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rockerverse.bib
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@Manual{R,
title = {R: A Language and Environment for Statistical Computing},
author = {{R Core Team}},
organization = {R Foundation for Statistical Computing},
address = {Vienna, Austria},
year = {2016},
note = {{ISBN} 3-900051-07-0},
url = {https://www.R-project.org/}
}
@article{RJ-2017-065,
author = {Carl Boettiger and Dirk Eddelbuettel},
title = {{An Introduction to Rocker: Docker Containers for R}},
year = {2017},
journal = {{The R Journal}},
doi = {10.32614/RJ-2017-065},
pages = {527--536},
volume = {9},
number = {2}
}
@article{Lang2017batchtools,
journal = {The Journal of Open Source Software},
doi = {10.21105/joss.00135},
issn = {2475-9066},
number = {10},
publisher = {The Open Journal},
title = {batchtools: Tools for R to work on batch systems},
volume = {2},
author = {Lang, Michel and Bischl, Bernd and Surmann, Dirk},
pages = {135},
date = {2017-02-22},
year = {2017},
month = {2},
day = {22}
}
@article{gentleman_bioconductor_2004,
title = {Bioconductor: open software development for computational biology and bioinformatics},
volume = {5},
issn = {1474-760X},
shorttitle = {Bioconductor},
doi = {10.1186/gb-2004-5-10-r80},
number = {10},
journal = {Genome Biology},
author = {Gentleman, Robert C. and Carey, Vincent J. and Bates, Douglas M. and Bolstad, Ben and Dettling, Marcel and Dudoit, Sandrine and Ellis, Byron and Gautier, Laurent and Ge, Yongchao and Gentry, Jeff and Hornik, Kurt and Hothorn, Torsten and Huber, Wolfgang and Iacus, Stefano and Irizarry, Rafael and Leisch, Friedrich and Li, Cheng and Maechler, Martin and Rossini, Anthony J. and Sawitzki, Gunther and Smith, Colin and Smyth, Gordon and Tierney, Luke and Yang, Jean YH and Zhang, Jianhua},
month = sep,
year = {2004},
pages = {R80}
}
@book{xie2018,
title = {R Markdown: The Definitive Guide},
author = {Xie, Yihui and Allaire, Joseph J and Grolemund, Garrett},
year = {2018},
publisher = {Chapman and Hall/CRC}
}
@Manual{liftr2019,
title = {liftr: Containerize R Markdown Documents for Continuous Reproducibility},
author = {Nan Xiao},
year = {2019},
note = {R package version 0.9.2},
url = {https://CRAN.R-project.org/package=liftr}
}
@misc{eddelbuettel_debugging_2019,
title = {Debugging with {Docker} and {Rocker} – {A} {Concrete} {Example} helping on {macOS}},
url = {http://dirk.eddelbuettel.com/blog/2019/08/05/},
urldate = {2019-11-06},
journal = {Thinking inside the box},
author = {Eddelbuettel, Dirk and Koenker, Roger},
month = aug,
year = {2019}
}
@article{marwick_packaging_2018,
title = {Packaging {Data} {Analytical} {Work} {Reproducibly} {Using} {R} (and {Friends})},
volume = {72},
issn = {0003-1305},
doi = {10.1080/00031305.2017.1375986},
number = {1},
journal = {The American Statistician},
author = {Marwick, Ben and Boettiger, Carl and Mullen, Lincoln},
month = jan,
year = {2018},
pages = {80--88}
}
@article{jupyter_binder_2018,
title = {Binder 2.0 - {Reproducible}, interactive, sharable environments for science at scale},
doi = {10.25080/Majora-4af1f417-011},
urldate = {2018-08-21},
journal = {Proceedings of the 17th Python in Science Conference},
author = {Jupyter, Project and Bussonnier, Matthias and Forde, Jessica and Freeman, Jeremy and Granger, Brian and Head, Tim and Holdgraf, Chris and Kelley, Kyle and Nalvarte, Gladys and Osheroff, Andrew and Pacer, M. and Panda, Yuvi and Perez, Fernando and Ragan-Kelley, Benjamin and Willing, Carol},
year = {2018},
pages = {113--120}
}
@article{kurtzer_singularity_2017,
title = {Singularity: {Scientific} containers for mobility of compute},
volume = {12},
issn = {1932-6203},
shorttitle = {Singularity},
doi = {10.1371/journal.pone.0177459},
number = {5},
journal = {PLOS ONE},
author = {Kurtzer, Gregory M. and Sochat, Vanessa and Bauer, Michael W.},
month = may,
year = {2017},
pages = {e0177459}
}
@article{boettiger_introduction_2015,
title = {An introduction to {Docker} for reproducible research, with examples from the {R} environment},
volume = {49},
issn = {01635980},
doi = {10.1145/2723872.2723882},
number = {1},
journal = {ACM SIGOPS Operating Systems Review},
author = {Boettiger, Carl},
month = jan,
year = {2015},
pages = {71--79}
}
@article{Bernstein2014,
doi = {10.1109/mcc.2014.51},
year = {2014},
month = sep,
publisher = {Institute of Electrical and Electronics Engineers ({IEEE})},
volume = {1},
number = {3},
pages = {81--84},
author = {David Bernstein},
title = {Containers and Cloud: From {LXC} to Docker to Kubernetes},
journal = {{IEEE} Cloud Computing}
}
@article{alam_orchestration_2018,
title = {Orchestration of {Microservices} for {IoT} {Using} {Docker} and {Edge} {Computing}},
volume = {56},
issn = {0163-6804, 1558-1896},
doi = {10.1109/MCOM.2018.1701233},
number = {9},
journal = {IEEE Communications Magazine},
author = {Alam, Muhammad and Rufino, Joao and Ferreira, Joaquim and Ahmed, Syed Hassan and Shah, Nadir and Chen, Yuanfang},
month = sep,
year = {2018},
pages = {118--123}
}
@misc{microsoft_cran_2019,
title = {{CRAN} {Time} {Machine} - {MRAN}},
url = {https://mran.microsoft.com/timemachine},
urldate = {2019-11-05},
journal = {Microsoft R Application Network},
author = {{Microsoft}},
year = {2019}
}
@misc{microsoft_linux_2019,
title = {Linux {Containers} on {Windows}},
url = {https://docs.microsoft.com/en-us/virtualization/windowscontainers/deploy-containers/linux-containers},
urldate = {2019-11-05},
author = {{Microsoft}},
month = sep,
year = {2019}
}
@misc{oci_open_2019,
title = {Open {Containers} {Initiative} - {About}},
url = {https://www.opencontainers.org/about},
urldate = {2019-11-05},
journal = {Open Containers Initiative},
author = {{OCI}},
year = {2019}
}
@misc{datadog_8_2018,
title = {8 surprising facts about real {Docker} adoption},
url = {https://www.datadoghq.com/docker-adoption/},
urldate = {2019-11-05},
journal = {8 surprising facts about real Docker adoption},
author = {{Datadog}},
month = jun,
year = {2018}
}
@misc{munoz_history_2019,
title = {The history of {Docker}'s climb in the container management market},
url = {https://searchservervirtualization.techtarget.com/feature/The-history-of-Dockers-climb-in-the-container-management-market},
urldate = {2019-11-05},
journal = {SearchServerVirtualization},
author = {Muñoz, Stefani},
month = jun,
year = {2019}
}
@misc{t-mobile_enterprise_2018,
title = {Enterprise {Web} {Services} with {Neural} {Networks} {Using} {R} and {TensorFlow}},
copyright = {Copyright 2017. All Rights Reserved.},
url = {https://opensource.t-mobile.com/blog/posts/r-tensorflow-api/},
urldate = {2019-12-13},
journal = {T-Mobile Open Source Blog},
author = {{T-Mobile} and Nolis, Jacqueline and Nolis, Heather},
month = nov,
year = {2018}
}
@misc{nolis_small_2019,
title = {Small data, big value},
url = {https://medium.com/tmobile-tech/small-data-big-value-f783ceca4fdb},
urldate = {2020-01-23},
journal = {T-Mobile Tech},
author = {Nolis, Jacqueline and Werdell, Joel},
month = dec,
year = {2019}
}
@misc{chan_zuckerberg_initiative_maintaining_2019,
title = {Maintaining {Rocker}: {Sustainability} for {Containerized} {Reproducible} {Analyses}},
shorttitle = {Maintaining {Rocker}},
url = {https://chanzuckerberg.com/eoss/proposals/maintaining-rocker-sustainability-for-containerized-reproducible-analyses/},
urldate = {2019-12-13},
journal = {Chan Zuckerberg Initiative},
author = {{Chan Zuckerberg Initiative} and Boettiger, Carl and Ross, Noam and Eddelbuettel, Dirk},
year = {2019}
}
@inproceedings{haydel_enhancing_2015,
series = {{UCC} '15},
title = {Enhancing the {Usability} and {Utilization} of {Accelerated} {Architectures} via {Docker}},
isbn = {978-0-7695-5697-0},
url = {http://dl.acm.org/citation.cfm?id=3233397.3233456},
urldate = {2019-12-16},
booktitle = {Proceedings of the 8th {International} {Conference} on {Utility} and {Cloud} {Computing}},
publisher = {IEEE Press},
author = {Haydel, Nicholas and Madey, Gregory and Gesing, Sandra and Dakkak, Abdul and de Gonzalo, Simon Garcia and Taylor, Ian and Hwu, Wen-mei W.},
year = {2015},
pages = {361--367}
}
@article{schmidhuber_deep_2015,
title = {Deep learning in neural networks: {An} overview},
volume = {61},
issn = {0893-6080},
shorttitle = {Deep learning in neural networks},
doi = {10.1016/j.neunet.2014.09.003},
urldate = {2019-12-16},
journal = {Neural Networks},
author = {Schmidhuber, Jürgen},
month = jan,
year = {2015},
pages = {85--117}
}
@Article{cran:2019,
author = {Kurt Hornik and Uwe Ligges and Achim Zeileis},
title = {Changes on CRAN},
journal = {The R Journal},
year = 2019,
volume = 11,
number = 1,
pages = {438--441},
month = jun,
url = {http://journal.r-project.org/archive/2019-1/cran.pdf}
}
@inproceedings{felter_updated_2015,
title = {An updated performance comparison of virtual machines and {Linux} containers},
doi = {10.1109/ISPASS.2015.7095802},
booktitle = {2015 {IEEE} {International} {Symposium} on {Performance} {Analysis} of {Systems} and {Software} ({ISPASS})},
author = {Felter, Wes and Ferreira, Alexandre and Rajamony, Ram and Rubio, Juan},
month = mar,
year = {2015},
pages = {171--172}
}
@misc{nust_rocker-win_2019,
title = {nuest/rocker-win: {Proof} on concept for {R} in {Windows}-based {Docker} {Containers}},
shorttitle = {nuest/rocker-win},
doi = {10.5281/zenodo.3584107},
publisher = {Zenodo},
author = {Daniel N\"ust},
month = dec,
year = {2019}
}
@article{wickham_welcome_2019,
title = {Welcome to the {Tidyverse}},
volume = {4},
issn = {2475-9066},
doi = {10.21105/joss.01686},
number = {43},
journal = {Journal of Open Source Software},
author = {Wickham, Hadley and Averick, Mara and Bryan, Jennifer and Chang, Winston and McGowan, Lucy and François, Romain and Grolemund, Garrett and Hayes, Alex and Henry, Lionel and Hester, Jim and Kuhn, Max and Pedersen, Thomas and Miller, Evan and Bache, Stephan and Müller, Kirill and Ooms, Jeroen and Robinson, David and Seidel, Dana and Spinu, Vitalie and Takahashi, Kohske and Vaughan, Davis and Wilke, Claus and Woo, Kara and Yutani, Hiroaki},
month = nov,
year = {2019},
pages = {1686}
}
@misc{ratesic_building_2018,
title = {Building a {Repository} of {Alpine}-based {Docker} {Images} for {R}, {Part} {II} – {Curiosity} {Killed} the {Cat} – (... but satisfaction brought it back.)},
url = {https://velaco.github.io/my-dockerfile-for-r-shiny-based-on-alpine-linux-II/},
urldate = {2020-01-10},
author = {Ratesic, Aleksandar},
month = nov,
year = {2018}
}
@misc{r-hub_docs_2019,
title = {R-hub {Docs}},
url = {https://docs.r-hub.io/},
urldate = {2020-01-10},
author = {{R-hub project}},
year = {2019}
}
@Manual{csardi_rhub_2019,
title = {rhub: Connect to 'R-hub'},
author = {Gábor Csárdi and Maëlle Salmon},
year = {2019},
note = {R package version 1.1.1},
url = {https://CRAN.R-project.org/package=rhub}
}
@misc{project_jupyter_jupyter_2018,
title = {Jupyter {Docker} {Stacks} — docker-stacks latest documentation},
url = {https://jupyter-docker-stacks.readthedocs.io/en/latest/},
urldate = {2020-01-10},
author = {Project Jupyter},
year = {2018}
}
@misc{lopp_package_2019,
title = {Package {Manager} 1.1.0 - {No} {Interruptions}},
url = {https://blog.rstudio.com/2019/11/07/package-manager-v1-1-no-interruptions/},
urldate = {2020-01-13},
journal = {RStudio Blog},
author = {Lopp, Sean},
month = jan,
year = {2019}
}
@misc{wikipedia_contributors_os-level_2020,
title = {{OS}-level virtualization},
copyright = {Creative Commons Attribution-ShareAlike License},
url = {https://en.wikipedia.org/w/index.php?title=OS-level_virtualization&oldid=935110975},
urldate = {2020-01-13},
journal = {Wikipedia},
author = {{Wikipedia contributors}},
month = jan,
year = {2020},
note = {Page Version ID: 935110975}
}
@article{donoho_50_2017,
title = {50 {Years} of {Data} {Science}},
volume = {26},
issn = {1061-8600},
doi = {10.1080/10618600.2017.1384734},
number = {4},
journal = {Journal of Computational and Graphical Statistics},
author = {Donoho, David},
month = oct,
year = {2017},
keywords = {Data analysis, Data science, Cross-study analysis, Meta analysis, Predictive modeling, Quantitative programming environments, Statistics},
pages = {745--766}
}
@Article{bennett_outsider_2020,
title = {outsider: Install and run programs, outside of R, inside of R (under review)},
author = {Bennett, Dominic and Hettling, Hannes and Silvestro, Daniele and Vos, Rutger and Antonelli, Alexandre},
journal = {Journal of Open Source Software},
year = {2020},
volume = {5},
number = {45},
pages = {2038},
doi = {10.21105/joss.02038}
}
@misc{rocker_geospatial_2019,
title = {rocker-org/geospatial},
publisher = {Zenodo},
author = {Boettiger, Carl and Lovelace, Robin and Howe, Mike and Lamb, James},
month = dec,
year = {2019},
doi = {10.5281/zenodo.1013940}
}
@Manual{core_writing_1999,
author = {{R Core Team}},
journal = {R Foundation for Statistical Computing},
url = {https://cran.r-project.org/doc/manuals/r-devel/R-exts.html},
urldate = {2020-01-15},
year = {1999}
}
@Manual{eddelbuettel_sanitizers_2014,
title = {sanitizers: C/C++ source code to trigger Address and Undefined Behaviour
Sanitizers},
author = {Dirk Eddelbuettel},
year = {2014},
note = {R package version 0.1.0},
url = {https://CRAN.R-project.org/package=sanitizers}
}
@misc{ye_docker_2019,
title = {Docker {Setup} for {R} package {Development}},
url = {https://haoye.us/post/2019-10-10-docker-for-r-package-development/},
urldate = {2020-01-15},
journal = {Hao Ye},
author = {Ye, Hao},
year = {2019}
}
@misc{eckert_building_2018,
title = {Building and testing {R} packages with latest {R}-{Devel}},
url = {https://alexandereckert.com/post/testing-r-packages-with-latest-r-devel/},
urldate = {2020-01-15},
author = {Eckert, Alexander},
month = feb,
year = {2018}
}
@misc{cardozo_faster_2018,
title = {Faster {Docker} builds in {Travis} {CI} for {R} packages},
url = {https://lecardozo.github.io/2018/03/01/automated-docker-build.html},
urldate = {2020-01-15},
author = {Cardozo, Lucas},
year = {2018}
}
@article{nust_containerit_2019,
title = {containerit: {Generating} {Dockerfiles} for reproducible research with {R}},
volume = {4},
issn = {2475-9066},
shorttitle = {containerit},
url = {https://joss.theoj.org/papers/10.21105/joss.01603},
doi = {10.21105/joss.01603},
number = {40},
journal = {Journal of Open Source Software},
author = {Nüst, Daniel and Hinz, Matthias},
month = aug,
year = {2019},
pages = {1603}
}
@article{emsley_framework_2018,
title = {A {Framework} for the {Preservation} of a {Docker} {Container} {\textbar} {International} {Journal} of {Digital} {Curation}},
volume = {12},
doi = {10.2218/ijdc.v12i2.509},
number = {2},
journal = {International Journal of Digital Curation},
author = {Emsley, Iain and De Roure, David},
month = apr,
year = {2018}
}
@article{nust_opening_2017,
title = {Opening the {Publication} {Process} with {Executable} {Research} {Compendia}},
volume = {23},
issn = {1082-9873},
doi = {10.1045/january2017-nuest},
number = {1/2},
journal = {D-Lib Magazine},
author = {Nüst, Daniel and Konkol, Markus and Pebesma, Edzer and Kray, Christian and Schutzeichel, Marc and Przibytzin, Holger and Lorenz, Jörg},
month = jan,
year = {2017}
}
@article{donoho_invitation_2010,
title = {An invitation to reproducible computational research},
volume = {11},
issn = {1465-4644},
doi = {10.1093/biostatistics/kxq028},
number = {3},
journal = {Biostatistics},
author = {Donoho, David L.},
month = jul,
year = {2010},
pages = {385--388}
}
@misc{marwick_how_2015,
title = {How computers broke science – and what we can do to fix it},
copyright = {Copyright © 2010–2019, The Conversation Trust (UK) Limited},
url = {http://theconversation.com/how-computers-broke-science-and-what-we-can-do-to-fix-it-49938},
urldate = {2017-07-05},
journal = {The Conversation},
author = {Marwick, Ben},
month = nov,
year = {2015}
}
@article{barba_terminologies_2018,
title = {Terminologies for {Reproducible} {Research}},
url = {http://arxiv.org/abs/1802.03311},
journal = {arXiv:1802.03311 [cs]},
author = {Barba, Lorena A.},
month = feb,
year = {2018},
note = {arXiv: 1802.03311}
}
@article{gentleman_statistical_2007,
title = {Statistical {Analyses} and {Reproducible} {Research}},
volume = {16},
issn = {1061-8600},
doi = {10.1198/106186007X178663},
number = {1},
journal = {Journal of Computational and Graphical Statistics},
author = {Gentleman, Robert and Lang, Duncan Temple},
month = mar,
year = {2007},
pages = {1--23}
}
@misc{oracle_labs_oraclefastr_2020,
title = {oracle/fastr},
url = {https://github.com/oracle/fastr},
urldate = {2020-01-16},
publisher = {Oracle},
author = {{Oracle Labs}},
month = jan,
year = {2020}
}
@Manual{horner_rapache_2013,
title = {rApache: Web application development with R and Apache.},
author = {Jeffrey Horner},
year = {2013},
url = {http://www.rapache.net/},
comment = {website seems down, https://web.archive.org/web/20190627101203/http://rapache.net/manual.html}
}
@article{brinckman2019,
title = {Computing environments for reproducibility: Capturing the “{W}hole {T}ale”},
author = {Brinckman, Adam and Chard, Kyle and Gaffney, Niall and Hategan, Mihael and Jones, Matthew B and Kowalik, Kacper and Kulasekaran, Sivakumar and Lud{\"a}scher, Bertram and Mecum, Bryce D and Nabrzyski, Jarek and others},
journal = {Future Generation Computer Systems},
volume = {94},
pages = {854--867},
year = {2019},
publisher = {Elsevier},
doi = {10.1016/j.future.2017.12.029}
}
@inproceedings{chard2019a,
author = {Chard, Kyle and Gaffney, Niall and Jones, Matthew B. and Kowalik, Kacper and Lud\"{a}scher, Bertram and Nabrzyski, Jarek and Stodden, Victoria and Taylor, Ian and Turk, Matthew J. and Willis, Craig},
title = {Implementing Computational Reproducibility in the Whole Tale Environment},
booktitle = {Proceedings of the 2nd International Workshop on Practical Reproducible Evaluation of Computer Systems},
series = {P-RECS '19},
year = {2019},
pages = {17--22},
doi = {10.1145/3322790.3330594}
}
@inproceedings{mecum2018,
title = {Preserving Reproducibility: Provenance and Executable Containers in DataONE Data Packages},
author = {Mecum, Bryce and Jones, Matthew B and Vieglais, Dave and Willis, Craig},
booktitle = {2018 IEEE 14th International Conference on e-Science (e-Science)},
pages = {45--49},
year = {2018},
organization = {IEEE},
doi = {10.1109/eScience.2018.00019}
}
@article{chard2019b,
author = {Chard, Kyle and Gaffney, Niall and Jones, Matthew B. and Kowalik,
Kacper and Lud\"{a}scher, Bertram and McPhillips, Timothy and Nabrzyski,
Jarek and Stodden, Victoria and Taylor, Ian and Thelen, Thomas and Turk, Matthew J. and Willis, Craig},
title = {{Application of BagIt-Serialized Research Object Bundles for Packaging and Re-execution of Computational Analyses}},
year=2019,
publisher = {Zenodo},
note = {{To appear in 2019 IEEE 15th International Conference on e-Science (e-Science).}},
doi = {10.5281/zenodo.3381754}
}
@article{mcphillips2019,
author = {McPhillips, Timothy and Willis, Craig and Gryk, Michael and Nunez-Corrales, Santiago and Lud\"{a}scher, Bertram},
title = {{Reproducibility by Other Means: Transparent Research Objects}},
year=2019,
publisher = {Zenodo},
note = {{To appear in 2019 IEEE 15th International Conference on e-Science (e-Science).}},
doi = {10.5281/zenodo.3382423}
}
@article{King1995,
title = {Replication, Replication},
volume = {28},
DOI = {10.2307/420301},
number = {3},
journal = {PS: Political Science \& Politics},
author = {King, Gary},
year = {1995},
month = {Sep},
pages = {444–452}
}
@article{Christian2018,
author = {Christian, Thu-Mai and Jacoby, William G and Lafferty-Hess, Sophia and Carsey, Thomas},
title = {Operationalizing the Replication Standard},
volume = {13},
journal = {International Journal of Digital Curation},
doi = {10.2218/ijdc.v13i1.555},
number = {1},
year = {2018}
}
@article{Alvarez2018,
title = {Research Replication: Practical Considerations},
volume = {51},
ISSN = {1049-0965, 1537-5935},
doi = {10.1017/S1049096517002566},
number = {2},
journal = {PS: Political Science \& Politics},
author = {Alvarez, R. Michael and Key, Ellen M. and Núñez, Lucas},
year = {2018},
month = {Apr},
pages = {422–426}
}
@article{Vilhuber2019,
title = {Report by the {AEA Data Editor}},
volume = {109},
ISSN = {2574-0768},
DOI = {10.1257/pandp.109.718},
journal = {AEA Papers and Proceedings},
author = {Vilhuber, Lars},
year = {2019},
month = {May},
pages = {718–729}
}
@article{Jacoby2017,
title = {Should Journals Be Responsible for Reproducibility?},
url = {https://www.insidehighered.com/blogs/rethinking-research/should-journals-be-responsible-reproducibility},
journal = {Inside Higher Ed},
author = {Jacoby, William G. and Lafferty-Hess, Sophia and Christian, Thu-Mai},
year = {2017},
month = {Jul},
urldate = {2020-01-20}
}
@article{Eubank2016,
title = {Lessons from a Decade of Replications at the {Quarterly Journal of Political Science}},
volume = {49},
ISSN = {1049-0965, 1537-5935},
DOI = {10.1017/S1049096516000196},
number = {2},
journal = {PS: Political Science \& Politics},
author = {Eubank, Nicholas},
year = {2016},
month = {Apr},
pages = {273–276}
}
@book{NASEM2019,
place = {Washington, D.C.},
title = {Reproducibility and Replicability in Science},
ISBN = {978-0-309-48616-3},
DOI = {10.17226/25303},
publisher = {National Academies Press},
author = {{Committee on Reproducibility and Replicability in Science}},
year = {2019}
}
@Manual{cannoodt_babelwhale_2019,
title = {babelwhale: Talking to 'Docker' and 'Singularity' Containers},
author = {Robrecht Cannoodt and Wouter Saelens},
year = {2019},
note = {R package version 1.0.1},
url = {https://CRAN.R-project.org/package=babelwhale}
}
@Manual{gdal_2019,
title = {{GDAL/OGR} Geospatial Data Abstraction software Library},
author = {{GDAL/OGR contributors}},
organization = {Open Source Geospatial Foundation},
year = {2019},
url = {https://gdal.org}
}
@misc{kjeldgaard_dockr_2019,
title = {'dockr': easy containerization for {R} - {pRopaganda} by smaakagen},
shorttitle = {'dockr'},
url = {http://smaakage85.netlify.com/2019/12/21/dockr-easy-containerization-for-r/},
urldate = {2020-01-23},
author = {Kjeldgaard, Lars},
month = dec,
year = {2019}
}
@Manual{cran_dockr,
title = {dockr: Creation of Lightweight Docker Images for Your Packages},
author = {Lars Kjeldgaard},
year = {2019},
note = {R package version 0.8.6},
url = {https://CRAN.R-project.org/package=dockr}
}
@Manual{renv2019,
title = {renv: Project Environments},
author = {Kevin Ushey},
year = {2020},
note = {R package version 0.9.3},
url = {https://CRAN.R-project.org/package=renv}
}
@misc{ushey_using_2019,
title = {Using renv with {Docker}},
url = {https://rstudio.github.io/renv/articles/docker.html},
urldate = {2020-01-23},
journal = {Project Environments • renv},
author = {Ushey, Kevin},
year = {2019}
}
@misc{ooms_opencpu_2017,
title = {{OpenCPU} - {Why} {Use} {Docker} with {R}? {A} {DevOps} {Perspective}},
url = {https://www.opencpu.org/posts/opencpu-with-docker/},
urldate = {2020-01-23},
author = {Ooms, Jeroen},
month = oct,
year = {2017}
}
@article{savini_epiexplorer_2019,
title = {{EpiExploreR}: {A} {Shiny} {Web} {Application} for the {Analysis} of {Animal} {Disease} {Data}},
volume = {7},
copyright = {http://creativecommons.org/licenses/by/3.0/},
shorttitle = {{EpiExploreR}},
doi = {10.3390/microorganisms7120680},
number = {12},
urldate = {2020-01-23},
journal = {Microorganisms},
author = {Savini, Lara and Candeloro, Luca and Perticara, Samuel and Conte, Annamaria},
month = dec,
year = {2019},
pages = {680}
}
@article{glouzon_structurexplor_2017,
title = {Structurexplor: a platform for the exploration of structural features of {RNA} secondary structures},
volume = {33},
issn = {1367-4803},
shorttitle = {Structurexplor},
doi = {10.1093/bioinformatics/btx323},
number = {19},
urldate = {2020-01-23},
journal = {Bioinformatics},
author = {Glouzon, Jean-Pierre Séhi and Perreault, Jean-Pierre and Wang, Shengrui},
month = oct,
year = {2017},
pages = {3117--3120}
}
@Manual{rselenium_2019,
title = {RSelenium: R Bindings for 'Selenium WebDriver'},
author = {John Harrison},
year = {2019},
note = {R package version 1.7.5},
url = {https://CRAN.R-project.org/package=RSelenium}
}
@Article{landau_drake_2019,
title = {The drake R package: a pipeline toolkit for reproducibility and high-performance computing},
author = {William Michael Landau},
journal = {Journal of Open Source Software},
year = {2018},
volume = {3},
number = {21}
}
@Manual{future_2020,
title = {future: Unified Parallel and Distributed Processing in R for Everyone},
author = {Henrik Bengtsson},
year = {2020},
note = {R package version 1.16.0},
url = {https://CRAN.R-project.org/package=future}
}
@Manual{googleComputeEngineR_2019,
title = {googleComputeEngineR: R Interface with Google Compute Engine},
author = {Mark Edmondson},
year = {2019},
note = {R package version 0.3.0},
url = {https://CRAN.R-project.org/package=googleComputeEngineR}
}
@misc{edmondson_r_2018,
title = {R on {Kubernetes} - serverless {Shiny}, {R} {APIs} and scheduled scripts},
url = {https://code.markedmondson.me/r-on-kubernetes-serverless-shiny-r-apis-and-scheduled-scripts/},
urldate = {2020-01-27},
author = {Edmondson, Mark},
month = may,
year = {2018}
}
@Manual{analogsea_2019,
title = {analogsea: Interface to 'Digital Ocean'},
author = {Scott Chamberlain and Hadley Wickham and Winston Chang},
year = {2019},
note = {R package version 0.7.2},
url = {https://CRAN.R-project.org/package=analogsea},
}
@Manual{AzureContainers_2019,
title = {AzureContainers: Interface to 'Container Instances', 'Docker Registry' and
'Kubernetes' in 'Azure'},
author = {Hong Ooi},
year = {2019},
note = {R package version 1.2.0},
url = {https://CRAN.R-project.org/package=AzureContainers},
}
@article{beaulieu-jones_reproducibility_2017,
title = {Reproducibility of computational workflows is automated using continuous analysis},
volume = {advance online publication},
issn = {1087-0156},
doi = {10.1038/nbt.3780},
journal = {Nature Biotechnology},
author = {Beaulieu-Jones, Brett K. and Greene, Casey S.},
month = mar,
year = {2017}
}
@article{cetinkaya-rundel_infrastructure_2018,
title = {Infrastructure and {Tools} for {Teaching} {Computing} {Throughout} the {Statistical} {Curriculum}},
volume = {72},
issn = {0003-1305},
doi = {10.1080/00031305.2017.1397549},
number = {1},
journal = {The American Statistician},
author = {Çetinkaya-Rundel, Mine and Rundel, Colin},
month = jan,
year = {2018},
pages = {58--65}
}
@misc{marwick_research_2017,
title = {Research compendium for the 1989 excavations at {Madjedbebe} rockshelter, {NT}, {Australia}},
author = {Marwick, Ben},
month = jul,
year = {2017},
doi = {10.6084/m9.figshare.1297059.v4}
}
@article{merchant_iplant_2016,
title = {The {iPlant} {Collaborative}: {Cyberinfrastructure} for {Enabling} {Data} to {Discovery} for the {Life} {Sciences}},
volume = {14},
issn = {1545-7885},
shorttitle = {The {iPlant} {Collaborative}},
doi = {10.1371/journal.pbio.1002342},
number = {1},
urldate = {2020-02-26},
journal = {PLOS Biology},
author = {Merchant, Nirav and Lyons, Eric and Goff, Stephen and Vaughn, Matthew and Ware, Doreen and Micklos, David and Antin, Parker},
month = jan,
year = {2016},
pages = {e1002342}
}
@article{devisetty_bringing_2016,
title = {Bringing your tools to {CyVerse} {Discovery} {Environment} using {Docker}},
volume = {5},
issn = {2046-1402},
doi = {10.12688/f1000research.8935.3},
urldate = {2020-02-26},
journal = {F1000Research},
author = {Devisetty, Upendra Kumar and Kennedy, Kathleen and Sarando, Paul and Merchant, Nirav and Lyons, Eric},
month = dec,
year = {2016},
pages = {1442}
}
@misc{rstudio_proxy_2020,
title = {Running RStudio Server with a Proxy},
url = {https://support.rstudio.com/hc/en-us/articles/200552326-Running-RStudio-Server-with-a-Proxy},
urldate = {2020-01-27},
publisher = {RStudio},
author = {{RStudio Support}},
month = jan,
year = {2020}
}
@Manual{cran_stevedore,
title = {stevedore: Docker Client},
author = {Rich FitzJohn},
year = {2020},
note = {R package version 0.9.3},
url = {https://CRAN.R-project.org/package=stevedore}
}
@Manual{cran_dockerfiler,
title = {dockerfiler: Easy Dockerfile Creation from R},
author = {Colin Fay},
year = {2019},
note = {R package version 0.1.3},
url = {https://CRAN.R-project.org/package=dockerfiler}
}
@Manual{cran_golem,
title = {golem: A Framework for Robust Shiny Applications},
author = {Vincent Guyader and Colin Fay and Sébastien Rochette and Cervan Girard},
year = {2019},
note = {R package version 0.1},
url = {https://CRAN.R-project.org/package=golem}
}
@Manual{cran_sys,
title = {sys: Powerful and Reliable Tools for Running System Commands in R},
author = {Jeroen Ooms},
year = {2019},
note = {R package version 3.3},
url = {https://CRAN.R-project.org/package=sys}
}
@Manual{cran_biocmanager,
title = {BiocManager: Access the Bioconductor Project Package Repository},
author = {Martin Morgan},
year = {2019},
note = {R package version 1.30.10},
url = {https://CRAN.R-project.org/package=BiocManager}
}
@Manual{cran_reticulate,
title = {reticulate: Interface to 'Python'},
author = {Kevin Ushey and JJ Allaire and Yuan Tang},
year = {2019},
note = {R package version 1.14},
url = {https://CRAN.R-project.org/package=reticulate}
}
@Manual{cran_shiny,
title = {shiny: Web Application Framework for R},
author = {Winston Chang and Joe Cheng and JJ Allaire and Yihui Xie and Jonathan McPherson},
year = {2019},
note = {R package version 1.4.0},
url = {https://CRAN.R-project.org/package=shiny}
}
@Manual{cran_checkpoint,
title = {checkpoint: Install Packages from Snapshots on the Checkpoint Server for
Reproducibility},
author = {Hong Ooi and Andrie {de Vries} and {Microsoft}},
year = {2020},
note = {R package version 0.4.9},
url = {https://CRAN.R-project.org/package=checkpoint}
}
@Article{pebesma_simple_2018,
author = {Edzer Pebesma},
title = {{Simple Features for R: Standardized Support for Spatial Vector Data}},
year = {2018},
journal = {{The R Journal}},
doi = {10.32614/RJ-2018-009},
pages = {439--446},
volume = {10},
number = {1}
}
@Manual{cran_rgdal,
title = {rgdal: Bindings for the 'Geospatial' Data Abstraction Library},
author = {Roger Bivand and Tim Keitt and Barry Rowlingson},
year = {2019},
note = {R package version 1.4-8},
url = {https://CRAN.R-project.org/package=rgdal}
}
@Manual{cran_future,
title = {future: Unified Parallel and Distributed Processing in R for Everyone},
author = {Henrik Bengtsson},
year = {2020},
note = {R package version 1.16.0},
url = {https://CRAN.R-project.org/package=future}
}
@Manual{cran_plumber,
title = {plumber: An API Generator for R},
author = {{Trestle Technology, LLC}},
year = {2018},
note = {R package version 0.4.6},
url = {https://CRAN.R-project.org/package=plumber}
}
@Manual{cran_rserve,
title = {Rserve: Binary R server},
author = {Simon Urbanek},
year = {2019},
note = {R package version 1.7-3.1},
url = {https://CRAN.R-project.org/package=Rserve}
}
@Manual{grosjean_sciviews_2019,
title = {{SciViews-R}: A GUI API for R},
author = {Philippe Grosjean},
organization = {UMONS},
address = {MONS, Belgium},