Vita

employment

education

publications

  1. 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:10.1086/508600 (arXiv)

  2. 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 (arXiv) (GitHub) (data)

  3. 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 (arXiv) (GitHub) (data)

  4. 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 (CRAN)

  5. 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 (arXiv) (GitHub)

  6. 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.2012.00247.x (preprint) (GitHub) (CRAN)

  7. 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 (preprint) (GitHub) (CRAN)

  8. 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 (arXiv) (GitHub) (data)

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

  10. Carl Boettiger*, Noam Ross*, Alan Hastings. (2013) Early warning signals: The charted and uncharted territories. Theoretical Ecology doi:10.1007/s12080-013-0192-6 (arXiv) (GitHub)

  11. 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 (arXiv) (GitHub)

  12. 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 (arXiv) (GitHub) (data)

  13. 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 (arXiv)

  14. 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 (arxiv) (GitHub) (CRAN)

  15. 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

  16. Carl Boettiger, Michael Bode, James N. Sanchirico, Jacob LaRiviere, Alan Hastings, and Paul Robert Armsworth. (2015) Optimal management of a stochastically varying population when policy adjustment is costly. Ecological Applications 26 (3) 808-817. doi:10.1890/15-0236 (arXiv) (GitHub)

grants

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

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

  3. Supercomputing grant (2011). DOE #DE-AC02-05CH11231. 50,000hrs.

  4. rOpenSci Project (2013, Co-PI). Alfred P. Sloan Foundation $180,000.

  5. NSF Biology Post-doc (2013). NSF #DBI-1306697, $138,000. (proposal)

  6. rOpenSci Project, phase II. (2014, Co-PI). Alfred P. Sloan Foundation $300,000.

  7. Codemeta project (2015). NSF EAGER, #1549758 $165,782. (proposal)

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

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

2015
  • Data Intensive Training Workshop, NCEAS, Santa Barbara, CA
  • rOpenSci unconference, San Fransisco CA.
  • PDGC Workshop, NIMBIOS, Knoxville TN
2014
2013 & prior

theses

  1. Carl Boettiger, David Huse (2006) Clonal Interference Models in Population Genetics. Princeton Physics Dept. doi:10.6084/m9.figshare.678305

  2. Carl Boettiger, Joshua Weitz, Simon Levin (2007) Adaptive Dynamics: Branching Phenomena and the Canonical Equation Princeton Physics Dept. doi:10.6084/m9.figshare.678306

  3. 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

  4. Carl Boettiger (2012). Regime shifts in ecology and evolution (PhD Dissertation). doi:10.6084/m9.figshare.97218

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:

  • Berkeley Research Computing Advisory Committee
  • Data Science Education 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 CRAN
  • Carl Boettiger (2013). knitcitations: Dynamic citations for dynamic documents. On CRAN.
  • Carl Boettiger, Scott Chamberlain, Karthik Ram, Edmund Hart (2013). rfigshare: Programmatic access to the figshare data repository. On CRAN.
  • Carl Boettiger (2012). pmc: Phylogenetic Monte Carlo. On CRAN.
  • Carl Boettiger & Duncan Temple Lang (2011). treebase: An R interface to TreeBASE. On CRAN.
  • Carl Boettiger (2011). rfishbase: Programmatic access to FishBase. On CRAN.

I am also a founding member of the rOpenSci project. My software impact is also measured relative to other academics by depsy.org

media interviews

  • 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