Vita

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. 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. 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)

  2. 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)

  3. 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.

  4. Carl Boettiger, Scott Chamberlain, Rutger Vos and Hilmar Lapp. (2015) 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)

  5. 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)

  6. 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)

  7. 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)

  8. 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)

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

  10. 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)

  11. 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)

  12. 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)

  13. 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)

  14. 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)

  15. 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)

  16. 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)

  17. 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 rOpenSci Project (2015-2018, Co-PI). Helmsley Trust 2,900,000 USD.

  • 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 USD.

  • NSF Biology Post-doc (2013-2015). National Science Foundation #DBI-1306697, 138,000 USD. (proposal)

  • The rOpenSci Project Phase I funding (2013, Co-PI). Alfred P. Sloan Foundation 180,000 USD.

  • IIASA YSSP fellowship (2009). National Academy of Sciences, OISE-0738129, 8,000 USD. (proposal)

  • Computational Science Graduate Fellowship (2008). Department of Energy, #DE-FG02-97ER25308, 149,000 USD. (proposal)

invited talks

2015

2014

  • Berkeley Initiative for Global Change Biology (student organized), UC Berkeley, CA.
  • DIMACS Global Change, Berkeley CA.
  • Zoology Seminar, University of Wisconsin, Madison, WI.
  • ESPM Seminar, UC Berkeley, CA.

2013 & prior

invited workshops

2016

2015

2014

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

national

  • NCEAS Scientific Advisory Board
  • rOpenSci Leadership team
  • Jestream NSF cloud computing Stakeholder Advisory Board

campus

  • UC Berkeley, Berkeley Research Computing Advisory Committee

reviewer for:

  • 2015 Proceedings of the National Academy of Sciences, Journal of Statistical Software, Bioinformatics, Chapman & Hall, Ecology Letters, Ecology, PeerJ, F1000 Research, Journal of Librarianship & Scholarly Communication, Nature Communications, Theoretical Ecology, Trends in Ecology & Evolution, Grid Computing

  • 2014 Theoretical Ecology, Biodiversity Data Journal, Ecology Letters, Journal of Theoretical Biology, American Naturalist, Proceedings of the National Academy of Sciences, Proceedings of the Royal Society B

  • 2013 Theoretical Ecology, Francis & Taylor, Ideas in Ecology and Evolution, The R Journal, National Science Foundation, Proceedings of the Royal Society B, Journal of Open Research Software, Canadian Journal of Fisheries and Aquatic Sciences

  • 2012 Theoretical Ecology, Evolution, Methods in Ecology and Evolution, Proceedings of the Royal Society B, PLoS ONE, Ecology, Conservation Letters, Ecology Letters

  • 2011 Theoretical Ecology, Ecological Modelling, Evolution, Methods in Ecology and Evolution, Ecosphere

  • 2010 & prior Theoretical Ecology, Journal of Mathematical Biology, Ecological Modelling, Ecology

selected software

  • Carl Boettiger, Scott Chamberlain, Rutger Vos and Hilmar Lapp. (2015) RNeXML: a package for reading and writing richly annotated phylogenetic, character, and trait data in R. On software
  • Carl Boettiger (2013). knitcitations: Dynamic citations for dynamic documents. On software.
  • Carl Boettiger, Scott Chamberlain, Karthik Ram, Edmund Hart (2013). rfigshare: Programmatic access to the figshare data repository. On software.
  • Carl Boettiger (2012). pmc: Phylogenetic Monte Carlo. On software.
  • Carl Boettiger & Duncan Temple Lang (2011). treebase: An R interface to TreeBASE. On software.
  • Carl Boettiger (2011). rfishbase: Programmatic access to FishBase. On software.

I am also a founding member of the rOpenSci project. 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