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

  1. 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

  2. Carl Boettiger, (2018). Managing Larger Data on a GitHub Repository. Journal of Open Source Software, 3(29), 971, doi:10.21105/joss.00971. (software).

  3. 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)

  4. 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)

  5. 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.

  6. Carl Boettiger (2017). Generating Codemeta Metadata for R Packages.
    The Journal of Open Source Software 2 (19), 454, doi:10.21105/joss.00454

  7. Getz, 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

  8. 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)

  9. 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)

  10. 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)

  11. 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)

  12. 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)

  13. 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.

  14. 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)

  15. 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)

  16. 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)

  17. 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)

  18. Carl Boettiger, Alan Hastings (2013). Tipping points: From patterns to predictions, Nature 493, 157–158. doi:10.1038/493157a.

  19. 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)

  20. 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)

  21. 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)

  22. 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)

  23. 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)

  24. 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)

  25. 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)

  26. 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

2017

2016

2015

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

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

selected software projects

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

SHA: e212aeccf


Profiles and Metrics

ImpactStory
Google Scholar
ORCID: 0000-0002-1642-628X



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