denis White},
  year = {2020},
  note = {R package version 1.3-9.1},
  url = {https://CRAN.R-project.org/package=tripack},
}

@Manual{R-xtable,
  title = {xtable: Export Tables to LaTeX or HTML},
  author = {David B. Dahl and David Scott and Charles Roosen and Arni Magnusson and Jonathan Swinton},
  year = {2019},
  note = {R package version 1.8-4},
  url = {http://xtable.r-forge.r-project.org/},
}

@Article{animation2013,
  title = {{animation}: An {R} Package for Creating Animations and Demonstrating Statistical Methods},
  author = {Yihui Xie},
  journal = {Journal of Statistical Software},
  year = {2013},
  volume = {53},
  number = {1},
  pages = {1--27},
  url = {https://doi.org/10.18637/jss.v053.i01},
}

@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},
  isbn = {978-1138700109},
  url = {https://bookdown.org/yihui/bookdown},
}

@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{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{lidR2020,
  author = {Jean-Romain Roussel and David Auty and Nicholas C. Coops and Piotr Tompalski and Tristan R.H. Goodbody and Andrew Sánchez Meador and Jean-François Bourdon and Florian {de Boissieu} and Alexis Achim},
  title = {lidR: An R package for analysis of Airborne Laser Scanning (ALS) data},
  journal = {Remote Sensing of Environment},
  volume = {251},
  pages = {112061},
  year = {2020},
  issn = {0034-4257},
  doi = {10.1016/j.rse.2020.112061},
  url = {https://www.sciencedirect.com/science/article/pii/S0034425720304314},
}

@Article{mgcv2011,
  title = {Fast stable restricted maximum likelihood and marginal 
likelihood estimation of semiparametric generalized linear models},
  journal = {Journal of the Royal Statistical Society (B)},
  volume = {73},
  number = {1},
  pages = {3-36},
  year = {2011},
  author = {S. N. Wood},
}

@Article{mgcv2016,
  title = {Smoothing parameter and model selection for general smooth models (with discussion)},
  author = {S.N. Wood and {N.} and {Pya} and B. S{"a}fken},
  journal = {Journal of the American Statistical Association},
  year = {2016},
  pages = {1548-1575},
  volume = {111},
}

@Article{mgcv2004,
  title = {Stable and efficient multiple smoothing parameter estimation for 
         generalized additive models},
  journal = {Journal of the American Statistical Association},
  volume = {99},
  number = {467},
  pages = {673-686},
  year = {2004},
  author = {S. N. Wood},
}

@Book{mgcv2017,
  title = {Generalized Additive Models: An Introduction with R},
  year = {2017},
  author = {S.N Wood},
  edition = {2},
  publisher = {Chapman and Hall/CRC},
}

@Article{mgcv2003,
  title = {Thin-plate regression splines},
  journal = {Journal of the Royal Statistical Society (B)},
  volume = {65},
  number = {1},
  pages = {95-114},
  year = {2003},
  author = {S. N. Wood},
}

@Book{nlme2000,
  title = {Mixed-Effects Models in S and S-PLUS},
  author = {José C. Pinheiro and Douglas M. Bates},
  year = {2000},
  publisher = {Springer},
  address = {New York},
  doi = {10.1007/b98882},
}

@Article{plyr2011,
  title = {The Split-Apply-Combine Strategy for Data Analysis},
  author = {Hadley Wickham},
  journal = {Journal of Statistical Software},
  year = {2011},
  volume = {40},
  number = {1},
  pages = {1--29},
  url = {https://www.jstatsoft.org/v40/i01/},
}

@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},
}

@Book{sf2023,
  author = {Edzer Pebesma and Roger Bivand},
  title = {{Spatial Data Science: With applications in R}},
  year = {2023},
  publisher = {{Chapman and Hall/CRC}},
  url = {https://r-spatial.org/book/},
  doi = {10.1201/9780429459016},
}

@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 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/},
}

@Article{topoDistance2020,
  author = {Ian J. Wang},
  title = {Topographic path analysis for modeling dispersal and functional connectivity: calculating topographic distances using the topoDistance R package},
  year = {2020},
  journal = {Methods in Ecology and Evolution},
  volume = {11},
  pages = {265-272},
  doi = {10.1111/2041-210X.13317},
}