Articles

  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). Noise can create or erase long transient dynamics. Theoretical Ecology doi:10.1007/s12080-021-00518-6, code, data

  40. Karatayev, Baskett, Kushner, Shears, Caselle, Boettiger (2021). Grazer behavior can regulate large-scale patterning of community states. Ecology Letters doi:10.1111/ele.13828

  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 doi:10.1016/j.oneear.2021.05.011, code

  42. Lapeyrolerie, Boettiger. (2021) Teaching machines to anticipate catastrophes. Proceedings of the National Academy of Sciences doi

  43. Chapman, Wiltshire, Baur, Bowles, Carlisle, Castillo, Esquivel, Gennet, Iles, Karp, Kremen, Liebert, Olimpi, Ory, Ryan, Sciligo, Thompson, Waterhouse, Boettiger. (2022). Social-ecological feedbacks drive tipping points in farming system diversification. One Earth doi:10.1016/j.oneear.2022.02.007 oa, code

  44. Chapman, Scoville, Lapeyrolerie, Boettiger. (2021). Power and Accountability in Reinforcement Learning Applications to Environmental Policy. 35th Conference on Neural Information Processing Systems (NeurIPS 2021) oa

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

Software projects

R Packages (Published on CRAN)

  • gbifdb: A High Performance Interface to GBIF. Carl Boettiger (2022).
    CRAN_Status_Badge peer reviewed

  • neonstore: NEON Data Store. Carl Boettiger and Quinn Thomas and Christine Laney and Claire Lunch (2020).
    CRAN_Status_Badge

  • contentid: An Interface for Content-Based Identifiers. Carl Boettiger and Jorrit Poelen (2020).
    CRAN_Status_Badge

  • taxalight: A Lightweight and Lightning-Fast Taxonomic Naming Interface. Carl Boettiger and Kari Norman (2020).
    CRAN_Status_Badge

  • sarsop: Approximate POMDP Planning Software. Carl Boettiger and Jeroen Ooms and Milad Memarzadeh (2020).
    CRAN_Status_Badge

  • taxadb: A High-Performance Local Taxonomic Database Interface. Carl Boettiger and Kari Norman and Jorrit Poelen and Scott Chamberlain, (2020).
    CRAN_Status_Badge peer reviewed

  • emld: Ecological Metadata as Linked Data. Carl Boettiger (2019).
    CRAN_Status_Badge peer reviewed

  • virtuoso: Interface to Virtuoso using ODBC. Carl Boettiger (2019).
    CRAN_Status_Badge peer reviewed

  • rdflib: Tools to Manipulate and Query Semantic Data. Carl Boettiger (2018).
    CRAN_Status_Badge peer reviewed

  • codemetar: Generate CodeMeta Metadata for R Packages. Carl Boettiger, Maëlle Salmon (2018).
    CRAN_Status_Badge peer reviewed

  • EcoNetGen: Simulate and Sample from Ecological Interaction Networks. Marcus de Aguiar, Erica Newman, Mathias Pires, Carl Boettiger (2018).
    CRAN_Status_Badge

  • piggyback: Managing Larger Data on a GitHub Repository. Carl Boettiger (2018).
    CRAN_Status_Badge peer reviewed

  • arkdb: Archive and Unarchive Databases Using Flat Files. Carl Boettiger (2018).
    CRAN_Status_Badge peer review

  • EML: Read and Write Ecological Metadata Language File. Carl Boettiger, Matt Jones (2016; v2 2019).
    CRAN_Status_Badge

  • RNeXML: Semantically Rich I/O for the NeXML Phylogenetics Format. Carl Boettiger, Scott Chamberlain, Hilmar Lapp, Rutger Voss (2014).
    CRAN_Status_Badge

  • pmc: Phylogenetic Monte Carlo. Carl Boettiger (2012).
    CRAN_Status_Badge

  • knitcitations: Citations for Knitr Markdown Files. Carl Boettiger (2012).
    CRAN_Status_Badge

  • rfishbase: R Interface to FishBase. Carl Boettiger, Scott Chamberlain, Duncan Temple Lang, Peter Wainwright (2011; v2 2015; v3 2019).
    CRAN_Status_Badge

Other Software

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.