packages.bib

@Manual{R-apexcharter,
  title = {apexcharter: Create Interactive Chart with the JavaScript ApexCharts
Library},
  author = {Victor Perrier and Fanny Meyer},
  year = {2020},
  note = {R package version 0.1.8},
  url = {https://CRAN.R-project.org/package=apexcharter},
}

@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 = {2020},
  url = {https://www.R-project.org/},
}

@Manual{R-blaze,
  title = {blaze: Observe URL Paths with Shiny},
  author = {Teetor, N.},
  note = {R package version 0.0.1},
  year = {2021},
}

@Manual{R-blogdown,
  title = {blogdown: Create Blogs and Websites with R Markdown},
  author = {Yihui Xie and Christophe Dervieux and Alison {Presmanes Hill}},
  year = {2021},
  note = {R package version 1.1},
  url = {https://github.com/rstudio/blogdown},
}

@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-brochure,
  title = {brochure: Multipage Shiny Apps},
  author = {Colin Fay},
  note = {R package version 0.0.0.9020},
  url = {https://github.com/colinfay/brochure},
  year = {2021},
}

@Manual{R-bs4Dash,
  title = {bs4Dash: A Bootstrap 4 Version of shinydashboard},
  author = {David Granjon},
  year = {2021},
  note = {R package version 2.0.3},
  url = {https://CRAN.R-project.org/package=bs4Dash},
}

@Manual{R-bslib,
  title = {bslib: Custom Bootstrap Sass Themes for Shiny and rmarkdown},
  author = {Carson Sievert and Joe Cheng},
  year = {2021},
  note = {R package version 0.3.0},
  url = {https://CRAN.R-project.org/package=bslib},
}

@Manual{R-CaPO4Sim,
  title = {CaPO4Sim: A Virtual Patient Simulator in the Context of Calcium and
Phosphate Homeostasis},
  author = {David Granjon},
  year = {2021},
  note = {R package version 0.2.0},
  url = {https://CRAN.R-project.org/package=CaPO4Sim},
}

@Manual{R-charpente,
  title = {charpente: Seamlessly Design Robust Shiny Extensions},
  author = {David Granjon and John Coene},
  note = {R package version 0.0.0.9000},
  url = {https://github.com/RinteRface/charpente},
  year = {2021},
}

@Manual{R-deminR,
  title = {deminR: deminR},
  author = {Gabrielle Devaux and David Granjon},
  note = {R package version 0.0.0.9000},
  year = {2021},
}

@Manual{R-deSolve,
  title = {deSolve: Solvers for Initial Value Problems of Differential Equations
(ODE, DAE, DDE)},
  author = {Karline Soetaert and Thomas Petzoldt and R. Woodrow Setzer},
  year = {2021},
  note = {R package version 1.29},
  url = {http://desolve.r-forge.r-project.org/},
}

@Manual{R-dplyr,
  title = {dplyr: A Grammar of Data Manipulation},
  author = {Hadley Wickham and Romain François and Lionel Henry and Kirill Müller},
  year = {2021},
  note = {R package version 1.0.3},
  url = {https://CRAN.R-project.org/package=dplyr},
}

@Manual{R-fresh,
  title = {fresh: Create Custom Bootstrap Themes to Use in Shiny},
  author = {Victor Perrier and Fanny Meyer},
  year = {2020},
  note = {R package version 0.2.0},
  url = {https://github.com/dreamRs/fresh},
}

@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 = {2020},
  note = {R package version 3.3.3},
  url = {https://CRAN.R-project.org/package=ggplot2},
}

@Manual{R-golem,
  title = {golem: A Framework for Robust Shiny Applications},
  author = {Colin Fay and Vincent Guyader and Sébastien Rochette and Cervan Girard},
  year = {2021},
  note = {R package version 0.3.1},
  url = {https://github.com/ThinkR-open/golem},
}

@Manual{R-htmltools,
  title = {htmltools: Tools for HTML},
  author = {Joe Cheng and Carson Sievert and Barret Schloerke and Winston Chang and Yihui Xie and Jeff Allen},
  year = {2021},
  note = {R package version 0.5.2},
  url = {https://github.com/rstudio/htmltools},
}

@Manual{R-httpuv,
  title = {httpuv: HTTP and WebSocket Server Library},
  author = {Joe Cheng and Winston Chang},
  year = {2021},
  note = {R package version 1.6.3},
  url = {https://github.com/rstudio/httpuv},
}

@Manual{R-httr,
  title = {httr: Tools for Working with URLs and HTTP},
  author = {Hadley Wickham},
  year = {2020},
  note = {R package version 1.4.2},
  url = {https://CRAN.R-project.org/package=httr},
}

@Manual{R-jsonlite,
  title = {jsonlite: A Simple and Robust JSON Parser and Generator for R},
  author = {Jeroen Ooms},
  year = {2020},
  note = {R package version 1.7.2},
  url = {https://CRAN.R-project.org/package=jsonlite},
}

@Manual{R-jstools,
  title = {jstools: Tools to Work with JavaScript and CSS},
  author = {Victor Perrier and Fanny Meyer},
  note = {R package version 0.1.0},
  url = {https://github.com/dreamRs/jstools},
  year = {2021},
}

@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-magrittr,
  title = {magrittr: A Forward-Pipe Operator for R},
  author = {Stefan Milton Bache and Hadley Wickham},
  year = {2020},
  note = {R package version 2.0.1},
  url = {https://CRAN.R-project.org/package=magrittr},
}

@Manual{R-OSUICode,
  title = {OSUICode: Standalone Code for "Outstanding Shiny User Interfaces"},
  author = {David Granjon},
  year = {2021},
  note = {R package version 0.0.0.9002},
}

@Manual{R-packer,
  title = {packer: An Opinionated Framework for Using JavaScript},
  author = {John Coene},
  year = {2021},
  note = {https://github.com/JohnCoene/packer, https://packer.john-coene.com},
}

@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-reactR,
  title = {reactR: React Helpers},
  author = {Facebook Inc and Michel Weststrate and Kent Russell and Alan Dipert},
  year = {2021},
  note = {R package version 0.4.4},
  url = {https://github.com/react-R/reactR},
}

@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-sass,
  title = {sass: Syntactically Awesome Style Sheets (Sass)},
  author = {Joe Cheng and Timothy Mastny and Richard Iannone and Barret Schloerke and Carson Sievert},
  year = {2021},
  note = {R package version 0.4.0},
  url = {https://github.com/rstudio/sass},
}

@Manual{R-scales,
  title = {scales: Scale Functions for Visualization},
  author = {Hadley Wickham and Dana Seidel},
  year = {2020},
  note = {R package version 1.1.1},
  url = {https://CRAN.R-project.org/package=scales},
}

@Manual{R-shiny,
  title = {shiny: Web Application Framework for R},
  author = {Winston Chang and Joe Cheng and JJ Allaire and Carson Sievert and Barret Schloerke and Yihui Xie and Jeff Allen and Jonathan McPherson and Alan Dipert and Barbara Borges},
  year = {2021},
  note = {R package version 1.6.0},
  url = {https://shiny.rstudio.com/},
}

@Manual{R-shiny.fluent,
  title = {shiny.fluent: Microsoft Fluent UI for Shiny Apps},
  author = {Marek Rogala and Kamil Zyla},
  note = {https://appsilon.github.io/shiny.fluent, https://github.com/appsilon/shiny.fluent},
  year = {2021},
}

@Manual{R-shiny.react,
  title = {shiny.react: Tools for Using React in Shiny},
  author = {Kamil Zyla and Marek Rogala},
  year = {2021},
  note = {R package version 0.2.3},
  url = {https://CRAN.R-project.org/package=shiny.react},
}

@Manual{R-shiny.router,
  title = {shiny.router: Basic Routing for Shiny Web Applications},
  author = {Filip Stachura and Dominik Krzemiński and Krystian Igras},
  year = {2021},
  note = {R package version 0.2.2},
  url = {https://CRAN.R-project.org/package=shiny.router},
}

@Manual{R-shinybulma,
  title = {shinybulma: Bulma for Shiny},
  author = {John Coene and David Granjon},
  note = {R package version 0.0.2.9000},
  url = {https://github.com/JohnCoene/shinybulma},
  year = {2021},
}

@Manual{R-shinydashboard,
  title = {shinydashboard: Create Dashboards with Shiny},
  author = {Winston Chang and Barbara {Borges Ribeiro}},
  year = {2018},
  note = {R package version 0.7.1},
  url = {http://rstudio.github.io/shinydashboard/},
}

@Manual{R-shinydashboardPlus,
  title = {shinydashboardPlus: Add More AdminLTE2 Components to shinydashboard},
  author = {David Granjon},
  year = {2021},
  note = {R package version 2.0.3},
  url = {https://CRAN.R-project.org/package=shinydashboardPlus},
}

@Manual{R-shinyjs,
  title = {shinyjs: Easily Improve the User Experience of Your Shiny Apps in Seconds},
  author = {Dean Attali},
  year = {2020},
  note = {R package version 2.0.0},
  url = {https://deanattali.com/shinyjs/},
}

@Manual{R-shinylogs,
  title = {shinylogs: Record Everything that Happens in a Shiny Application},
  author = {Fanny Meyer and Victor Perrier},
  year = {2019},
  note = {R package version 0.1.7},
  url = {https://github.com/dreamRs/shinylogs},
}

@Manual{R-shinyMobile,
  title = {shinyMobile: Mobile Ready shiny Apps with Standalone Capabilities},
  author = {David Granjon and Victor Perrier and Isabelle Rudolf},
  year = {2021},
  note = {R package version 0.9.1},
  url = {https://CRAN.R-project.org/package=shinyMobile},
}

@Manual{R-shinyWidgets,
  title = {shinyWidgets: Custom Inputs Widgets for Shiny},
  author = {Victor Perrier and Fanny Meyer and David Granjon},
  year = {2021},
  note = {R package version 0.5.7},
  url = {https://github.com/dreamRs/shinyWidgets},
}

@Manual{R-tablerDash,
  title = {tablerDash: Tabler API for Shiny},
  author = {David Granjon},
  note = {https://rinterface.github.io/tablerDash/, https://github.com/RinteRface/tablerDash/},
  year = {2021},
}

@Manual{R-testthat,
  title = {testthat: Unit Testing for R},
  author = {Hadley Wickham},
  year = {2021},
  note = {R package version 3.0.2},
  url = {https://CRAN.R-project.org/package=testthat},
}

@Manual{R-thematic,
  title = {thematic: Unified and Automatic Theming of ggplot2, lattice, and
base R Graphics},
  author = {Carson Sievert and Barret Schloerke and Joe Cheng},
  year = {2021},
  note = {R package version 0.1.2},
  url = {https://CRAN.R-project.org/package=thematic},
}

@Manual{R-waiter,
  title = {waiter: Loading Screen for Shiny},
  author = {John Coene},
  year = {2021},
  note = {R package version 0.2.3},
  url = {https://CRAN.R-project.org/package=waiter},
}

@Manual{R-websocket,
  title = {websocket: WebSocket Client Library},
  author = {Winston Chang and Joe Cheng and Alan Dipert and Barbara Borges},
  year = {2020},
  note = {R package version 1.3.1},
  url = {https://CRAN.R-project.org/package=websocket},
}

@Book{blogdown2017,
  title = {blogdown: Creating Websites with {R} Markdown},
  author = {Yihui Xie and Alison Presmanes Hill and Amber Thomas},
  publisher = {Chapman and Hall/CRC},
  address = {Boca Raton, Florida},
  year = {2017},
  note = {ISBN 978-0815363729},
  url = {https://github.com/rstudio/blogdown},
}

@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},
}

@Article{deSolve2010,
  title = {Solving Differential Equations in {R}: Package de{S}olve},
  author = {Karline Soetaert and Thomas Petzoldt and R. Woodrow Setzer},
  journal = {Journal of Statistical Software},
  volume = {33},
  number = {9},
  pages = {1--25},
  year = {2010},
  coden = {JSSOBK},
  issn = {1548-7660},
  url = {https://www.jstatsoft.org/v33/i09},
  doi = {10.18637/jss.v033.i09},
  keywords = {ordinary differential equations, partial differential
    equations, differential algebraic equations, initial value problems,
    R, FORTRAN, C},
}

@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{jsonlite2014,
  title = {The jsonlite Package: A Practical and Consistent Mapping Between JSON Data and R Objects},
  author = {Jeroen Ooms},
  journal = {arXiv:1403.2805 [stat.CO]},
  year = {2014},
  url = {https://arxiv.org/abs/1403.2805},
}

@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},
}

@Article{testthat2011,
  author = {Hadley Wickham},
  title = {testthat: Get Started with Testing},
  journal = {The R Journal},
  year = {2011},
  volume = {3},
  pages = {5--10},
  url = {https://journal.r-project.org/archive/2011-1/RJournal_2011-1_Wickham.pdf},
}