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author = {Przemyslaw Biecek and Marcin Kosinski},
year = {2017},
title = {{archivist}: An {R} Package for Managing, Recording and Restoring Data Analysis Results},
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volume = {82},
number = {11},
pages = {1--28},
doi = {10.18637/jss.v082.i11}
}
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publisher = {Chapman and Hall/CRC},
title = {{blogdown}: Creating Websites with {R} Markdown},
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address = {Boca Raton, Florida},
author = {Yihui Xie},
note = {ISBN 978-1138700109},
publisher = {Chapman and Hall/CRC},
title = {{bookdown}: Authoring Books and Technical Documents with {R} Markdown},
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note = {R package version 3.3.2},
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year = {2019}
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@manual{checkpoint,
author = {Hong Ooi},
note = {R package version 0.4.7},
title = {{checkpoint}: Install Packages from Snapshots on the Checkpoint Server for
Reproducibility},
url = {https://CRAN.R-project.org/package=checkpoint},
year = {2019}
}
@manual{devtools,
author = {Hadley Wickham and Jim Hester and Winston Chang},
note = {R package version 2.1.0},
title = {{devtools}: Tools to Make Developing R Packages Easier},
url = {https://CRAN.R-project.org/package=devtools},
year = {2019}
}
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author = {William Michael Landau},
year = {2018},
title = {The {drake} {R} package: a pipeline toolkit for reproducibility and high-performance computing},
journal = {Journal of Open Source Software},
volume = {3},
number = {21}
}
@article{dryad,
author = {Vision, Todd},
year = {2010},
title = {The dryad digital repository: published evolutionary data as part of the greater data ecosystem}
}
@manual{git2r,
author = {Stefan Widgren and others},
note = {R package version 0.26.1},
title = {{git2r}: Provides Access to Git Repositories},
url = {https://CRAN.R-project.org/package=git2r},
year = {2019}
}
@manual{glue,
author = {Jim Hester},
note = {R package version 1.3.1},
title = {{glue}: Interpreted String Literals},
url = {https://CRAN.R-project.org/package=glue},
year = {2019}
}
@misc{john_blischak_2019_3241801,
author = {John Blischak and
Peter Carbonetto and
Jiaxiang Li and
Zaynaib (Ola) Giwa and
Wouter van Amsterdam and
E. David Aja and
Pierre Formont and
Tim Trice and
Steve Peak and
Luke Zappia and
Josh Johnson and
Ethan White and
Ania Tassinari},
doi = {10.5281/zenodo.3241801},
month = {jun},
title = {jdblischak/workflowr: workflowr 1.4.0},
url = {https://doi.org/10.5281/zenodo.3241801},
year = {2019},
doi = {10.5281/zenodo.3241801}
}
@book{kitzes2017,
author = {Kitzes, Justin and Turek, Daniel and Deniz, Fatma},
publisher = {Univ of California Press},
title = {The practice of reproducible research: case studies and lessons from the data-intensive sciences},
year = {2017}
}
@manual{knitrpkg,
author = {Yihui Xie},
note = {R package version 1.23},
title = {{knitr}: A General-Purpose Package for Dynamic Report Generation in R},
url = {https://yihui.name/knitr/},
year = {2019}
}
@article{marwick2017,
author = {Marwick, Ben},
year = {2017},
title = {Computational reproducibility in archaeological research: basic principles and a case study of their implementation},
journal = {Journal of Archaeological Method and Theory},
volume = {24},
number = {2},
pages = {424--450}
}
@manual{packrat,
author = {Kevin Ushey and Jonathan McPherson and Joe Cheng and Aron Atkins and JJ Allaire},
note = {R package version 0.5.0},
title = {{packrat}: A Dependency Management System for Projects and their R Package
Dependencies},
url = {https://CRAN.R-project.org/package=packrat},
year = {2018}
}
@manual{pkgdown,
author = {Hadley Wickham and Jay Hesselberth},
note = {R package version 1.4.1},
title = {{pkgdown}: Make Static HTML Documentation for a Package},
url = {https://CRAN.R-project.org/package=pkgdown},
year = {2019}
}
@manual{projecttemplate,
author = {John Myles White},
note = {R package version 0.9.0},
title = {{ProjectTemplate}: Automates the Creation of New Statistical Analysis Projects},
url = {https://CRAN.R-project.org/package=ProjectTemplate},
year = {2019}
}
@manual{rmarkdownpkg,
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 
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note = {R package version 1.13},
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url = {https://rmarkdown.rstudio.com},
year = {2019}
}
@manual{rprojroot,
author = {Kirill Müller},
note = {R package version 1.2},
title = {{rprojroot}: Finding Files in Project Subdirectories},
url = {https://CRAN.R-project.org/package=rprojroot},
year = {2017}
}
@manual{rrtools,
author = {Ben Marwick},
note = {R package version 0.1.0},
title = {{rrtools}: Creates a Reproducible Research Compendium},
url = {https://github.com/benmarwick/rrtools},
year = {2019}
}
@manual{rstudio,
address = {Boston, MA},
author = {{RStudio Team}},
organization = {RStudio, Inc.},
title = {RStudio: Integrated Development Environment for R},
url = {http://www.rstudio.com/},
year = {2018}
}
@manual{rsuite,
author = {Walerian Sokolowski and Wit Jakuczun and Yulia Yakimechko and Mateusz Kalinowski and Ryszard Szymanski},
note = {R package version 0.37-253},
title = {{RSuite}: Supports Developing, Building and Deploying R Solution},
url = {https://CRAN.R-project.org/package=RSuite},
year = {2019}
}
@article{snakemake,
author = {K{\"o}ster, Johannes and Rahmann, Sven},
year = {2012},
title = {Snakemake—a scalable bioinformatics workflow engine},
journal = {Bioinformatics},
volume = {28},
number = {19},
pages = {2520--2522}
}
@article{switchr,
author = {Gabriel Becker and Cory Barr and Robert Gentleman and Michael Lawrence},
year = {2017},
title = {Enhancing Reproducibility and Collaboration via Management of {R} Package Cohorts},
journal = {Journal of Statistical Software},
volume = {82},
number = {1},
pages = {1--17},
doi = {10.18637/jss.v082.i01}
}
@manual{usethis,
author = {Hadley Wickham and Jennifer Bryan},
note = {R package version 1.5.1},
title = {{usethis}: Automate Package and Project Setup},
url = {https://CRAN.R-project.org/package=usethis},
year = {2019}
}