packages.bib

@Manual{R-agridat,
  title = {agridat: Agricultural Datasets},
  author = {Kevin Wright},
  year = {2022},
  note = {R package version 1.21},
  url = {https://kwstat.github.io/agridat/},
}

@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 = {2023},
  url = {https://www.R-project.org/},
}

@Manual{R-bookdown,
  title = {bookdown: Authoring Books and Technical Documents with R Markdown},
  author = {Yihui Xie},
  year = {2023},
  note = {R package version 0.35},
  url = {https://CRAN.R-project.org/package=bookdown},
}

@Manual{R-breedR,
  title = {breedR: Statistical Methods for Forest Genetic Resources Analysts},
  author = {Facundo Muñoz and Leopoldo Sanchez},
  year = {2020},
  note = {R package version 0.12-5},
  url = {https://github.com/famuvie/breedR},
}

@Manual{R-desplot,
  title = {desplot: Plotting Field Plans for Agricultural Experiments},
  author = {Kevin Wright},
  year = {2023},
  note = {R package version 1.10},
  url = {https://kwstat.github.io/desplot/},
}

@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 1.1.2},
  url = {https://CRAN.R-project.org/package=dplyr},
}

@Manual{R-emmeans,
  title = {emmeans: Estimated Marginal Means, aka Least-Squares Means},
  author = {Russell V. Lenth},
  year = {2023},
  note = {R package version 1.8.8},
  url = {https://github.com/rvlenth/emmeans},
}

@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 = {2023},
  note = {R package version 3.4.3},
  url = {https://CRAN.R-project.org/package=ggplot2},
}

@Manual{R-gstat,
  title = {gstat: Spatial and Spatio-Temporal Geostatistical Modelling, Prediction
and Simulation},
  author = {Edzer Pebesma and Benedikt Graeler},
  year = {2023},
  note = {R package version 2.1-1},
  url = {https://github.com/r-spatial/gstat/},
}

@Manual{R-knitr,
  title = {knitr: A General-Purpose Package for Dynamic Report Generation in R},
  author = {Yihui Xie},
  year = {2023},
  note = {R package version 1.43},
  url = {https://yihui.org/knitr/},
}

@Manual{R-lme4,
  title = {lme4: Linear Mixed-Effects Models using Eigen and S4},
  author = {Douglas Bates and Martin Maechler and Ben Bolker and Steven Walker},
  year = {2023},
  note = {R package version 1.1-34},
  url = {https://github.com/lme4/lme4/},
}

@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 3.1-162},
  url = {https://svn.r-project.org/R-packages/trunk/nlme/},
}

@Manual{R-psych,
  title = {psych: Procedures for Psychological, Psychometric, and Personality
Research},
  author = {William Revelle},
  year = {2023},
  note = {R package version 2.3.6},
  url = {https://personality-project.org/r/psych/
https://personality-project.org/r/psych-manual.pdf},
}

@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://CRAN.R-project.org/package=purrr},
}

@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 = {2023},
  note = {R package version 2.24},
  url = {https://CRAN.R-project.org/package=rmarkdown},
}

@Manual{R-sf,
  title = {sf: Simple Features for R},
  author = {Edzer Pebesma},
  year = {2023},
  note = {R package version 1.0-14},
  url = {https://CRAN.R-project.org/package=sf},
}

@Manual{R-sp,
  title = {sp: Classes and Methods for Spatial Data},
  author = {Edzer Pebesma and Roger Bivand},
  year = {2023},
  note = {R package version 2.0-0},
  url = {https://CRAN.R-project.org/package=sp},
}

@Manual{R-spaMM,
  title = {spaMM: Mixed-Effect Models, with or without Spatial Random Effects},
  author = {François Rousset and Jean-Baptiste Ferdy and Alexandre Courtiol},
  year = {2023},
  note = {R package version 4.3.20},
  url = {https://CRAN.R-project.org/package=spaMM},
}

@Manual{R-SpATS,
  title = {SpATS: Spatial Analysis of Field Trials with Splines},
  author = {{Maria Xose Rodriguez-Alvarez} and {Martin Boer} and {Paul Eilers}},
  year = {2022},
  note = {R package version 1.0-18},
  url = {https://CRAN.R-project.org/package=SpATS},
}

@Manual{R-spdep,
  title = {spdep: Spatial Dependence: Weighting Schemes, Statistics},
  author = {Roger Bivand},
  year = {2023},
  note = {R package version 1.2-8},
  url = {https://CRAN.R-project.org/package=spdep},
}

@Manual{R-tidyr,
  title = {tidyr: Tidy Messy Data},
  author = {Hadley Wickham and Davis Vaughan and Maximilian Girlich},
  year = {2023},
  note = {R package version 1.3.0},
  url = {https://CRAN.R-project.org/package=tidyr},
}

@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{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},
}

@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{lme42015,
  title = {Fitting Linear Mixed-Effects Models Using {lme4}},
  author = {Douglas Bates and Martin M{\"a}chler and Ben Bolker and Steve Walker},
  journal = {Journal of Statistical Software},
  year = {2015},
  volume = {67},
  number = {1},
  pages = {1--48},
  doi = {10.18637/jss.v067.i01},
}

@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},
}

@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{spaMM2014,
  title = {Testing environmental and genetic effects in the presence of spatial autocorrelation},
  author = {François Rousset and Jean-Baptiste Ferdy},
  journal = {Ecography},
  year = {2014},
  volume = {37},
  number = {8},
  pages = {781-790},
  url = {https://dx.doi.org/10.1111/ecog.00566},
}

@Article{SpATS2017,
  title = {Correcting for spatial heterogeneity in plant breeding experiments with P-splines},
  author = {Mar{\'i}a Xos{\'e} Rodr{\'i}guez-{\'A}lvarez and Martin P. Boer and Fred A. {van Eeuwijk} and Paul H.C. Eilers},
  journal = {Spatial Statistics},
  year = {2017},
  volume = {23},
  pages = {52 - 71},
  url = {https://doi.org/10.1016/j.spasta.2017.10.003},
}

@Article{spdep2018,
  author = {Roger Bivand and David W. S. Wong},
  title = {Comparing implementations of global and local indicators of spatial association},
  journal = {TEST},
  year = {2018},
  volume = {27},
  number = {3},
  pages = {716--748},
  doi = {10.1007/s11749-018-0599-x},
}

@Article{spdep2022,
  author = {{Roger Bivand}},
  title = {R Packages for Analyzing Spatial Data: A Comparative Case Study with Areal Data},
  journal = {Geographical Analysis},
  year = {2022},
  volume = {54},
  number = {3},
  pages = {488-518},
  doi = {10.1111/gean.12319},
}

@Book{spdep2013,
  author = {Roger S. Bivand and Edzer Pebesma and Virgilio Gómez-Rubio},
  title = {Applied spatial data analysis with {R}, Second edition},
  year = {2013},
  publisher = {Springer, NY},
  url = {https://asdar-book.org/},
}

@Book{spdep2023,
  author = {Edzer Pebesma and Roger S. Bivand},
  title = {Spatial Data Science With Applications in {R}},
  year = {2023},
  publisher = {Chapman & Hall},
  url = {https://r-spatial.org/book/},
}