packages.bib

@Manual{R-assertthat,
  title = {assertthat: Easy Pre and Post Assertions},
  author = {Hadley Wickham},
  year = {2019},
  note = {R package version 0.2.1},
  url = {https://CRAN.R-project.org/package=assertthat},
}

@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 = {2021},
  url = {https://www.R-project.org/},
}

@Manual{R-bookdown,
  title = {bookdown: Authoring Books and Technical Documents with R Markdown},
  author = {Yihui Xie},
  year = {2021},
  note = {R package version 0.22},
  url = {https://CRAN.R-project.org/package=bookdown},
}

@Manual{R-data.table,
  title = {data.table: Extension of `data.frame`},
  author = {Matt Dowle and Arun Srinivasan},
  year = {2021},
  note = {R package version 1.14.2},
  url = {https://CRAN.R-project.org/package=data.table},
}

@Manual{R-doParallel,
  title = {doParallel: Foreach Parallel Adaptor for the parallel Package},
  author = {Microsoft Corporation and Steve Weston},
  year = {2020},
  note = {R package version 1.0.16},
  url = {https://CRAN.R-project.org/package=doParallel},
}

@Manual{R-dplyr,
  title = {dplyr: A Grammar of Data Manipulation},
  author = {Hadley Wickham and Romain François and Lionel Henry and Kirill Müller},
  year = {2022},
  note = {R package version 1.0.9},
  url = {https://CRAN.R-project.org/package=dplyr},
}

@Manual{R-forcats,
  title = {forcats: Tools for Working with Categorical Variables (Factors)},
  author = {Hadley Wickham},
  year = {2021},
  note = {R package version 0.5.1},
  url = {https://CRAN.R-project.org/package=forcats},
}

@Manual{R-foreach,
  title = {foreach: Provides Foreach Looping Construct},
  author = {{Revolution Analytics} and Steve Weston}},
  year = {2022},
  note = {R package version 1.5.2},
  url = {https://github.com/RevolutionAnalytics/foreach},
}

@Manual{R-fs,
  title = {fs: Cross-Platform File System Operations Based on libuv},
  author = {Jim Hester and Hadley Wickham},
  year = {2020},
  note = {R package version 1.5.0},
  url = {https://CRAN.R-project.org/package=fs},
}

@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 = {2022},
  note = {R package version 3.3.6},
  url = {https://CRAN.R-project.org/package=ggplot2},
}

@Manual{R-ggpubr,
  title = {ggpubr: ggplot2 Based Publication Ready Plots},
  author = {Alboukadel Kassambara},
  year = {2020},
  note = {R package version 0.4.0},
  url = {https://rpkgs.datanovia.com/ggpubr/},
}

@Manual{R-ggridges,
  title = {ggridges: Ridgeline Plots in ggplot2},
  author = {Claus O. Wilke},
  year = {2021},
  note = {R package version 0.5.3},
  url = {https://wilkelab.org/ggridges/},
}

@Manual{R-ggthemes,
  title = {ggthemes: Extra Themes, Scales and Geoms for ggplot2},
  author = {Jeffrey B. Arnold},
  year = {2021},
  note = {R package version 4.2.4},
  url = {https://github.com/jrnold/ggthemes},
}

@Manual{R-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{R-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},
}

@Manual{R-iterators,
  title = {iterators: Provides Iterator Construct},
  author = {Revolution Analytics and Steve Weston},
  year = {2022},
  note = {R package version 1.0.14},
  url = {https://github.com/RevolutionAnalytics/iterators},
}

@Manual{R-knitr,
  title = {knitr: A General-Purpose Package for Dynamic Report Generation in R},
  author = {Yihui Xie},
  year = {2021},
  note = {R package version 1.33},
  url = {https://yihui.org/knitr/},
}

@Manual{R-lazyeval,
  title = {lazyeval: Lazy (Non-Standard) Evaluation},
  author = {Hadley Wickham},
  year = {2019},
  note = {R package version 0.2.2},
  url = {https://CRAN.R-project.org/package=lazyeval},
}

@Manual{R-maps,
  title = {maps: Draw Geographical Maps},
  author = {Ray Brownrigg},
  year = {2021},
  note = {R package version 3.4.0},
  url = {https://CRAN.R-project.org/package=maps},
}

@Manual{R-Matrix,
  title = {Matrix: Sparse and Dense Matrix Classes and Methods},
  author = {Douglas Bates and Martin Maechler},
  year = {2021},
  note = {R package version 1.4-0},
  url = {https://CRAN.R-project.org/package=Matrix},
}

@Manual{R-metafor,
  title = {metafor: Meta-Analysis Package for R},
  author = {Wolfgang Viechtbauer},
  year = {2021},
  note = {R package version 3.0-2},
  url = {https://CRAN.R-project.org/package=metafor},
}

@Manual{R-mgcv,
  title = {mgcv: Mixed GAM Computation Vehicle with Automatic Smoothness
Estimation},
  author = {Simon Wood},
  year = {2021},
  note = {R package version 1.8-38},
  url = {https://CRAN.R-project.org/package=mgcv},
}

@Manual{R-nlme,
  title = {nlme: Linear and Nonlinear Mixed Effects Models},
  author = {José Pinheiro and Douglas Bates and {R-core}},
  year = {2021},
  note = {R package version 3.1-153},
  url = {https://svn.r-project.org/R-packages/trunk/nlme/},
}

@Manual{R-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{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-readr,
  title = {readr: Read Rectangular Text Data},
  author = {Hadley Wickham and Jim Hester},
  year = {2020},
  note = {R package version 1.4.0},
  url = {https://CRAN.R-project.org/package=readr},
}

@Manual{R-reshape2,
  title = {reshape2: Flexibly Reshape Data: A Reboot of the Reshape Package},
  author = {Hadley Wickham},
  year = {2020},
  note = {R package version 1.4.4},
  url = {https://github.com/hadley/reshape},
}

@Manual{R-rmarkdown,
  title = {rmarkdown: Dynamic Documents for R},
  author = {JJ Allaire and Yihui Xie 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 = {2021},
  note = {R package version 2.11},
  url = {https://CRAN.R-project.org/package=rmarkdown},
}

@Manual{R-scales,
  title = {scales: Scale Functions for Visualization},
  author = {Hadley Wickham and Dana Seidel},
  year = {2022},
  note = {R package version 1.2.0},
  url = {https://CRAN.R-project.org/package=scales},
}

@Manual{R-stringr,
  title = {stringr: Simple, Consistent Wrappers for Common String Operations},
  author = {Hadley Wickham},
  year = {2019},
  note = {R package version 1.4.0},
  url = {https://CRAN.R-project.org/package=stringr},
}

@Manual{R-survey,
  title = {survey: Analysis of Complex Survey Samples},
  author = {Thomas Lumley},
  year = {2020},
  note = {R package version 4.0},
  url = {http://r-survey.r-forge.r-project.org/survey/},
}

@Manual{R-survival,
  title = {survival: Survival Analysis},
  author = {Terry M Therneau},
  year = {2021},
  note = {R package version 3.2-13},
  url = {https://github.com/therneau/survival},
}

@Manual{R-tibble,
  title = {tibble: Simple Data Frames},
  author = {Kirill Müller and Hadley Wickham},
  year = {2022},
  note = {R package version 3.1.8},
  url = {https://CRAN.R-project.org/package=tibble},
}

@Manual{R-tidyr,
  title = {tidyr: Tidy Messy Data},
  author = {Hadley Wickham and Maximilian Girlich},
  year = {2022},
  note = {R package version 1.2.0},
  url = {https://CRAN.R-project.org/package=tidyr},
}

@Manual{R-tidyselect,
  title = {tidyselect: Select from a Set of Strings},
  author = {Lionel Henry and Hadley Wickham},
  year = {2022},
  note = {R package version 1.1.2},
  url = {https://CRAN.R-project.org/package=tidyselect},
}

@Manual{R-tidyverse,
  title = {tidyverse: Easily Install and Load the Tidyverse},
  author = {Hadley Wickham},
  year = {2021},
  note = {R package version 1.3.1},
  url = {https://CRAN.R-project.org/package=tidyverse},
}

@Manual{R-viridis,
  title = {viridis: Colorblind-Friendly Color Maps for R},
  author = {Simon Garnier},
  year = {2021},
  note = {R package version 0.6.1},
  url = {https://CRAN.R-project.org/package=viridis},
}

@Manual{R-viridisLite,
  title = {viridisLite: Colorblind-Friendly Color Maps (Lite Version)},
  author = {Simon Garnier},
  year = {2021},
  note = {R package version 0.4.0},
  url = {https://CRAN.R-project.org/package=viridisLite},
}

@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/},
}

@Manual{R-zoo,
  title = {zoo: S3 Infrastructure for Regular and Irregular Time Series (Z's
Ordered Observations)},
  author = {Achim Zeileis and Gabor Grothendieck and Jeffrey A. Ryan},
  year = {2021},
  note = {R package version 1.8-9},
  url = {https://zoo.R-Forge.R-project.org/},
}

@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},
  note = {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},
}

@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{metafor2010,
  title = {Conducting meta-analyses in {R} with the {metafor} package},
  author = {Wolfgang Viechtbauer},
  journal = {Journal of Statistical Software},
  year = {2010},
  volume = {36},
  number = {3},
  pages = {1--48},
  url = {https://doi.org/10.18637/jss.v036.i03},
}

@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},
}

@Article{reshape22007,
  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/},
}

@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},
  note = {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},
  note = {ISBN 9780367563837},
  url = {https://bookdown.org/yihui/rmarkdown-cookbook},
}

@Article{survey2004,
  year = {2004},
  author = {Thomas Lumley},
  title = {Analysis of Complex Survey Samples},
  journal = {Journal of Statistical Software},
  volume = {9},
  number = {1},
  pages = {1-19},
  note = {R package verson 2.2},
}

@Book{survey2010,
  year = {2010},
  author = {Thomas Lumley},
  title = {Complex Surveys: A Guide to Analysis Using R: A Guide to Analysis Using R},
  publisher = {John Wiley and Sons},
}

@Book{survival-book,
  title = {Modeling Survival Data: Extending the {C}ox Model},
  author = {{Terry M. Therneau} and {Patricia M. Grambsch}},
  year = {2000},
  publisher = {Springer},
  address = {New York},
  isbn = {0-387-98784-3},
}

@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{zoo2005,
  title = {zoo: S3 Infrastructure for Regular and Irregular Time Series},
  author = {Achim Zeileis and Gabor Grothendieck},
  journal = {Journal of Statistical Software},
  year = {2005},
  volume = {14},
  number = {6},
  pages = {1--27},
  doi = {10.18637/jss.v014.i06},
}