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. 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)

  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. (oa, code, 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, (oa, code, data)

  4. Jeremy M. Beaulieu, Dwueng-Chwuan Jhwueng, Carl Boettiger, 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)

  5. Carl Boettiger, 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)

  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.2012.00247x. (oa, code, software)

  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. (oa, code, software)

  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. (oa, code, 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. (oa, code)

  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. (oa, code)

  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. (oa, code, data). F1000 recommended

  13. Carl Boettiger (2015). An introduction to Docker for reproducible research. ACM SIGOPS Operating Systems Review 49(1), 71-79. doi:10.1145/2723872.2723882. (oa)

  14. 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.

  15. 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)

  16. 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)

  17. 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)

  18. 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)

  19. 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)

  20. Getz, Marshall, Carlson, Giuggioli, Ryan, Romañach, Boettiger, Chamberlain, Larsen, D’Odorico, O’Sullivan (2017). Making ecological models adequate. Ecology Letters. doi:10.1111/ele.12893

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

  22. Carl Boettiger, Dirk Eddelbuettel (2018). An Introduction to Rocker: Docker Containers for R. The R Journal. doi:10.32614/RJ-2017-065

  23. 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)

  24. 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)

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

  26. 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

  27. Katz, Allen, Barba, Berg, Bik, Boettiger, et al. (2018). The principles of tomorrow’s university. F1000Research, 7:1926 doi:10.12688/f1000research.17425.1. (32 co-authors.)

  28. Carl Boettiger (2019). Ecological Metadata as Linked Data. Journal of Open Source Software, 4(34), 1276, doi:10.21105/joss.01276 (software).

  29. Dan Sholler, Karthik Ram, Carl Boettiger, Daniel S Katz (2019). Enforcing public data archiving policies in academic publishing: A study of ecology journals. Big Data & Society 6(1) 1-18. doi:10.1177/2053951719836258

  30. Milad Memarzadeh, Carl Boettiger (2019). Resolving the Measurement Uncertainty Paradox in Ecological Management. American Naturalist. doi:10.1086/702704. (oa, code, data). F1000 recommended

  31. Carl Boettiger, Ryan Batt (2019). Bifurcation or state tipping: assessing transition type in a model trophic cascade. Journal of Mathematical Biology. doi:10.1007/s00285-019-01358-z (oa, code)

  32. Milad Memarzadeh, Gregory L. Britten, Boris Worm, Carl Boettiger (2019). Rebuilding global fisheries under uncertainty. Proceedings of the National Academy of Sciences. doi:10.1073/pnas.1902657116

  33. de Aguiar, Newman, Pires, Yeakel, Boettiger, Burkle, Gravel, Guimarães Jr, O’Donnell, Poisot, Fortin, Hembry (2019). Revealing biases in the sampling of ecological interaction networks, PeerJ, doi:10.7717/peerj.7566. software.

  34. Carl Boettiger (2020). Ecological management of stochastic systems with long transients. Theoretical Ecology. doi:10.1007/s12080-020-00477-4, code

  35. Kari Norman, Scott Chamberlain, Carl Boettiger (2020). taxadb: A high‐performance local taxonomic database interface. Methods in Ecology and Evolution. doi:10.1111/2041-210X.13440 software

  36. Pascal, Memarzadeh, Boettiger, Lloyd, Chadès (2020). A Shiny r app to solve the problem of when to stop managing or surveying species under imperfect detection Methods in Ecology and Evolution. doi:10.1111/2041-210X.13501 software

  37. Carl Boettiger (2020). [Rp] Fluctuation domains in adaptive evolution. ReScience C 6, 1, #15, https://rescience.github.io/bibliography/Boettiger_2020.html, doi:10.5281/zenodo.4081202, code

  38. Caleb Scoville, Melissa Chapman, Razvan Amironesei, Carl Boettiger (2021). Algorithmic conservation in a changing climate. Current Opinion in Environmental Sustainability 51, 30-35, doi:10.1016/j.cosust.2021.01.009.

  39. Reimer, Arroyo-Esquivel, Jiang, Scharf, Wolkovich, Zhu, Boettiger (2021). Detection of long transient dynamics in noisy time series. Theoretical Ecology (Accepted)

  40. Karatayev, Baskett, Kushner, Shears, Caselle, Boettiger (2021). Grazer behavior can regulate large-scale patterning of community states. Ecology Letters (Accepted)

  41. Chapman, Oestreich, Frawley, Boettiger, Diver, Santos, Scoville, Armstrong, Blondin, Chand, Haulsee, Knight, Crowder (2021). Promoting equity in the use of algorithms for high seas conservation. One Earth (In Press)

Grants

  • CAREER: Harnessing the data revolution for predicting and managing ecosystem regime shifts. Carl Boettiger. (2020-2025). National Science Foundation #DBI-1942280. $504,335.00

  • The Rocker Project. Carl Boettiger, Noam Ross, Dirk Eddelbuettel. (2019 - 2020). Chan-Zuckerberg Initiative: Essential Open Source Software for Science. $75,912

  • 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

  • The rOpenSci Project. Karthik Ram, Carl Boettiger, Scott Chamberlain. (renewal, 2019-2021). Helmsley Charitable Trust, award 2016PG-BRI004. $1,000,000

  • Detecting Change in Global Biodiversity through Large Scale Network Analysis. Carl Boettiger, Rosemary Gillespie, Rasmus Nielsen. (2018). Berkeley Institute for Data Science, $67,000

  • Big Data, Big Uncertainty: Ecological Decision- Making in the 21st Century. (2018-2020). Hellman Fellows Award, The Hellman Foundation. $37,600

  • Berkeley Collegium Award for Narrowing the Gap Between Teaching and Research. (2018-2019) $16,867.50

  • Managing ecosystems under extreme uncertainty. (2016 - 2019) NSF XSEDE TG-DEB160003. NSF Estimated value of computing resources: $34,558

  • Reproducible and Collaborative Data Science. NSF XSEDE TG-DEB160021. (2016 - 2019) NSF Estimated value of computing resources: $20,028

  • James S McDonnell Foundation Post-doctoral Fellowship in Complex Systems (Awarded to post-doctoral scholar Allison Barner, who then chose to bring this award to my group at UC Berkeley) $200,000.

  • The rOpenSci Project (2015-2018, Co-PI). Karthik Ram, Carl Boettiger, Scott Chamberlain. Helmsley Charitable Trust, award 2016PG-BRI004. $2,875,071

  • The CodeMeta Project (2015). National Science Foundation #ACI-1549758 $165,782. (proposal here)

  • The rOpenSci Project, Phase II funding (2014, Co-PI). Karthik Ram, Carl Boettiger, Scott Chamberlain. Alfred P. Sloan Foundation $300,000

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

  • The rOpenSci Project Phase I funding (2013 Co-PI). Karthik Ram, Carl Boettiger, Scott Chamberlain. Alfred P. Sloan Foundation $180,000

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

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

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

2019

2018

2017

2016

2015

2014

2013 & prior

Awards

  • 2020 Early Career Fellow, Ecological Society of America
  • 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

Service

Campus

  • 2019 - current. Faculty Working Group for the formation of the Division of Data Science & Information
  • 2018 - 2019. Faculty Task Force for Data Science Minor Design
  • 2018 - current. Faculty Advisory Committee of the Vice Chancellor for Undergraduate Education
  • 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
  • 2017 - current. Steering Committee for NSF Research Traineeship (NRT): Environment and Society: Data Science for the 21st Century (DS421)
  • 2015 - 2019. Berkeley Research Computing Advisory Committee

Extra-campus

Software

R Packages

  • emld: Ecological Metadata as Linked Data. Carl Boettiger (2019).
  • virtuoso: Interface to Virtuoso using ODBC. Carl Boettiger (2019).
  • rdflib: Tools to Manipulate and Query Semantic Data. Carl Boettiger (2018).
  • codemetar: Generate CodeMeta Metadata for R Packages. Carl Boettiger, Maëlle Salmon (2018).
  • EcoNetGen: Simulate and Sample from Ecological Interaction Networks. Marcus de Aguiar, Erica Newman, Mathias Pires, Carl Boettiger (2018).
  • piggyback: Managing Larger Data on a GitHub Repository. Carl Boettiger (2018).
  • arkdb: Archive and Unarchive Databases Using Flat Files. Carl Boettiger (2018).
  • EML: Read and Write Ecological Metadata Language File. Carl Boettiger, Matt Jones (2016; v2 2019).
  • RNeXML: Semantically Rich I/O for the NeXML Phylogenetics Format. Carl Boettiger, Scott Chamberlain, Hilmar Lapp, Rutger Voss (2014).
  • pmc: Phylogenetic Monte Carlo. Carl Boettiger (2012).
  • knitcitations: Citations for Knitr Markdown Files. Carl Boettiger (2012).
  • rfishbase: R Interface to FishBase. Carl Boettiger, Scott Chamberlain, Duncan Temple Lang, Peter Wainwright (2011; v2 2015; v3 2019).

Other Software

  • Carl Boettiger, Dirk Eddelbuettel. The Rocker Project: Docker images for the R environment. https://rocker-project.org. (Language: Dockerfile)
  • Carl Boettiger, Matt Jones, et al. The CodeMeta Project: Software Metadata Exchange https://codemeta.github.io (Language: JSON-LD)

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