This is my full PhD thesis in R Markdown (using the bookdown package), containing a PDF and EPUB file, and a website in the ‘docs’ folder with the integral content of the book. https://git.io/PhDthesisAMR
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@Manual{R-AMR,
title = {AMR: Antimicrobial Resistance Data Analysis},
author = {Matthijs S. Berends and Christian F. Luz and Alexander W. Friedrich and Bhanu N. M. Sinha and Casper J. Albers and Corinna Glasner},
year = {2021},
note = {https://github.com/msberends/AMR, https://msberends.github.io/AMR},
}
@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 0.24},
url = {https://CRAN.R-project.org/package=bookdown},
}
@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-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 2.10},
url = {https://CRAN.R-project.org/package=rmarkdown},
}
@Article{AMR2021,
title = {AMR - An R Package for Working with Antimicrobial Resistance Data},
author = {M S Berends and C F Luz and A W Friedrich and B N M Sinha and C J Albers and C Glasner},
doi = {10.1101/810622},
journal = {Journal of Statistical Software},
pages = {Accepted for publication},
year = {2021},
url = {https://www.biorxiv.org/content/10.1101/810622v4},
}
@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{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},
}
@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},
}