reproducible-research.bib

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@article{boettigerIntroductionRockerDocker2017a,
	Author = {Boettiger, Carl and Eddelbuettel, Dirk},
	Date = {2017},
	Doi = {https://doi.org/10.32614/RJ-2017-065},
	Issn = {2073-4859},
	Journaltitle = {The R Journal},
	Langid = {english},
	Number = {2},
	Pages = {527},
	Shortjournal = {The R Journal},
	Shorttitle = {An {{Introduction}} to {{Rocker}}},
	Title = {An Introduction to Rocker: Docker Containers for {{R}}},
	Url = {https://journal.r-project.org/archive/2017/RJ-2017-065/index.html},
	Urldate = {2019-08-14},
	Volume = {9},
	Bdsk-Url-1 = {https://journal.r-project.org/archive/2017/RJ-2017-065/index.html},
	Bdsk-Url-2 = {https://doi.org/10.32614/RJ-2017-065}}

@manual{baseR,
	Address = {Vienna, Austria},
	Author = {{R Core Team}},
	Organization = {R Foundation for Statistical Computing},
	Title = {R: A Language and Environment for Statistical Computing},
	Url = {https://www.R-project.org/},
	Year = {2020},
	Bdsk-Url-1 = {https://www.R-project.org/}}

@manual{liftr,
	Author = {Nan Xiao},
	Note = {R package version 0.9.2},
	Title = {{liftr}: Containerize {R} Markdown Documents for Continuous Reproducibility},
	Url = {https://CRAN.R-project.org/package=liftr},
	Year = {2019},
	Bdsk-Url-1 = {https://CRAN.R-project.org/package=liftr}}

@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},
	Bdsk-Url-1 = {https://github.com/benmarwick/rrtools}}

@online{revolutionanalyticsReproducibilityUsingFixed2019,
	Author = {{Revolution Analytics}},
	Date = {2019},
	Journaltitle = {Microsoft R Application Network},
	Title = {Reproducibility: Using Fixed {CRAN} Repository Snapshots. {{MRAN}}},
	Url = {https://mran.microsoft.com/documents/rro/reproducibility},
	Urldate = {2019-08-14},
	Bdsk-Url-1 = {https://mran.microsoft.com/documents/rro/reproducibility}}

@online{dockerinc.DockerHub2019,
	Author = {{Docker Inc.}},
	Date = {2019},
	Title = {Docker {{Hub}}},
	Url = {https://hub.docker.com/},
	Urldate = {2019-08-14},
	Bdsk-Url-1 = {https://hub.docker.com/}}

@manual{redoc,
	Author = {Noam Ross},
	Note = {R package version 0.1.0.9000},
	Title = {{redoc}: Reversible Reproducible Documents},
	Url = {https://github.com/noamross/redoc},
	Year = {2019},
	Bdsk-Url-1 = {https://github.com/noamross/redoc}}

@article{hodgesStatisticalMethodsResearch2019,
	Archiveprefix = {arXiv},
	Author = {Hodges, James S.},
	Date = {2019-05-20},
	Eprint = {1905.08381},
	Eprinttype = {arxiv},
	Title = {Statistical Methods Research Done as Science Rather than Mathematics},
	Url = {http://arxiv.org/abs/1905.08381},
	Urldate = {2019-08-14},
	Bdsk-Url-1 = {http://arxiv.org/abs/1905.08381}}

@article{ruleTenSimpleRules2019,
	Author = {Rule, Adam and Birmingham, Amanda and Zuniga, Cristal and Altintas, Ilkay and Huang, Shih-Cheng and Knight, Rob and Moshiri, Niema and Nguyen, Mai H. and Rosenthal, Sara Brin and P{\'e}rez, Fernando and Rose, Peter W.},
	Date = {2019-07-25},
	Doi = {https://doi.org/10.1371/journal.pcbi.1007007},
	Issn = {1553-7358},
	Journaltitle = {PLOS Computational Biology},
	Keywords = {Analysts,Computer and information sciences,Computer hardware,Data processing,Ecosystems,Graphical user interfaces,Metadata,Reproducibility},
	Langid = {english},
	Number = {7},
	Pages = {e1007007},
	Shortjournal = {PLOS Computational Biology},
	Title = {Ten Simple Rules for Writing and Sharing Computational Analyses in {{Jupyter Notebooks}}},
	Url = {https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007007},
	Urldate = {2019-08-17},
	Volume = {15},
	Bdsk-Url-1 = {https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007007},
	Bdsk-Url-2 = {https://doi.org/10.1371/journal.pcbi.1007007}}

@article{barbaHardRoadReproducibility2016,
	Author = {Barba, Lorena A.},
	Date = {2016-10-07},
	Doi = {https://doi.org/10.1126/science.354.6308.142},
	Eprint = {27846503},
	Eprinttype = {pmid},
	Issn = {0036-8075, 1095-9203},
	Journaltitle = {Science},
	Langid = {english},
	Number = {6308},
	Pages = {142},
	Title = {The Hard Road to Reproducibility},
	Url = {https://science.sciencemag.org/content/354/6308/142},
	Urldate = {2019-08-17},
	Volume = {354},
	Bdsk-Url-1 = {https://science.sciencemag.org/content/354/6308/142},
	Bdsk-Url-2 = {https://doi.org/10.1126/science.354.6308.142}}

@article{pengReproducibleResearchComputational2011,
	Author = {Peng, Roger D.},
	Date = {2011-12-02},
	Doi = {https://doi.org/10.1126/science.1213847},
	Eprint = {22144613},
	Eprinttype = {pmid},
	Issn = {0036-8075, 1095-9203},
	Journaltitle = {Science},
	Langid = {english},
	Number = {6060},
	Pages = {1226-1227},
	Title = {Reproducible {{Research}} in {{Computational Science}}},
	Url = {https://science.sciencemag.org/content/334/6060/1226},
	Urldate = {2019-08-17},
	Volume = {334},
	Bdsk-Url-1 = {https://science.sciencemag.org/content/334/6060/1226},
	Bdsk-Url-2 = {https://doi.org/10.1126/science.1213847}}

@article{wilsonGoodEnoughPractices2017,
	Author = {Wilson, Greg and Bryan, Jennifer and Cranston, Karen and Kitzes, Justin and Nederbragt, Lex and Teal, Tracy K.},
	Date = {2017-06-22},
	Doi = {https://doi.org/10.1371/journal.pcbi.1005510},
	Issn = {1553-7358},
	Journaltitle = {PLOS Computational Biology},
	Keywords = {Data processing,Reproducibility,Computer software,Control systems,Data management,Programming languages,Software tools,Source code},
	Langid = {english},
	Number = {6},
	Pages = {e1005510},
	Shortjournal = {PLOS Computational Biology},
	Title = {Good Enough Practices in Scientific Computing},
	Url = {https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005510},
	Urldate = {2019-08-17},
	Volume = {13},
	Bdsk-Url-1 = {https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005510},
	Bdsk-Url-2 = {https://doi.org/10.1371/journal.pcbi.1005510}}

@article{sandveTenSimpleRules2013,
	Author = {Sandve, Geir Kjetil and Nekrutenko, Anton and Taylor, James and Hovig, Eivind},
	Date = {2013-10-24},
	Doi = {https://doi.org/10.1371/journal.pcbi.1003285},
	Issn = {1553-7358},
	Journaltitle = {PLOS Computational Biology},
	Keywords = {Computer and information sciences,Reproducibility,Source code,Archives,Computer applications,Habits,Replication studies,Sequence analysis},
	Langid = {english},
	Number = {10},
	Pages = {e1003285},
	Shortjournal = {PLOS Computational Biology},
	Title = {Ten {{Simple Rules}} for {{Reproducible Computational Research}}},
	Url = {https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003285},
	Urldate = {2019-08-17},
	Volume = {9},
	Bdsk-Url-1 = {https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003285},
	Bdsk-Url-2 = {https://doi.org/10.1371/journal.pcbi.1003285}}

@article{taschukTenSimpleRules2017,
	Author = {Taschuk, Morgan and Wilson, Greg},
	Date = {2017-04-13},
	Doi = {https://doi.org/10.1371/journal.pcbi.1005412},
	Issn = {1553-7358},
	Journaltitle = {PLOS Computational Biology},
	Keywords = {Reproducibility,Computer software,Software tools,Bioinformatics,Operating systems,Sequence alignment,Software development,Software engineering},
	Langid = {english},
	Number = {4},
	Pages = {e1005412},
	Shortjournal = {PLOS Computational Biology},
	Title = {Ten Simple Rules for Making Research Software More Robust},
	Url = {https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005412},
	Urldate = {2019-08-17},
	Volume = {13},
	Bdsk-Url-1 = {https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005412},
	Bdsk-Url-2 = {https://doi.org/10.1371/journal.pcbi.1005412}}

@article{novellaContainerbasedBioinformaticsPachyderm2019,
	Author = {Novella, Jon Ander and Emami Khoonsari, Payam and Herman, Stephanie and Whitenack, Daniel and Capuccini, Marco and Burman, Joachim and Kultima, Kim and Spjuth, Ola},
	Date = {2019-03-01},
	Doi = {https://doi.org/10.1093/bioinformatics/bty699},
	Issn = {1367-4803},
	Journaltitle = {Bioinformatics},
	Langid = {english},
	Number = {5},
	Pages = {839-846},
	Shortjournal = {Bioinformatics},
	Title = {Container-Based Bioinformatics with {{Pachyderm}}},
	Url = {https://academic.oup.com/bioinformatics/article/35/5/839/5068160},
	Urldate = {2019-08-17},
	Volume = {35},
	Bdsk-Url-1 = {https://academic.oup.com/bioinformatics/article/35/5/839/5068160},
	Bdsk-Url-2 = {https://doi.org/10.1093/bioinformatics/bty699}}

@article{ivieReproducibilityScientificComputing2018,
	Author = {Ivie, Peter and Thain, Douglas},
	Date = {2018-07},
	Doi = {https://doi.org/10.1145/3186266},
	Issn = {0360-0300},
	Journaltitle = {ACM Comput. Surv.},
	Keywords = {Reproducibility,computational science,replicability,reproducible,scientific computing,scientific workflow,scientific workflows,workflow,workflows},
	Number = {3},
	Pages = {63:1--63:36},
	Title = {Reproducibility in {{Scientific Computing}}},
	Urldate = {2019-08-17},
	Volume = {51},
	Bdsk-Url-1 = {https://doi.org/10.1145/3186266}}

@article{clyburne-sherinComputationalReproducibilityContainers2018,
	Author = {Clyburne-Sherin, April and Fei, Xu and Green, Seth Ariel},
	Date = {2018-02-16},
	Doi = {https://doi.org/10.31234/osf.io/mf82t},
	Title = {Computational {{Reproducibility}} via {{Containers}} in {{Social Psychology}}},
	Url = {https://osf.io/mf82t},
	Urldate = {2019-08-17},
	Bdsk-Url-1 = {https://osf.io/mf82t},
	Bdsk-Url-2 = {https://doi.org/10.31234/osf.io/mf82t}}

@article{hardwicketome.DataAvailabilityReusability,
	Author = {{Hardwicke Tom E.} and {Mathur Maya B.} and {MacDonald Kyle} and {Nilsonne Gustav} and {Banks George C.} and {Kidwell Mallory C.} and {Hofelich Mohr Alicia} and {Clayton Elizabeth} and {Yoon Erica J.} and {Henry Tessler Michael} and {Lenne Richie L.} and {Altman Sara} and {Long Bria} and {Frank Michael C.}},
	Doi = {https://doi.org/10.1098/rsos.180448},
	Journaltitle = {Royal Society Open Science},
	Number = {8},
	Pages = {180448},
	Shortjournal = {Royal Society Open Science},
	Shorttitle = {Data Availability, Reusability, and Analytic Reproducibility},
	Title = {Data Availability, Reusability, and Analytic Reproducibility: Evaluating the Impact of a Mandatory Open Data Policy at the Journal {{Cognition}}},
	Url = {https://royalsocietypublishing.org/doi/full/10.1098/rsos.180448},
	Urldate = {2019-08-17},
	Volume = {5},
	Bdsk-Url-1 = {https://royalsocietypublishing.org/doi/full/10.1098/rsos.180448},
	Bdsk-Url-2 = {https://doi.org/10.1098/rsos.180448}}

@article{askrenUsingMakeReproducible2016,
	Author = {Askren, Mary K. and McAllister-Day, Trevor K. and Koh, Natalie and Mestre, Zo{\'e} and Dines, Jennifer N. and Korman, Benjamin A. and Melhorn, Susan J. and Peterson, Daniel J. and Peverill, Matthew and Qin, Xiaoyan and Rane, Swati D. and Reilly, Melissa A. and Reiter, Maya A. and Sambrook, Kelly A. and Woelfer, Karl A. and Grabowski, Thomas J. and Madhyastha, Tara M.},
	Date = {2016},
	Doi = {https://doi.org/10.3389/fninf.2016.00002},
	Issn = {1662-5196},
	Journaltitle = {Frontiers in Neuroinformatics},
	Keywords = {workflow,Neuroimaging methods,neuroimaging pipelines,Quality Assurance,reproducibility},
	Langid = {english},
	Shortjournal = {Front. Neuroinform.},
	Title = {Using {{Make}} for {{Reproducible}} and {{Parallel Neuroimaging Workflow}} and {{Quality}}-{{Assurance}}},
	Url = {https://www.frontiersin.org/articles/10.3389/fninf.2016.00002/full},
	Urldate = {2019-08-17},
	Volume = {10},
	Bdsk-Url-1 = {https://www.frontiersin.org/articles/10.3389/fninf.2016.00002/full},
	Bdsk-Url-2 = {https://doi.org/10.3389/fninf.2016.00002}}

@article{gentlemanStatisticalAnalysesReproducible2007,
	Author = {Gentleman, Robert and Lang, Duncan Temple},
	Date = {2007-03-01},
	Doi = {https://doi.org/10.1198/106186007X178663},
	Issn = {1061-8600},
	Journaltitle = {Journal of Computational and Graphical Statistics},
	Keywords = {Compendium,Dynamic documents,Literate programming,Markup language,Perl,Python,R},
	Number = {1},
	Pages = {1-23},
	Title = {Statistical {{Analyses}} and {{Reproducible Research}}},
	Urldate = {2019-08-20},
	Volume = {16},
	Bdsk-Url-1 = {https://doi.org/10.1198/106186007X178663}}

@article{marwickPackagingDataAnalytical2018,
	Author = {Marwick, Ben and Boettiger, Carl and Mullen, Lincoln},
	Date = {2018-01-02},
	Doi = {https://doi.org/10.1080/00031305.2017.1375986},
	Issn = {0003-1305},
	Journaltitle = {The American Statistician},
	Keywords = {Computational science,Data science,Open source software,Reproducible research},
	Number = {1},
	Pages = {80-88},
	Title = {Packaging Data Analytical Work Reproducibly Using {R} (and Friends)},
	Urldate = {2019-08-20},
	Volume = {72},
	Bdsk-Url-1 = {https://doi.org/10.1080/00031305.2017.1375986}}

@article{bryanExcuseMeYou2018,
	Author = {Bryan, Jennifer},
	Date = {2018-01-02},
	Doi = {https://doi.org/10.1080/00031305.2017.1399928},
	Issn = {0003-1305},
	Journaltitle = {The American Statistician},
	Keywords = {Data science,Git,GitHub,R language; R Markdown,Reproducibility,Workflow},
	Number = {1},
	Pages = {20-27},
	Title = {Excuse {{Me}}, {{Do You Have}} a {{Moment}} to {{Talk About Version Control}}?},
	Urldate = {2019-08-20},
	Volume = {72},
	Bdsk-Url-1 = {https://doi.org/10.1080/00031305.2017.1399928}}

@manual{gohel2019officer,
	Author = {David Gohel},
	Note = {R package version 0.3.5},
	Title = {{officer}: Manipulation of Microsoft Word and PowerPoint Documents},
	Url = {https://CRAN.R-project.org/package=officer},
	Year = {2019},
	Bdsk-Url-1 = {https://CRAN.R-project.org/package=officer}}

@article{stoddenEnhancingReproducibilityComputational2016,
	Author = {Stodden, Victoria and McNutt, Marcia and Bailey, David H. and Deelman, Ewa and Gil, Yolanda and Hanson, Brooks and Heroux, Michael A. and Ioannidis, John P. A. and Taufer, Michela},
	Date = {2016-12-09},
	Doi = {https://doi.org/10.1126/science.aah6168},
	Eprint = {27940837},
	Eprinttype = {pmid},
	Issn = {0036-8075, 1095-9203},
	Journaltitle = {Science},
	Langid = {english},
	Number = {6317},
	Pages = {1240-1241},
	Title = {Enhancing Reproducibility for Computational Methods},
	Url = {https://science.sciencemag.org/content/354/6317/1240},
	Urldate = {2019-08-23},
	Volume = {354},
	Bdsk-Url-1 = {https://science.sciencemag.org/content/354/6317/1240},
	Bdsk-Url-2 = {https://doi.org/10.1126/science.aah6168}}

@article{fosterOpenScienceFramework2017,
	Author = {Foster, Erin D. and Deardorff, Ariel},
	Date = {2017-04},
	Doi = {https://doi.org/10.5195/jmla.2017.88},
	Eprinttype = {pmid},
	Issn = {1536-5050},
	Journaltitle = {Journal of the Medical Library Association},
	Number = {2},
	Pages = {203-206},
	Pmcid = {PMC5370619},
	Shortjournal = {J Med Libr Assoc},
	Title = {Open {{Science Framework}} ({{OSF}})},
	Url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5370619/},
	Urldate = {2019-08-26},
	Volume = {105},
	Bdsk-Url-1 = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5370619/},
	Bdsk-Url-2 = {https://doi.org/10.5195/jmla.2017.88}}

@manual{workflowr,
	Author = {John Blischak and Peter Carbonetto and Matthew Stephens},
	Title = {{workflowr}: A Framework for Reproducible and Collaborative Data Science},
	Url = {https://github.com/jdblischak/workflowr},
	Version = {1.4.0.9001},
	Year = {2019},
	Bdsk-Url-1 = {https://github.com/jdblischak/workflowr}}

@article{drake,
	Author = {William Michael Landau},
	Journal = {Journal of Open Source Software},
	Number = {21},
	Title = {The {drake} {R} package: a pipeline toolkit for reproducibility and high-performance computing},
	Url = {https://doi.org/10.21105/joss.00550},
	Volume = {3},
	Year = {2018},
	Bdsk-Url-1 = {https://doi.org/10.21105/joss.00550}}

@manual{holepunch,
	Author = {Karthik Ram},
	Note = {R package version 0.1.25.9000},
	Title = {{holepunch}: Configure Your {R} Project for 'binderhub'},
	Url = {https://github.com/karthik/holepunch},
	Year = {2019},
	Bdsk-Url-1 = {https://github.com/karthik/holepunch}}

@manual{renv,
	Author = {Kevin Ushey},
	Note = {R package version 0.9.3},
	Title = {{renv}: Project Environments},
	Url = {https://CRAN.R-project.org/package=renv},
	Year = {2020},
	Bdsk-Url-1 = {https://CRAN.R-project.org/package=renv}}

@manual{reprex,
	Author = {Jennifer Bryan and Jim Hester and David Robinson and Hadley Wickham},
	Title = {{reprex}: Prepare Reproducible Example Code via the Clipboard},
	Url = {https://CRAN.R-project.org/package=reprex},
	Version = {0.3.0},
	Year = {2019},
	Bdsk-Url-1 = {https://CRAN.R-project.org/package=reprex}}

@article{yenniDevelopingModernData2018,
	Author = {Yenni, Glenda M. and Christensen, Erica M. and Bledsoe, Ellen K. and Supp, Sarah R. and Diaz, Renata M. and White, Ethan P. and Ernest, S. K. Morgan},
	Date = {2018-06-12},
	Doi = {https://doi.org/10.1101/344804},
	Journaltitle = {bioRxiv},
	Langid = {english},
	Pages = {344804},
	Title = {Developing a Modern Data Workflow for Living Data},
	Url = {https://www.biorxiv.org/content/10.1101/344804v1},
	Urldate = {2019-08-29},
	Bdsk-Url-1 = {https://www.biorxiv.org/content/10.1101/344804v1},
	Bdsk-Url-2 = {https://doi.org/10.1101/344804}}

@book{turingway2020,
	Author = {{The Turing Way Community} and Becky Arnold and Louise Bowler and Sarah Gibson; Patricia Herterich and Rosie Higman and Anna Krystalli and Alexander Morley and Martin O'Reilly and Kirstie Whitaker},
	Doi = {http://doi.org/10.5281/zenodo.3233986},
	Title = {The {Turing} Way: A Handbook for Reproducible Data Science (v0.0.4)},
	Year = {2019},
	Bdsk-Url-1 = {http://doi.org/10.5281/zenodo.3233986}}

@article{beaulieu-jonesReproducibilityComputationalWorkflows2017,
	Author = {Beaulieu-Jones, Brett K. and Greene, Casey S.},
	Date = {2017-04},
	Doi = {https://doi.org/10.1038/nbt.3780},
	Issn = {1546-1696},
	Journaltitle = {Nature Biotechnology},
	Langid = {english},
	Number = {4},
	Pages = {342-346},
	Shortjournal = {Nat Biotechnol},
	Title = {Reproducibility of Computational Workflows Is Automated Using Continuous Analysis},
	Url = {https://www.nature.com/articles/nbt.3780},
	Urldate = {2019-08-29},
	Volume = {35},
	Bdsk-Url-1 = {https://www.nature.com/articles/nbt.3780},
	Bdsk-Url-2 = {https://doi.org/10.1038/nbt.3780}}

@article{kurtzerSingularityScientificContainers2017,
	Author = {Kurtzer, Gregory M. and Sochat, Vanessa and Bauer, Michael W.},
	Date = {2017-05-11},
	Doi = {https://doi.org/10.1371/journal.pone.0177459},
	Issn = {1932-6203},
	Journaltitle = {PLOS ONE},
	Keywords = {Computer software,Open source software,Operating systems,Research validity,Software design,Software development,Software tools,Tar},
	Langid = {english},
	Number = {5},
	Pages = {e0177459},
	Shortjournal = {PLOS ONE},
	Shorttitle = {Singularity},
	Title = {Singularity: {{Scientific}} Containers for Mobility of Compute},
	Url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0177459},
	Urldate = {2019-08-29},
	Volume = {12},
	Bdsk-Url-1 = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0177459},
	Bdsk-Url-2 = {https://doi.org/10.1371/journal.pone.0177459}}

@article{perkelToolkitDataTransparency2018,
	Author = {Perkel, Jeffrey M.},
	Date = {2018-08-20},
	Doi = {https://doi.org/10.1038/d41586-018-05990-5},
	Journaltitle = {Nature},
	Langid = {english},
	Pages = {513-515},
	Title = {A Toolkit for Data Transparency Takes Shape},
	Url = {http://www.nature.com/articles/d41586-018-05990-5},
	Urldate = {2019-08-29},
	Volume = {560},
	Bdsk-Url-1 = {http://www.nature.com/articles/d41586-018-05990-5},
	Bdsk-Url-2 = {https://doi.org/10.1038/d41586-018-05990-5}}

@article{perkelPioneeringLivecodeArticle2019,
	Author = {Perkel, Jeffrey M.},
	Date = {2019-02-28},
	Doi = {https://doi.org/10.1038/d41586-019-00724-7},
	Journaltitle = {Nature},
	Langid = {english},
	Pages = {17-18},
	Title = {Pioneering `Live-Code' Article Allows Scientists to Play with Each Other's Results},
	Url = {http://www.nature.com/articles/d41586-019-00724-7},
	Urldate = {2019-08-29},
	Volume = {567},
	Bdsk-Url-1 = {http://www.nature.com/articles/d41586-019-00724-7},
	Bdsk-Url-2 = {https://doi.org/10.1038/d41586-019-00724-7}}

@article{piccoloToolsTechniquesComputational2016,
	Author = {Piccolo, Stephen R. and Frampton, Michael B.},
	Date = {2016-07-11},
	Doi = {https://doi.org/10.1186/s13742-016-0135-4},
	Issn = {2047-217X},
	Journaltitle = {GigaScience},
	Number = {1},
	Pages = {30},
	Shortjournal = {GigaScience},
	Title = {Tools and Techniques for Computational Reproducibility},
	Urldate = {2019-08-29},
	Volume = {5},
	Bdsk-Url-1 = {https://doi.org/10.1186/s13742-016-0135-4}}

@inproceedings{claerboutElectronicDocumentsGive1992,
	Author = {Claerbout, Jon F. and Karrenbach, Martin},
	Booktitle = {{{SEG Technical Program Expanded Abstracts}} 1992},
	Date = {1992-01},
	Doi = {https://doi.org/10.1190/1.1822162},
	Eventtitle = {{{SEG Technical Program Expanded Abstracts}} 1992},
	Langid = {english},
	Pages = {601-604},
	Publisher = {{Society of Exploration Geophysicists}},
	Title = {Electronic Documents Give Reproducible Research a New Meaning},
	Url = {http://library.seg.org/doi/abs/10.1190/1.1822162},
	Urldate = {2019-08-29},
	Bdsk-Url-1 = {http://library.seg.org/doi/abs/10.1190/1.1822162},
	Bdsk-Url-2 = {https://doi.org/10.1190/1.1822162}}

@report{herouxCompatibleReproducibilityTaxonomy2018,
	Author = {Heroux, Michael A. and Barba, Lorena and Parashar, Manish and Stodden, Victoria and Taufer, Michela},
	Date = {2018-10-01},
	Doi = {https://doi.org/10.2172/1481626},
	Institution = {{Sandia National Lab. (SNL-NM), Albuquerque, NM}},
	Langid = {english},
	Number = {SAND2018-11186},
	Title = {Toward a Compatible Reproducibility Taxonomy for Computational and Computing Sciences.},
	Url = {https://www.osti.gov/biblio/1481626},
	Urldate = {2019-08-29},
	Bdsk-Url-1 = {https://www.osti.gov/biblio/1481626},
	Bdsk-Url-2 = {https://doi.org/10.2172/1481626}}

@report{stoddenEnablingReproducibleResearch2009,
	Author = {Stodden, Victoria},
	Date = {2009-03-03},
	Institution = {{Social Science Research Network}},
	Keywords = {Enabling Reproducible Research: Open Licensing for Scientific Innovation,SSRN,Victoria Stodden},
	Langid = {english},
	Location = {{Rochester, NY}},
	Number = {ID 1362040},
	Shorttitle = {Enabling {{Reproducible Research}}},
	Title = {Enabling {{Reproducible Research}}: {{Open Licensing}} for {{Scientific Innovation}}},
	Type = {SSRN Scholarly Paper},
	Url = {https://papers.ssrn.com/abstract=1362040},
	Urldate = {2019-08-29},
	Bdsk-Url-1 = {https://papers.ssrn.com/abstract=1362040}}

@manual{jetpack,
	Author = {Andrew Kane},
	Note = {R package version 0.4.3},
	Title = {{jetpack}: A Friendly Package Manager},
	Url = {https://github.com/ankane/jetpack},
	Year = {2019},
	Bdsk-Url-1 = {https://github.com/ankane/jetpack}}

@manual{miniCRAN,
	Author = {Andrie {de Vries}},
	Note = {R package version 0.2.12},
	Title = {{miniCRAN}: Create a Mini Version of CRAN Containing Only Selected Packages},
	Url = {https://CRAN.R-project.org/package=miniCRAN},
	Year = {2019},
	Bdsk-Url-1 = {https://CRAN.R-project.org/package=miniCRAN}}

@manual{checkpoint,
	Author = {Microsoft Corporation},
	Title = {{checkpoint}: Install Packages from Snapshots on the Checkpoint Server for Reproducibility},
	Url = {https://CRAN.R-project.org/package=checkpoint},
	Version = {0.4.6},
	Year = {2019},
	Bdsk-Url-1 = {https://CRAN.R-project.org/package=checkpoint}}

@article{marwickPackagingDataAnalytical2018,
	Author = {Marwick, Ben and Boettiger, Carl and Mullen, Lincoln},
	Date = {2018-01-02},
	Doi = {https://doi.org/10.1080/00031305.2017.1375986},
	Issn = {0003-1305},
	Journaltitle = {The American Statistician},
	Number = {1},
	Pages = {80-88},
	Shortjournal = {The American Statistician},
	Title = {Packaging {{Data Analytical Work Reproducibly Using R}} (and {{Friends}})},
	Url = {https://amstat.tandfonline.com/doi/full/10.1080/00031305.2017.1375986},
	Urldate = {2019-08-28},
	Volume = {72},
	Bdsk-Url-1 = {https://amstat.tandfonline.com/doi/full/10.1080/00031305.2017.1375986},
	Bdsk-Url-2 = {https://doi.org/10.1080/00031305.2017.1375986}}

@manual{boot,
	Author = {Angelo Canty and B. D. Ripley},
	Title = {{boot}: Bootstrap R (S-Plus) Functions},
	Url = {https://CRAN.R-project.org/package=boot},
	Version = {1.3-23},
	Year = {2019},
	Bdsk-Url-1 = {https://CRAN.R-project.org/package=boot}}

@article{lavaan2012,
	Author = {Yves Rosseel},
	Journal = {Journal of Statistical Software},
	Number = {2},
	Pages = {1--36},
	Title = {{lavaan}: An {R} Package for Structural Equation Modeling},
	Url = {http://www.jstatsoft.org/v48/i02/},
	Volume = {48},
	Year = {2012},
	Bdsk-Url-1 = {http://www.jstatsoft.org/v48/i02/}}

@article{knuth1984literate,
	Author = {Knuth, Donald Ervin},
	Journal = {The Computer Journal},
	Number = {2},
	Pages = {97--111},
	Publisher = {Oxford University Press},
	Title = {Literate programming},
	Volume = {27},
	Year = {1984}}

@article{epskamp2019rep,
	Author = {Sacha Epskamp},
	Doi = {https://doi.org/10.1177/2515245919847421},
	Journal = {Advances in Methods and Practices in Psychological Science},
	Number = {2},
	Pages = {145-155},
	Title = {Reproducibility and Replicability in a Fast-Paced Methodological World},
	Volume = {2},
	Year = {2019},
	Bdsk-Url-1 = {https://doi.org/10.1177/2515245919847421}}

@article{dfg2019,
	Author = {{Deutsche Forschungsgemeinschaft}},
	Date = {2019},
	Langid = {german},
	Title = {Leitlinien zur Sicherung guter wissenschaftlicher Praxis},
	Url = {https://www.dfg.de/download/pdf/foerderung/rechtliche_rahmenbedingungen/gute_wissenschaftliche_praxis/kodex_gwp.pdf},
	Bdsk-Url-1 = {https://www.dfg.de/download/pdf/foerderung/rechtliche_rahmenbedingungen/gute_wissenschaftliche_praxis/kodex_gwp.pdf}}

@manual{xie2019,
	Author = {Yihui Xie},
	Title = {{knitr}: A General-Purpose Package for Dynamic Report Generation in {R}},
	Url = {https://yihui.name/knitr/},
	Version = {1.22},
	Year = {2019},
	Bdsk-Url-1 = {https://yihui.name/knitr/}}

@book{xie2015,
	Address = {Boca Raton, Florida},
	Author = {Yihui Xie},
	Edition = {2nd},
	Note = {ISBN 978-1498716963},
	Publisher = {Chapman and Hall/CRC},
	Title = {Dynamic Documents with {R} and knitr},
	Url = {https://yihui.name/knitr/},
	Year = {2015},
	Bdsk-Url-1 = {https://yihui.name/knitr/}}

@manual{papaja2018,
	Author = {Frederik Aust and Marius Barth},
	Title = {{papaja}: {Create} {APA} manuscripts with {R Markdown}},
	Url = {https://github.com/crsh/papaja},
	Version = {0.1.0.9842},
	Year = {2018},
	Bdsk-Url-1 = {https://github.com/crsh/papaja}}

@manual{stargazer2018,
	Address = {Bratislava, Slovakia},
	Author = {Marek Hlavac},
	Organization = {Central European Labour Studies Institute (CELSI)},
	Title = {{stargazer}: Well-Formatted Regression and Summary Statistics Tables},
	Url = {https://CRAN.R-project.org/package=stargazer},
	Version = {5.2.2},
	Year = {2018},
	Bdsk-Url-1 = {https://CRAN.R-project.org/package=stargazer}}

@manual{r2019,
	Address = {Vienna, Austria},
	Author = {{R Core Team}},
	Organization = {R Foundation for Statistical Computing},
	Title = {R: A Language and Environment for Statistical Computing},
	Url = {https://www.R-project.org/},
	Year = {2019},
	Bdsk-Url-1 = {https://www.R-project.org/}}
	
@Book{rmarkdown2019,
  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{chaconProGit2014,
	Author = {Chacon, Scott and Straub, Ben},
	Date = {2014-11-09},
	Edition = {2nd ed. edition},
	Isbn = {978-1-4842-0077-3},
	Langid = {english},
	Location = {{New York, NY}},
	Pagetotal = {456},
	Publisher = {{Apress}},
	Title = {Pro {{Git}}}}

@article{feldmanMakeProgramMaintaining1979,
	Author = {Feldman, Stuart I.},
	Date = {1979-04},
	Doi = {https://doi.org/10.1002/spe.4380090402},
	Issn = {00380644, 1097024X},
	Journaltitle = {Software: Practice and Experience},
	Langid = {english},
	Number = {4},
	Pages = {255-265},
	Shortjournal = {Softw: Pract. Exper.},
	Title = {Make --- a Program for Maintaining Computer Programs},
	Urldate = {2019-10-28},
	Volume = {9},
	Bdsk-Url-1 = {https://doi.org/10.1002/spe.4380090402}}

@article{merkelDockerLightweightLinux2014,
	Author = {Merkel, Dirk},
	Date = {2014-03},
	Issn = {1075-3583},
	Journaltitle = {Linux J.},
	Number = {239},
	Shorttitle = {Docker},
	Title = {Docker: Lightweight Linux Containers for Consistent Development and Deployment},
	Url = {http://dl.acm.org/citation.cfm?id=2600239.2600241},
	Urldate = {2019-10-28},
	Volume = {2014},
	Bdsk-Url-1 = {http://dl.acm.org/citation.cfm?id=2600239.2600241}}

@manual{here2017,
	Author = {Kirill M{\"u}ller},
	Title = {{here}: A Simpler Way to Find Your Files},
	Url = {https://CRAN.R-project.org/package=here},
	Version = {0.1},
	Year = {2017},
	Bdsk-Url-1 = {https://CRAN.R-project.org/package=here}}

@manual{digest2019,
	Author = {Dirk Eddelbuettel and Antoine Lucas and Jarek Tuszynski and Henrik Bengtsson and Simon Urbanek and Mario Frasca and Bryan Lewis and Murray Stokely and Hannes Muehleisen and Duncan Murdoch and Jim Hester and Wush Wu and Qiang Kou and Thierry Onkelinx and Michel Lang and Viliam Simko and Kurt Hornik and Radford Neal and Kendon Bell and Matthew {de Queljoe} and Ion Suruceanu and Bill Denney},
	Title = {digest: Create Compact Hash Digests of R Objects},
	Url = {https://CRAN.R-project.org/package=digest},
	Version = {0.6.21},
	Year = {2019},
	Bdsk-Url-1 = {https://CRAN.R-project.org/package=digest}}

@inproceedings{binder2018,
	Author = {{Project Jupyter} and Matthias Bussonnier and Jessica Forde and Jeremy Freeman and Brian Granger and Tim Head and Chris Holdgraf and Kyle Kelley and Gladys Nalvarte and Andrew Osheroff and M. Pacer and Yuvi Panda and Fernando Perez and Benjamin {Ragan-Kelley} and Carol Willing},
	Booktitle = {{P}roceedings of the 17th {P}ython in {S}cience {C}onference},
	Doi = {https://doi.org/10.25080/Majora-4af1f417-011},
	Editor = {{F}atih {A}kici and {D}avid {L}ippa and {D}illon {N}iederhut and {M} {P}acer},
	Pages = {113 - 120},
	Title = {{B}inder 2.0 - {R}eproducible, interactive, sharable environments for science at scale},
	Year = {2018},
	Bdsk-Url-1 = {https://doi.org/10.25080/Majora-4af1f417-011}}
	
	To cite package ‘worcs’ in publications use:

  Caspar J. van Lissa (2020). worcs: Workflow for Open Reproducible Code in
  Science. R package version 0.1.1. https://github.com/cjvanlissa/worcs

A BibTeX entry for LaTeX users is

@Manual{worcs,
    title = {{worcs}: Workflow for Open Reproducible Code in Science},
    author = {Caspar J. {van Lissa} and Aaron Peikert and Andreas M. Brandmaier},
    year = {2020},
    note = {R package version 0.1.1},
    url = {https://github.com/cjvanlissa/worcs},
  }
  
@article{worcspaper,
  title = {{WORCS}: A Workflow for Open Reproducible Code in Science},
  author={Caspar J. {van Lissa} and Loek Brinkman and Barbara Vreede and Rens van de Schoot and Aaron Peikert and Andreas M. Brandmaier},
  year={2020},
  doi={10.17605/OSF.IO/ZCVBS},
  url={https://osf.io/zcvbs/}
  
  
  }
  
  
  @article{nosek2012scientific,
  title={Scientific utopia: I. Opening scientific communication},
  author={Nosek, Brian A and Bar-Anan, Yoav},
  journal={Psychological Inquiry},
  volume={23},
  number={3},
  pages={217--243},
  year={2012},
  publisher={Taylor \& Francis}
}