Scott Chamberlain homo sapien

Vita

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Scott Chamberlain

Work

  • 2011-present   rOpenSci: co-founded developer collective to make R (#rstats) packages to facilitate use of open source journals and data sets. Website; Code. rOpenSci is now housed within UC Berkeley.
  • 2012-2014   Postdoctoral Scholar: Simon Fraser University - Plant-pollinator networks

Education

  • 2012 Ph.D Dept. of Ecology & Evolutionary Biology, Rice University
  • 2009 M.A. Dept. of Ecology & Evolutionary Biology, Rice University
  • 2003 B.S. Biological Sciences, California State University

Programming

  • R » I have developed R software for 14 years, for research projects, and as packages (see them on GitHub). I co-founded a developer collective to make R software tools for scientists called rOpenSci (https://ropensci.org/).
  • Python » I have programmed in Python for 7 years, and am relatively comfortable throughtout the language, having used it for a variety of simulations, and maintain 3 python libraries on pypi.
  • Ruby » I have programmed in Ruby for about 6 years. I have deployed an app to Heroku to monitor the many web APIs that we at rOpenSci consume, and b) I wrote a tiny gem to get Bibtex style references by inputting a DOI here), and I write many RESTful APIs in Ruby Sinatra. I have 5 gems on Rubygems.
  • HTML/CSS » I use HTML often for my own website and blog, and occasionally customize CSS.
  • Databases » I am familiar with and use many databases, including SQL (MySQL, SQLite, PostgreSQL) and NoSQL (CouchDB). I am also familiar with Elasticsearch and Solr, and have created R clients for both of them.

Publications

  • Mitchell, N., Chamberlain, S. A., & Whitney, K. D. (2021). Proximity to crop relatives determines some patterns of natural selection in a wild sunflower. Evolutionary Applications. https://doi.org/10.1111/eva.13201
  • Guzman, L. M., Chamberlain, S. A., & Elle, E. (2020). Phenology and Robustness in plant-pollinator networks. BioRxiv Preprint. https://doi.org/10.1101/2020.10.30.362616
  • Conde, D. A., Staerk, J., Colchero, F., Chamberlain, S., et al. 2019. Data gaps and opportunities for comparative and conservation biology. PNAS, 116(19), 9658–9664. https://doi.org/10.1073/pnas.1816367116
  • Ram, K., Boettiger, C., Chamberlain, S., et al. 2019. A Community of Practice Around Peer Review for Long-Term Research Software Sustainability. Computing in Science & Engineering, 21(2), 59–65. https://doi.org/10.1109/MCSE.2018.2882753
  • D Pearse, W., & A Chamberlain, S. 2018. Suppdata: Downloading Supplementary Data from Published Manuscripts. Journal of Open Source Software, 3(25), 721. https://doi.org/10.21105/joss.00721
  • Foster ZSL, Chamberlain S and Grünwald NJ. 2018. taxa: An R package implementing data standards and methods for taxonomic data. F1000Research, 7:272 https://doi.org/10.12688/f1000research.14013.2
  • Chamberlain, S., C. Boettiger. 2017. R Python, and Ruby clients for GBIF species occurrence data. PeerJ Preprints. https://peerj.com/preprints/3304v1/
  • Winslow, L. A., Chamberlain, S., et al. (2016). sbtools: A package connecting R to cloud-based data for collaborative online research. The R Journal, 8(1), 387-398. https://doi.org/10.1371/journal.pone.0127781
  • Boettiger C, Chamberlain S, et al. RNeXML: A Package for Reading and Writing Richly Annotated Phylogenetic, Character, and Trait Data in R. Methods in Ecology & Evolution, 7, 352-357. https://doi.org/10.1111/2041-210X.12469
  • Boettiger, C., Chamberlain, S., et al. 2015. RNeXML: a package for reading and writing richly annotated phylogenetic, character and trait data in R. Methods in Ecology & Evolution, 7(3), 352–357. https://doi.org/10.1111/2041-210x.12469
  • Boettiger, C., Chamberlain, S., Hart, E., & Ram, K. 2015. Building software, building community: lessons from the rOpenSci project. Journal of Open Research Software, 3(1). https://doi.org/10.5334/jors.bu
  • Guo H, Chamberlain SA, Elhaik E, Jalli I, Lynes A-R, et al. 2015. Geographic Variation in Plant Community Structure of Salt Marshes: Species, Functional and Phylogenetic Perspectives. PLoS ONE 10(5): e0127781. doi: 10.1371/journal.pone.0127781 web pdf
  • Mair, P, and S. Chamberlain. 2014. Web Technologies Task View. The R Journal 6(1): 178-181. web pdf
  • Revell, L., S.A. Chamberlain. 2014. Rphylip: An R interface for PHYLIP. Methods in Ecology & Evolution web pdf
  • Chamberlain, S.A., et al. 2014. Traits and phylogenetic history contribute to network structure across Canadian plant-pollinator communities. Oecologia web
  • Chamberlain, S.A., et al. 2014. Phylogenetic tree shape and the structure of mutualistic networks. Journal of Ecology web pdf
  • Chamberlain, S.A., J.A. Rudgers, and J.L. Bronstein. 2014. How context-dependent are species interactions. Ecology Letters web pdf
  • Barraquand F, Ezard TH, Jørgensen PS, Zimmerman N, Chamberlain S et al. 2014 Lack of quantitative training among early-career ecologists: a survey of the problem and potential solutions. PeerJ 2:e285 web pdf xml
  • Vamosi, J.; Chamberlain, S.A., Garcha, N.; Moray, C.; Mooers, A. 2014. Pollinators visit related plant species across 29 plant-pollinator networks. Ecology & Evolution
  • Chamberlain SA, Szöcs E. 2013. taxize: taxonomic search and retrieval in R [v1; ref status: indexed, http://f1000r.es/1pv] F1000Research 2013, 2:191 (doi: 10.12688/f1000research.2-191.v1) github pdf
  • Chamberlain, S.A., J.A. Rudgers, & K.D. Whitney. 2013. Proximity to agriculture alters abundance and community composition of wild sunflower mutualists and antagonists. Ecosphere. pdf
  • Chamberlain, S.A. 2013. Consuming Article-Level Metrics: Observations and Lessons from Comparing Aggregator Provider Data. Information Standards Quarterly. github pdf web
  • Chamberlain, S.A., S.M. Hovick,…et al…K.D. Whitney. 2012. Does phylogeny matter? Assessing the impact of phylogenetic information in ecological meta-analysis. Ecology Letters 15(6):627-636. pdf
  • Chamberlain, S.A., & J.A. Rudgers. 2012. How do plants balance multiple mutualists? Correlations among traits for attracting protective bodyguards and pollinators in cotton (Gossypium). Evolutionary Ecology 26:65-77. pdf
  • Holland, J.N., _Chamberlain, S.A.__and T.E.X. Miller. 2011. Consequences of ants and extrafloral nectar for a pollinating seed-consuming mutualism: ant satiation, floral distraction, or plant defense? _Oikos. pdf
  • Chamberlain, S.A., J.K. Kilpatrick, & J.N. Holland. 2010. Do extrafloral nectar resources, abundances, and body sizes contribute to the structure of ant-plant mutualistic networks? Oecologia 164:741-750. pdf
  • Holland, J.N., Chamberlain, S.A.,& K.C. Horn. 2010. Temporal variation in extrafloral nectar secretion by reproductive tissues of the senita cactus, Pachycereus schottii (Cactaceae), in the Sonoran Desert of Mexico. Journal of Arid Environments 74(6):712-714. pdf
  • Chamberlain, S.A., & J.N. Holland. 2009. Quantitative synthesis of context-dependency in ant-plant protection mutualisms. Ecology 90(9):2384-2392. pdf ***
  • Holland, J.N., S.A.Chamberlain, A.M. Waguespack, and A.S. Kinyo. 2009. Effects of pollen load and donor diversity on variation in seed and fruit size in a columnar cactus, Pachycereus schottii (Cactaceae). International Journal of Plant Sciences 170:467-475. pdf
  • Chamberlain, S.A.& J.N. Holland. 2009. Body size predicts degree in ant-plant mutualistic networks. Functional Ecology 23:196-202. pdf
  • Holland, J.N., Chamberlain, S.A.,& K.C. Horn. 2009. Constitutive and induced extrafloral nectar production: optimal defense theory predicts plant resource investment in a protection mutualism. Journal of Ecology 97(1):89-96. pdf
  • Chamberlain, S.A. & J.N. Holland. 2008. Density-mediated and context-dependent consumer-resource interactions between ants and extrafloral nectar plants. Ecology 89(5):1364-1374. pdf
  • Chamberlain, S.A.& R.A. Schlising. 2008. Role of honey bees (Hymenoptera: Apidae) in the pollination biology of a California native plant, Triteleia laxa (Asparagales: Themidaceae). Environmental Entomology 37(3):808-816. pdf
  • Holland, J.N. & S.A. Chamberlain. 2007. Ecological and evolutionary mechanisms for low seed:ovule ratios: need for a pluralistic approach? Ecology 88(3):706-715. pdf
  • Schlising, R.A. & S.A. Chamberlain. 2006. Biology of the geophytic lily, Triteleia laxa (Themidaceae), in grasslands of the Northern Sacramento Valley. Madroño 53(4):321-341. pdf

Academic Presentations

  • 2019 useR, Toulouse, France. talk
  • 2019 R user group meeting, Portland, OR. talk
  • 2018 Biodiversity Information Standards (TDWG), Dunedin, New Zealand. talk
  • 2018 Joint Statistical Meeting, Vancouver, Canada. talk
  • 2018 Bioinformatics Open Source Conference (BOSC), Portland, OR. talk
  • 2018 Digital Data in Biodiversity Research Conference, Berkeley, CA. poster
  • 2018 Digital Data in Biodiversity Research Conference, Berkeley, CA. talk
  • 2018 CDC R user group. talk
  • 2017 University of Oregon, Eugene, OR. guest lecture
  • 2017 Biodiversity Information Standards (TDWG) meeting, Ottawa, Canada. talk
  • 2017 Ecological Society of America conference, Portland, OR. talk
  • 2017 University of Oregon, Eugene, OR. guest lecture
  • 2017 Open Source Systems in the Public Sector. two talk’s
  • 2016 Philo­sophy And His­tory Of Open Science symposium. talk
  • 2016 R meetup group, Portland, OR. talk
  • 2015 Crossref Annual Meeting. keynote & talk
  • 2015 SFBay Apache Lucene/Solr Meetup at Stanford University. talk
  • 2014 Simon Fraser University Statistics Department. seminar
  • 2014 University of Georgia Odum School of Ecology. seminar
  • 2014 QCBS meeting, Montreal, Canada. talk
  • 2013 Simon Fraser University Library. talk
  • 2013 Ecological Society of America conference. lightning talk
  • 2012 British Ecological Society conference. talk & workshop
  • 2012 University of Calgary Biological Sciences Department. seminar
  • 2012 Ecological Society of America conference. poster
  • 2011 Ecological Society of America conference. talk
  • 2011 Rice University-University of Houston Joint Graduate Student Conference. talk
  • 2009 Ecological Society of America conference. talk
  • 2009 Southeastern Ecol. and Evol. Conference, Univ. Florida. talk
  • 2009 Ecological Integration Symposium at Texas A&M University. talk
  • 2008 Entomological Society of America conference. talk
  • 2008 Ecological Society of America conference. talk
  • 2007 California Botanical Society 22nd Graduate Student conference. talk
  • 2003 CALFED Bay-Delta conference. poster

Grants

  • 2012 Public Library of Science & Mendeley Binary Battle - 3rd place in code competition ($1,000) - together with Carl Boettiger and Karthik Ram
  • 2011 Ecological Society of America Population Biology Section Travel Award to the 2011 ESA Conference ($250)
  • 2010-2011 Lodieska Stockbridge Vaughn Fellowship ($16,250 towards stipend)
  • 2010 Prairie Biotic Research, Inc. ($896)
  • 2009 Envision Grant, Leadership Rice, Rice University ($1,618) – together with Rice undergraduates Samuel Jacobson and Myra Lara
  • 2009 Best Thesis, Department of Ecology and Evolutionary Biology, Rice University
  • 2006-2007 Wray-Todd Graduate Fellowship
  • 2008 Best Graduate Student Paper, presented by Department of Ecology and Evolutionary Biology, Rice University ($100)
  • 2002 National Science Foundation REU (Research Experience for Undergraduates), California State University, Chico ($3,000)

Student mentoring

Larry Liu (Summer 2008), Rameez Anwar (Fall 2008-Spring 2009), Yosuke Akiyama (Fall 2008-Spring 2009), Rohini Sigireddi(Summer 2009), Neha Deshpande(Summer 2009), Matt King (Spring 2010), Tianshi Ji (Fall 2010), Morgan Black (Fall 2010-2011), Roy Wu (Fall 2010), Thanh Vu (Spring 2011-2012), Charles Danan (Spring 2011-2012)

Extramural service and community outreach

  • 2010 Organized the Rice University-University of Houston Joint Graduate Student Conference
  • 2008-2009 Board Member, Rice University Bicycle Safety Committee, Graduate Student Representative to prepare a bicycle safety policy for Rice University
  • 2007-2010 Treasurer/Secretary, Ecology & Evolutionary Biology Graduate Student Association, Rice University.
  • 2004-2005 Board Member, Friends of Bidwell Park Board of Directors, Chico, California. Advocacy for sound environmental stewardship of parks.

Peer review service

  • Subject Editor: Biodiversity Data Journal

  • Grant Proposals: Chan Zuckerberg Initiative, 2x

  • Peer Review (55 total): African Journal of Agricultural Research, Agricultural & Forest Entomology (2), The American Naturalist, Annals of Botany (2), Biodiversity Data Journal, Biological Invasions, Ecography (4), Ecological Complexity, Ecological Entomology, Ecological Complexity, Ecology (3), Ecology Letters, Ecology and Evolution, Environmental Management, Evolutionary Ecology, Florida Entomologist (2), Journal of Avian Biology, Journal of Ecology (4), Journal of Tropical Ecology, Methods in Ecology and Evolution (7), New Phytologist, Oecologia, Oikos (3), Plant Ecology, PLOS One (2), Population Ecology (2), Proceedings of the Royal Society B, The R Journal (2), Scientific Data (3), PeerJ, F1000Research

References

  • Dr. Elizabeth Elle, Biology Dept., Simon Fraser University, eelle@sfu.ca
  • Dr. Robert Schlising, Biology Dept., California State University, Chico, rschlising@csuchico.edu
  • Dr. Jennifer Rudgers, Biology Dept., University of New Mexico, jrudgers@unm.edu
  • Dr. Ken Whitney, Biology Dept., University of New Mexico, kwhitney@unm.edu