references.bib

@article{knuth84,
  author = {Knuth, Donald E.},
  title = {Literate Programming},
  year = {1984},
  issue_date = {May 1984},
  publisher = {Oxford University Press, Inc.},
  address = {USA},
  volume = {27},
  number = {2},
  issn = {0010-4620},
  url = {https://doi.org/10.1093/comjnl/27.2.97},
  doi = {10.1093/comjnl/27.2.97},
  journal = {Comput. J.},
  month = may,
  pages = {97–111},
  numpages = {15}
}

@misc{Bell2006,
    year = {2006},
    title = {Issues with Open Source Statistical Software in Industry: Validation, Legal
    Issues, and Regulatory Requirements
  },
    howpublished = {\url{https://ww2.amstat.org/meetings/jsm/2006/onlineprogram/index.cfm?fuseaction=people_index&letter=B}
  },
    author = {Bell, B.}
}

@misc{Soukup2007,
    note = {Accessed: 2024-03-18},
    year = {2007},
    title = {Using R: Perspectives of a FDA Statistical RevieweR},
    publisher = {useR},
    howpublished = {\url{https://www.r-project.org/conferences/useR-2007/program/presentations/soukup.pdf}
  },
    author = {Soukup, M.}
}

@misc{Schuette2018,
    note = {Accessed on: 2024-03-18},
    year = {2018},
    title = {Using R in a regulatory environment: some FDA perspectives},
    howpublished = {\url{https://rinpharma.com/publication/rinpharma_7/}},
    author = {Schuette, P.}
}

@misc{FDA2015,
    note = {Accessed on: 2024-03-18},
    year = {2015},
    title = {Statistical Software Clarifying Statement},
    howpublished = {\url{https://www.fda.gov/media/161196/download}},
    author = {U.S. Food & Drug Administration (FDA)}
}

@misc{Novo2023,
    note = {Accessed on: 2024-03-18},
    year = {2023},
    title = {Novo Nordisk's Journey to an R based FDA Submission},
    howpublished = {\url{https://www.youtube.com/watch?v=t33dS17QHuA}},
    author = {Knoph, A.S., Larsen, S.F., Bilgrau, A.E.}
}

@misc{Roche2023,
    note = {Accessed on: 2024-03-18},
    year = {2023},
    title = {Shifting to an Open-Source Backbone in Clinical Trials with Roche},
    howpublished = {\url{https://www.youtube.com/watch?v=nqJsLSLd39A}},
    author = {Neitman, T., Martin, K., Leng, N., Black, J.}
}

@misc{SubmissionsWG2021,
    note = {Accessed on: 2024-03-18},
    year = {2021},
    title = {R Consortium Submissions Working Group},
    howpublished = {\url{https://rconsortium.github.io/submissions-wg/}},
    author = {}
}

@misc{OSNDAs,
    note = {Accessed on: 2024-03-20},
    title = {Open-Source-in-New-Drug-Applications-NDAs-FDA},
    howpublished = {\url{https://github.com/philbowsher/Open-Source-in-New-Drug-Applications-NDAs-FDA}},
    author = {Bowsher, P.}
}

@misc{RValidation,
    note = {Accessed on: 2024-03-20},
    title = {R Validation Hub},
    howpublished = {\url{https://www.pharmar.org/}},
    author = {}
}

@Manual{riskmetric,
  title = {riskmetric: Risk Metrics to Evaluating R Packages},
  author = {{R Validation Hub} and Doug Kelkhoff and Marly Gotti and Eli Miller and Kevin K and Yilong Zhang and Eric Milliman and Juliane Manitz},
  year = {2024},
  note = {R package version 0.2.4.9000, https://github.com/pharmaR/riskmetric},
  url = {https://pharmar.github.io/riskmetric/},
      note = {Accessed on: 2024-03-20}
}

@Manual{riskassessment,
  title = {riskassessment: A web app designed to interface with the `riskmetric` package},
  author = {Aaron Clark and Robert Krajcik and Jeff Thompson and Lars Andersen and Andrew Borgman and Marly Gotti and Maya Gans and Aravind Reddy Kallem and {Fission Labs India Pvt Ltd}},
  year = {2023},
  note = {R package version 3.0.0},
  url = {https://github.com/pharmaR/riskassessment},
      note = {Accessed on: 2024-03-20}
      }
      
@misc{Merck_Validation,
    note = {Accessed on: 2024-03-20},
    title = {R Validation Hub},
    howpublished = {\url{https://www.pharmar.org/}},
    author = {}
}

@book{RPackages,
  title         = {R Packages},
  author        = {Wickham, Hadley and Bryan, Jenny},
  year          = {2023},
  publisher     = {O'Reilly Media, Incorporated},
  isbn          = {9781098134945},
  abstract      = {Organize, Test, Document, and Share Your Code},
  language      = {en}
}

@Manual{covr,
  title = {covr: Test Coverage for Packages},
  author = {Jim Hester},
  year = {2023},
  note = {R package version 3.6.4, https://github.com/r-lib/covr},
  url = {https://covr.r-lib.org},
}

@Manual{covtracer,
  title = {covtracer: Tools for contextualizing tests},
  author = {Doug Kelkhoff and Andrew McNeil},
  year = {2024},
  note = {R package version 0.0.0.9016},
  url = {https://github.com/genentech/covtracer},
}

@Manual{roxygen2,
  title = {roxygen2: In-Line Documentation for R},
  author = {Hadley Wickham and Peter Danenberg and Gábor Csárdi and Manuel Eugster},
  year = {2024},
  note = {R package version 7.3.1, https://github.com/r-lib/roxygen2},
  url = {https://roxygen2.r-lib.org/},
}

@Manual{pkgdown,
  title = {pkgdown: Make Static HTML Documentation for a Package},
  author = {Hadley Wickham and Jay Hesselberth and Maëlle Salmon},
  year = {2023},
  note = {R package version 2.0.7, https://github.com/r-lib/pkgdown},
  url = {https://pkgdown.r-lib.org},
}

@Manual{RStudioIDE, 
  title = {RStudio: Integrated Development Environment for R}, 
  author = {{RStudio Team}}, 
  organization = {RStudio, PBC.}, 
  address = {Boston, MA}, 
  year = {2020}, 
  url = {http://www.rstudio.com/}, 
}

@misc{tidyValidation,
    note = {Accessed: 2024-03-27},
    year = {2020},
    title = {tidyverse, tidymodels, r-lib, and gt R packages: Regulatory Compliance and Validation Issues},
    publisher = {Posit / RStudio PBC},
    url = {https://www.rstudio.com/assets/img/validation-tidy.pdf}
}

@Manual{renv,
  title = {renv: Project Environments},
  author = {Kevin Ushey and Hadley Wickham},
  year = {2024},
  note = {R package version 1.0.5, https://github.com/rstudio/renv},
  url = {https://rstudio.github.io/renv/},
}

@misc{Podman, 
  title = {Getting Started with Podman}, 
  author = {Podman Team},
  year = {2024}, 
  url = {https://podman.io/docs}, 
  note = {Accessed: 2024-03-27},
}

@misc{PPM, 
  title = {Posit Public Package Manager}, 
  url = {https://packagemanager.posit.co/}, 
  note = {Accessed: 2024-03-27},
}

@Manual{sessioninfo,
  title = {sessioninfo: R Session Information},
  author = {Hadley Wickham and Winston Chang and Robert Flight and Kirill Müller and Jim Hester},
  year = {2022},
  note = {https://github.com/r-lib/sessioninfo#readme, https://r-lib.github.io/sessioninfo/},
}

@Manual{logrx,
  title = {logrx: A Logging Utility Focus on Clinical Trial Programming Workflows},
  author = {Nathan Kosiba and Thomas Bermudez and Ben Straub and Michael Rimler and Nicholas Masel and Sam Parmar},
  year = {2023},
  note = {R package version 0.3.0},
  url = {https://github.com/pharmaverse/logrx},
}