Curriculum Vitae

Education

• Ph.D., Graduate Group in Ecology 2015
  UC Davis Davis, CA
• B.Sc., Center for Environmental Studies 2006
  Brown University Providence, RI

Professional Experience

• Principal Scientist, Computational Research 2019-
  EcoHealth Alliance New York, NY
• Senior Research Scientist 2017-2019
  EcoHealth Alliance New York, NY
• Disease Ecologist 2015-2017
  EcoHealth Alliance New York, NY
• Senior Analyst 2008-2009
  GreenOrder New York, NY
• Analyst 2006-2008
  GreenOrder New York, NY

Selected Software Packages

• citesdb: A high-performance database of shipment-level CITES trade data. (2019)    
• fasterize: High performance raster conversion for modern spatial data. (2018)    
• rchie: An R parser for ArchieML. (2018)        
  “Structured text, for an unstructured world.” rchie parses a free-text data format developed by the New York Times interactives team, designed to allow writers and developers to collaborate on data-driven outputs like apps and infographics. Paired with googledrive package, it allows rapid iteration and collaboration.
• redoc: Reversible reproducible documents with R Markdown and Microsoft Word. (2019)      
  redoc is an attempt at the holy grail of mixed-workflow collaboration: it enables analysts to produce Microsoft Word douments using R Markdown that can be edited and then de-compiled into R Markdown again witout loss of information. It’s goal is for teams with different tools to be able to work together with minimal need to adopt each other’s workflows.

Courses and Workshops

• Simulating Epidemiological Models with R, EcoHealth Net Workshop, George Mason University, Fairfax, Virgina, Jun 4, 2019    
  The EcoHealth Net program brings together scientists and STEM undergraduate and graduate students for internships and a week-long intensive workshop on One Health research.
• Generalized Additive Models in R: A Free Interactive Course, (online), May 30, 2019    
  You can take this course online! Originally created for a commerical online learning company, I’ve ported this course to a free, interactive website that allows you to exercises live.
• Fitting Non-Linear Models in R with the mgcv Package, Ecological Society of America Annual Meeting, New Orleans, Louisiana, May 10, 2018    
  This course is designed and run in conjucation with David Miller, Gavin Simpson, and Eric Pedersen and has run at ESA for a number of years. Lots of materials and resources available at the link!
• Simulating Epidemiological Models with R, EcoHealth Net Workshop, Tufts University, Meford, Massachusettss, Jun 5, 2017  
• Fitting Non-Linear Models in R with the mgcv Package, Ecological Society of America Annual Meeting, New Orleans, Louisiana, May 10, 2017  

Presentations

• R, Coronavirus, and Pandemic Prevention, New York Open Statistical Programming Meetup, Apr 20, 2020        
  For the New York R Meetup, I spoke about the types of models and software virus hunters and epidemiologists use to understand emerging diseases, and how they relate to problems and models familiar to data scientists.
• Building Software and Communities With Peer Review: rOpenSci, pyOpenSci, and Beyond, PyData NYC, Nov 5, 2019      
• One Health Surveillance Data: Sharing, Standards, and Stories, Bat One Health Research Network Meeting, Phuket, Thailand, Aug 28, 2019    
  This presentation kicked off the BOHRN working sessions on data sharing for synthesis and collaboration. How can we structure disease surveillance data so we can better integrate them for macro-level insights?
• Epidemiological Modeling: From Basics to Artificial Intelligence, Department of Homeland Security Biosurveillance Presentation Series, Jun 19, 2019  
• Reproducibility in an Office world: tools for crossing the abyss, New York R Conference, May 11, 2019  
• Reproducibility in an Office world: a brief history of failures, R-Ladies NYC, Nov 6, 2018  
• Generating better macroecological data from literature: a case study of antimicrobial resistance emergence, Ecological Society of America Annual Meeting, New Orleans, Louisiana, Aug 10, 2018    
• DockeR for the UseR, New York Open Statistical Programming Meetup, Jul 11, 2018        
  An introduction to Docker with demonstration of different workflows and applications for R users. Lots of resources and links included.
• The Modern R Data Package, New York R Conference, Apr 21, 2018  
• Nonlinear models in R: the wonderful world of mgcv, New York Open Statistical Programming Meetup, Nov 21, 2017      
• Better packages through peer review: lessons from rOpenSci, New York R Conference, Apr 22, 2017  
• Joint circulation of viral diseases in a bat population, Ecological Society of America Annual Meeting, Ft. Lauderdale., Florida, Aug 9, 2016    
• Optimal control of disease with individual-based models, Ecological Society of America Annual Meeting, Baltimore, Maryland, Aug 11, 2015    
• Modeling forest disease using a macroparasite framework, Ecological Society of America Annual Meeting, Sacramento, California, Aug 13, 2014    

Publications

•  
  Greg Albery interned at EcoHealth Alliance for the end of his Ph.D. and did this excellent work using GAMs to understand patterns in what mammals carry common viruses.
•  
  This is my first and only paper that actually started on a bar napkin.
• Daniel Nüst, Dirk Eddelbuettel, Dom Bennett, Robrecht Cannoodt, Dav Clark, Gergely Daroczi, Mark Edmondson, Colin Fay, Ellis Hughes, Lars Kjeldgaard, Sean Lopp, Ben Marwick, Heather Nolis, Jacqueline Nolis, Hong Ooi, Karthik Ram, Noam Ross, Lori Shepherd, Péter Sólymos, Tyson Lee Swetnam, Nitesh Turaga, Charlotte Van Petegem, Jason Williams, Craig Willis and Nan Xiao (2020, preprint) The Rockerverse: Packages and Applications for Containerization with R. doi: