packages.bib

@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 0.37, 
https://pkgs.rstudio.com/bookdown/},
  url = {https://github.com/rstudio/bookdown},
}

@Manual{R-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 = {http://florianhartig.github.io/DHARMa/},
}

@Manual{R-gamlss,
  title = {gamlss: Generalised Additive Models for Location Scale and Shape},
  author = {Mikis Stasinopoulos and Robert Rigby},
  year = {2023},
  note = {R package version 5.4-20},
  url = {https://www.gamlss.com/},
}

@Manual{R-ggeffects,
  title = {ggeffects: Create Tidy Data Frames of Marginal Effects for ggplot from
Model Outputs},
  author = {Daniel Lüdecke},
  year = {2024},
  note = {R package version 1.5.0},
  url = {https://strengejacke.github.io/ggeffects/},
}


@Manual{R-glmmTMB,
  title = {glmmTMB: Generalized Linear Mixed Models using Template Model Builder},
  author = {Mollie Brooks and Ben Bolker and Kasper Kristensen and Martin Maechler and Arni Magnusson and Hans Skaug and Anders Nielsen and Casper Berg and Koen {van Bentham}},
  year = {2023},
  note = {R package version 1.1.8},
  url = {https://github.com/glmmTMB/glmmTMB},
}


@Manual{R-knitr,
  title = {knitr: A General-Purpose Package for Dynamic Report Generation in R},
  author = {Yihui Xie},
  year = {2023},
  note = {R package version 1.45},
  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 1.1-35.1},
  url = {https://github.com/lme4/lme4/},
}

@Manual{R-marginaleffects,
  title = {marginaleffects: Predictions, Comparisons, Slopes, Marginal Means, and Hypothesis
Tests},
  author = {Vincent Arel-Bundock},
  year = {2024},
  note = {R package version 0.18.0},
  url = {https://marginaleffects.com/},
}

@Manual{R-MASS,
  title = {MASS: Support Functions and Datasets for Venables and Ripley's MASS},
  author = {Brian Ripley},
  year = {2023},
  note = {R package version 7.3-60},
  url = {http://www.stats.ox.ac.uk/pub/MASS4/},
}

@Manual{R-mclogit,
  title = {mclogit: Multinomial Logit Models, with or without Random Effects or
Overdispersion},
  author = {Martin Elff},
  year = {2022},
  note = {R package version 0.9.6, https://github.com/melff/mclogit/},
  url = {http://mclogit.elff.eu},
}



@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 3.1-163},
  url = {https://svn.r-project.org/R-packages/trunk/nlme/},
}

@Manual{R-ordinal,
  title = {ordinal: Regression Models for Ordinal Data},
  author = {Rune Haubo Bojesen Christensen},
  year = {2023},
  note = {R package version 2023.12-4},
  url = {https://github.com/runehaubo/ordinal},
}

@Manual{R-pbkrtest,
  title = {pbkrtest: Parametric Bootstrap, Kenward-Roger and Satterthwaite Based
Methods for Test in Mixed Models},
  author = {Ulrich Halekoh and Søren Højsgaard},
  year = {2023},
  note = {R package version 0.5.2},
  url = {https://people.math.aau.dk/~sorenh/software/pbkrtest/},
}

@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-RLRsim,
  title = {RLRsim: Exact (Restricted) Likelihood Ratio Tests for Mixed and Additive
Models},
  author = {Fabian Scheipl},
  year = {2022},
  note = {R package version 3.1-8},
  url = {https://github.com/fabian-s/RLRsim},
}

@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 2.25, 
https://pkgs.rstudio.com/rmarkdown/},
  url = {https://github.com/rstudio/rmarkdown},
}



@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},
}

@Article{gamlss2005,
  title = {Generalized additive models for location, scale and shape,(with discussion)},
  journal = {Applied Statistics},
  volume = {54},
  part = {3},
  pages = {507-554},
  year = {2005},
  author = {{R. A. Rigby} and {D. M. Stasinopoulos}},
}

@Article{ggeffects2018,
  title = {ggeffects: Tidy Data Frames of Marginal Effects from Regression Models.},
  volume = {3},
  doi = {10.21105/joss.00772},
  number = {26},
  journal = {Journal of Open Source Software},
  author = {Daniel Lüdecke},
  year = {2018},
  pages = {772},
}

@Article{glmmTMB2017,
  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},
}

@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},
}

@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{MASS2002,
  title = {Modern Applied Statistics with S},
  author = {W. N. Venables and B. D. Ripley},
  publisher = {Springer},
  edition = {Fourth},
  address = {New York},
  year = {2002},
  note = {ISBN 0-387-95457-0},
  url = {https://www.stats.ox.ac.uk/pub/MASS4/},
}

@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{pbkrtest2014,
  title = {A Kenward-Roger Approximation and Parametric Bootstrap Methods for Tests in Linear Mixed Models -- The {R} Package {pbkrtest}},
  author = {Ulrich Halekoh and S{\o}ren H{\o}jsgaard},
  journal = {Journal of Statistical Software},
  year = {2014},
  volume = {59},
  number = {9},
  pages = {1--30},
  url = {https://www.jstatsoft.org/v59/i09/},
}

@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{RLRsim2008,
  title = {Size and power of tests for a zero random effect variance or polynomial
               regression in additive and linear mixed models.},
  author = {Fabian Scheipl and Sonja Greven and Helmut Kuechenhoff},
  year = {2008},
  journal = {Computational Statistics & Data Analysis},
  volume = {52},
  number = {7},
  pages = {3283--3299},
}

@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{scatterplot3d2003,
  title = {Scatterplot3d - an R Package for Visualizing Multivariate Data},
  author = {Uwe Ligges and Martin M{\"a}chler},
  journal = {Journal of Statistical Software},
  year = {2003},
  pages = {1--20},
  number = {11},
  volume = {8},
  doi = {10.18637/jss.v008.i11},
}

@Article{statmod2016a,
  author = {Goknur Giner and Gordon K. Smyth},
  year = {2016},
  title = {statmod: probability calculations for the inverse Gaussian distribution},
  journal = {R Journal},
  volume = {8},
  number = {1},
  pages = {339-351},
}

@Article{statmod2010a,
  author = {Belinda Phipson and Gordon K. Smyth},
  year = {2010},
  title = {Permutation p-values should never be zero: calculating exact p-values when permutations are randomly drawn},
  journal = {Statistical Applications in Genetics and Molecular Biology},
  volume = {9},
  number = {1},
  pages = {Article 39},
}

@Article{statmod2009a,
  author = {Yifang Hu and Gordon K. Smyth},
  year = {2009},
  title = {ELDA: extreme limiting dilution analysis for comparing depleted and enriched populations in stem cell and other assays},
  journal = {Journal of Immunological Methods},
  volume = {347},
  number = {1},
  pages = {70-78},
}

@Article{statmod2005a,
  author = {Gordon K. Smyth},
  title = {Optimization and nonlinear equations},
  journal = {Encyclopedia of Biostatistics},
  year = {2005},
  publisher = {John Wiley and Sons, Ltd},
  pages = {3088-3095},
}

@Article{statmod2005b,
  author = {Gordon K. Smyth},
  title = {Numerical integration},
  journal = {Encyclopedia of Biostatistics},
  year = {2005},
  publisher = {John Wiley and Sons, Ltd},
  pages = {3088-3095},
}

@Article{statmod2002a,
  author = {Gordon K. Smyth},
  year = {2002},
  title = {An efficient algorithm for REML in heteroscedastic regression},
  journal = {Journal of Computational and Graphical Statistics},
  volume = {11},
  pages = {836-847},
}

@Article{statmod1996a,
  author = {Peter K. Dunn and Gordon K. Smyth},
  year = {1996},
  title = {Randomized quantile residuals},
  journal = {J. Comput. Graph. Statist},
  volume = {5},
  pages = {236-244},
}