employment
2015-current Assistant Professor, Department of Environmental Science, Policy and Management, University of California, Berkeley.
2013-2015 NSF Post-doctoral Scholar in the Department of Applied Mathematics and Statistics, University of California, Santa Cruz. Mentors: Marc Mangel, Stephan Munch
education
2012 Ph.D Population Biology, University of California, Davis. Mentor: Alan Hastings
2007 A.B in Physics, Princeton University, with honors and certificates in biophysics and applied and computational mathematics.
publications
Karthik Ram, Carl Boettiger, Scott Chamberlain, Noam Ross, Maelle Salmon, & Stephanie Butland. (2018). A Community of Practice Around Peer-review for Long-term Research Software Sustainability. Computing in Science & Engineering, 9615(c), 1–1. doi:10.1109/MCSE.2018.2882753
Carl Boettiger, (2018). Managing Larger Data on a GitHub Repository. Journal of Open Source Software, 3(29), 971, doi:10.21105/joss.00971. (software).
Milad Memarzadeh, Carl Boettiger (2018). Adaptive management of ecological systems under partial observability. Biological Conservation. 224, 9-15. doi:10.1016/j.biocon.2018.05.009. (software)
Carl Boettiger (2018). From noise to knowledge: how randomness generates novel phenomena and reveals information. Ecology Letters. doi:10.1111/ele.13085 (oa, code, data)
Carl Boettiger, Dirk Eddelbuettel (2018). An Introduction to Rocker: Docker Containers for R. The R Journal. https://journal.r-project.org/archive/2017/RJ-2017-065/index.html.
Carl Boettiger (2017). Generating Codemeta Metadata for R Packages.
The Journal of Open Source Software 2 (19), 454, doi:10.21105/joss.00454Getz, Marshall, Carlson, Giuggioli, Ryan, Romañach, Boettiger, Chamberlain, Larsen, D'Odorico, O'Sullivan, D. (2017). Making ecological models adequate. Ecology Letters. doi:10.1111/ele.12893
Ben Marwick, Carl Boettiger, Lincoln Mullen (2017). Packaging data analytical work reproducibly using R (and friends). The American Statistician. doi:10.1080/00031305.2017.1375986. (oa)
Hampton, Jones, Wasser, Schuldhauer, Supp, Brun, Herandez, Boettiger, Collins, Gross, Fernandez, Budden, White, Teal, Labou & Aukema. (2017) Skills and Knowledge for Data Intensive Research. BioScience. doi:10.1093/biosci/bix025. (oa)
T Alex Perkins, Carl Boettiger, Benjamin L. Philips. (2016) After the games are over: life-history trade-offs drive dispersal attenuation following range expansion. Ecology and Evolution 6 (18) 6425-6434. doi:10.1002/ece3.2314. (oa, code)
Carl Boettiger, Michael Bode, James N. Sanchirico, Jacob LaRiviere, Alan Hastings, and Paul Robert Armsworth. (2016) Optimal management of a stochastically varying population when policy adjustment is costly. Ecological Applications 26 (3) 808-817. doi:10.1890/15-0236. (oa, code)
Carl Boettiger, Scott Chamberlain, Rutger Vos and Hilmar Lapp. (2016) RNeXML: a package for reading and writing richly annotated phylogenetic, character, and trait data in R. Methods in Ecology and Evolution. doi:10.1111/2041-210X.12469. (oa, code, software)
Carl Boettiger, Scott Chamberlain, Edmund Hart, Karthik Ram. (2015) Building Software, Building Community: Lessons from the rOpenSci Project. Journal of Open Research Software 3: e8, doi:10.5334/jors.bu.
Carl Boettiger. (2015) An introduction to Docker for reproducible research. ACM SIGOPS Operating Systems Review, Special Issue on Repeatability and Sharing of Experimental Artifacts. 49(1), 71-79. doi:10.1145/2723872.2723882. (oa)
Carl Boettiger, Marc Mangel, Stephan Munch. (2015) Avoiding tipping points in fisheries management through Gaussian process dynamic programming. Proceedings of the Royal Society B 282(1801), 8–11. doi:10.1098/rspb.2014.1631. (oa, code, data)
Carl Boettiger, Alan Hastings. (2013) No early warning signals for stochastic transitions: insights from large deviation theory. Proceedings of the Royal Society B. doi:10.1098/rspb.2013.1372. (oa, code)
Carl Boettiger*, Noam Ross*, Alan Hastings. (2013) Early warning signals: The charted and uncharted territories. Theoretical Ecology doi:10.1007/s12080-013-0192-6. (oa, code)
Carl Boettiger, Alan Hastings (2013). Tipping points: From patterns to predictions, Nature 493, 157–158. doi:10.1038/493157a.
Carl Boettiger, Alan Hastings (2012). Early Warning Signals and the Prosecutor’s Fallacy, Proceedings of the Royal Society B 279 (1748) 4734-4739. doi:10.1098/rspb.2012.2085. (oa, code, data)
Carl Boettiger, Duncan Temple Lang, Peter Wainwright (2012). rfishbase: exploring, manipulating and visualizing FishBase data from R, Journal of Fish Biology. 81 (6) 2030–2039. doi:10.1111/j.1095-8649.2012.03464.x. (oa, code, software)
Carl Boettiger, Duncan Temple Lang (2012). Treebase: An R package for discovery, access and manipulation of online phylogenies, Methods in Ecology and Evolution 3 (6) 1060–1066. doi:10.1111/j.2041-210X.2012.00247x. (oa, code, software)
Carl Boettiger and Alan Hastings (2012). Quantifying Limits to Detection of Early Warning for Critical Transitions, Journal of the Royal Society: Interface 9 (75) 2527-2539. doi:10.1098/rsif.2012.0125. (oa, code)
Jeremy M. Beaulieu, Dwueng-Chwuan Jhwueng, Carl Boettiger and Brian O’Meara, (2012). Modeling Stabilizing Selection: Expanding the Ornstein-Uhlenbeck Model of Adaptive Evolution, Evolution 66 (8) 2369-2383. doi:10.1111/j.1558-5646.2012.01619.x (software)
Carl Boettiger, Graham Coop, Peter Ralph (2012) Is your phylogeny informative? Measuring the power of comparative methods, Evolution 66 (7) 2240-51. doi:10.1111/j.1558-5646.2011.01574.x, (oa, code, data)
Carl Boettiger, Jonathan Dushoff, Joshua S Weitz (2010) Fluctuation domains in adaptive evolution, Theoretical Population Biology 77 (1) 6-13. doi:10.1016/j.tpb.2009.10.003. (oa, code, data)
James J. Wray, Neta A. Bahcall, Paul Bode, Carl Boettiger, Phillip Hopkins. (2006) The Shape, Multiplicity, and Evolution of Superclusters in Lambda-CDM Cosmology, The Astrophysical Journal 652 (2) 907-916. doi:10.1086/50860. (oa)
grants
The Influence of Conflicting Policies and Supply-Chain Pressures on Farmers' Decisions and Tradeoffs with Respect to Biodiversity, Profitability, and Sustainability. Timothy Bowles (PI), Alastair Iles, Claire Kremen, Carl Boettiger. (2018-2022). National Science Foundation #CNH-1824871 $1,301,737
Detecting Change in Global Biodiversity through Large Scale Network Analysis. (2018-2020) Berkeley Institute for Data Science, $67,000
Hellman Fellows Award (2018-2020) The Hellman Foundation. $37,600
Berkeley Collegium Award for Excellence in Undergraduate Education. (2018-2019) $16,867.50
Managing ecosystems under extreme uncertainty. (2016-03 - 2019-09) NSF XSEDE TG-DEB160003. NSF Estimated value of computing resources: $34,558
Reproducible and Collaborative Data Science. NSF XSEDE TG-DEB160021. NSF Estimated value of computing resources: $20,028
The rOpenSci Project (2015-2018, Co-PI). Helmsley Charitable Trust, award 2016PG-BRI004. $2,900,000
The Codemeta project (2015). National Science Foundation #ACI-1549758 165,782 USD. (proposal)
The rOpenSci Project, Phase II funding (2014, Co-PI). Alfred P. Sloan Foundation $300,000
NSF Biology Post-doc (2013-2015). National Science Foundation #DBI-1306697, $138,000 (proposal)
The rOpenSci Project Phase I funding (2013, Co-PI). Alfred P. Sloan Foundation $180,000
IIASA YSSP fellowship (2009). National Academy of Sciences, OISE-0738129, $8,000. (proposal)
Computational Science Graduate Fellowship (2008). United States Department of Energy, #DE-FG02-97ER25308, $149,000. (proposal)
book chapters
- Carl Boettiger (2017). A Reproducible R Notebook Using Docker. In J. Kitzes, D. Turek, & F. Deniz (Eds.), The Practice of Reproducible Research: Case Studies and Lessons from the Data-Intensive Sciences (1st ed., pp. 109–117). Oakland, CA: UC Press. https://www.ucpress.edu/book.php?isbn=9780520294752
invited talks & workshops
2018
- NSF SI2 PIs Meeting, Washington, DC
- rOpenSci unconference, Seattle, WA
- Faculty Learning Program Fellows Workshop Berkeley, CA
- GraphXD, Berkeley, CA
- Digital Data in Biodiversity UC Berkeley. (co-organizer)
2017
- CROSS Symposium Speaker UC Santa Cruz.
- Imagining Tomorrow's University Chicago, IL.
- rOpenSci unconference, Los Angeles, CA
- Prov-a-thon: Practical Tools for Reproducible Science, Tamaya, NM.
- NSF Translational Data Science Workshop, Berkeley Institute for Data Science, Berkeley, CA.
2016
- Force16 Codemeta Workshop, Portland OR (organizer)
- CodeMeta NSF Workshop Portland, OR (organizer)
- rOpenSci unconference, San Francisco, CA
2015
- Invited Speaker, Empirical Dynamical Modeling and Forecasting in Nonlinear Systems, NTU, Taiwan.
- Moore-Sloan Data Science Environments: Second Annual Data Science Summit
- Data Intensive Training Workshop, NCEAS, Santa Barbara, CA
- NSF Big Data Hubs Design Charette, Western Region.
- rOpenSci unconference, San Francisco CA.
- Pretty Darn Good Control Working group, NIMBIOS, Knoxville TN
2014
- Invited speaker, Berkeley Initiative for Global Change Biology Workshop (student organized), UC Berkeley, CA.
- Invited speaker, DIMACS Global Change, Berkeley CA.
- Invited speaker, Zoology Seminar, University of Wisconsin, Madison, WI.
- Invited speaker, ESPM Seminar, UC Berkeley, CA.
- rOpenSci unconference, San Francisco CA.
- Reproducible Science: Curriculum & Workflow Workshop, NESCent, Durham, NC.
- WSSSPE 2.0 Meeting. New Orleans, LA.
- Workflows Working Group, NCEAS, Santa Barbara, CA.
2013 & prior
- invited speaker, MBI, Sustainable Management of Living Natural Resources, Columbus, OH.
- invited seminar speaker, WHOI, Woods Hole, MA.
- invited seminar speaker, UC Davis Dept of Environmental Resources and Economics; Davis, CA.
- invited speaker, SSB Symposium, Evolution Conference, Ottawa, CAN.
- Sustainable Management of Living Natural Resources Workshop, MBI Columbus, OH.
- Academic software & workforce development Workshop, ISEES. Oakland, CA.
- Software Lifecycle Workshop, ISEES, Santa Barbara, CA.
- Pretty Darn Good Control Working group, NIMBIOS, Knoxville, TN
- Stochastic spatial modeling in population dynamics Workshop, AIM, Palo Alto, CA.
awards
- 2011 Volterra Award (Best student talk, ESA Theory Section)
- 2007 Elected to Membership in the Society of Sigma Xi
- 2007 Allen G. Shenstone Prize in Physics, Princeton University
- 2007 The Class of 1870 Old English Prize, Princeton University
- 2006 Kusaka Memorial Prize in Physics, Princeton University
- 2006 Plasma Physics Fellow, PPPL
service
campus
- 2018 - current. Governance Committee for Data Science Programs
- 2017 - 2018. ESPM Remote Sensing Faculty Search, committee member & equity liaison
- 2017 - 2018. ad hoc Data Science Degree Proposal Committee
- 2015 - current. Berkeley Research Computing Advisory Committee
extra-campus
- NCEAS Scientific Advisory Board
- rOpenSci Leadership Team
- Jetstream Cloud Computing Stakeholder Advisory Board, XSEDE.
selected software projects
- 2012 - current: The rOpenSci Project, co-founder. https://ropensci.org
- 2014 - current: Carl Boettiger, Dirk Eddelbuettel. The Rocker Project: Docker images for the R environment. https://rocker-project.org
- 2015 - current: Carl Boettiger, Matt Jones, et al. The CodeMeta Project: Software Metadata Exchange https://codemeta.github.io
My software impact is also measured relative to other academics by depsy.org
theses
- Carl Boettiger, David Huse (2006) Clonal Interference Models in Population Genetics. Princeton Physics Dept. doi:10.6084/m9.figshare.678305.
- Carl Boettiger, Joshua Weitz, Simon Levin (2007) Adaptive Dynamics: Branching Phenomena and the Canonical Equation Princeton Physics Dept. doi:10.6084/m9.figshare.678306.
- Carl Boettiger, Stephen Pacala, David Huse (2007) Ensemble Behavior from Individual Dynamics in Multispecies Forest Populations. Princeton Physics Dept. doi:10.6084/m9.figshare.678304.
- Carl Boettiger (2012). Regime shifts in ecology and evolution (PhD Dissertation). doi:10.6084/m9.figshare.97218.
media interviews
- Seltenrich, N. (2016). "Scaling the Heights of Data Science." Breakthroughs Magazine. https://nature.berkeley.edu/breakthroughs/opensci-data
- Tachibana, C. (2014). "The paperless lab" Science 345(6195) pp. 468-470. 10.1126/science.opms.p1400087
- Mascarelli, A. (2014) "Research tools: Jump off the page." Nature 507, 523–525. doi:10.1038/nj7493-523a
- Check Hayden E (2013). "Mozilla Plan Seeks to Debug Scientific Code." Nature, 501, pp. 472-472. doi:10.1038/501472a
- Van Noorden R (2013). "Data-Sharing: Everything on Display." Nature, 500, pp. 243-245. doi:10.1038/nj7461-243a
- Gewin, Virginia (2013). "Turning Point: Carl Boettiger" Nature, 493 p 711 doi:10.1038/nj7434-711a
- Wald, Chelsea (2010). "Scientists Embrace Openness" Science. doi:10.1126/science.caredit.a1000036