Hello! I’m Dr. Noam Ross, and welcome to my personal website. I’m a Senior Research Scientist and computational disease ecologist at EcoHealth Alliance. I study the dynamics of wildlife diseases and how those diseases spill over between species, including into humans. I’m interested in how we predict these spillovers in time and space, and in using models that mix mechanistic and non-parametric components to do so.

I am a practitioner and advocate of reproducible research, open science, and justice and inclusion in my fields. I am a founding editor for software peer-review at rOpenSci, and have a variety of projects related to reproducibility using R statistical computer language.

Musings, Explorations, and Announcements

I’m recruiting a Research Software Engineer to join my team at EcoHealth Alliance in New York. Details and how to apply can be found at https://www.ecohealthalliance.org/career/research-software-engineer.

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Drake, Docker, and Gitlab-CI

24 September 2019

For a number of reasons I’ve been trying out GitLab as a replacement for for both GitHub and various continuous integration systems, and have been exploring configurations useful for model-fitting pipelines. I turned one of these into an example repository that shows how to use GitLab together with the Rocker Docker images and the drake build system to reproducibly run a project pipeline, using the cacheing functionality across all three tools to make things reasonably speedy and enable both local and remote builds.

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A New Website

9 August 2019

For me, the task of building a personal website is fraught with so many of my technical, aesthetic, and personal hangups that I hadn’t updated mine since mid-graduate school. Thanks to consistent pestering by Maëlle, though, I finally got around to re-building this one using a modern toolkit. Hopefully I can keep it up to date.

Here are some of the pieces that I used to build it:

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See my original post for background and updates. I was glad to see the announcement from the DataCamp Board that, after a long period of silence and inaction, the company is taking seriously an incident of sexual misconduct and re-examining its approach to the issue and its relationship with concerned instructors. The CEO’s leave of absence and the engagement of Ms. Bhargava indicate a turn in the right direction.

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Please note there are MANY updates below, and a separate post following DataCamp’s April 24th announcement.

Last week (April 4, 2019) DataCamp published a blog post stating that “one of DataCamp’s executives danced inappropriately and made uninvited physical contact with another employee,” an action meeting many definitions of sexual assault. While the post makes the claim that DataCamp does not condone this behavior, it also makes clear that the disciplinary actions against the executive were limited to “sensitivity training, personal coaching, and a strong warning.”

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Recent Works

  • Hongying Li, Emma Mendelsohn, Chen Zong, Wei Zhang, Emily Hagan, Ning Wang, Shiyue Li, Hong Yan, Huimin Huang, Guangjian Zhu, Noam Ross, Aleksei Chmura, Philip Terry, Mark Fielder, Maureen Miller, Zhengli Shi and Peter Daszak (2019) Human-animal interactions and bat coronavirus spillover potential among rural residents in Southern China. doi:10.1016/j.bsheal.2019.10.004
  • Building Software and Communities With Peer Review: rOpenSci, pyOpenSci, and Beyond, PyData NYC, Nov 5, 2019      
  • Evan A. Eskew, Allison M. White, Noam Ross, Kristine M. Smith, Katherine F. Smith, Jon Paul Rodríguez, Carlos Zambrana-Torrelio, William B. Karesh and Peter Daszak (2019, preprint) United States wildlife and wildlife product imports from 2000-2014. doi:10.1101/780197
  • One Health Surveillance Data: Sharing, Standards, and Stories, Bat One Health Research Network Meeting, Phuket, Thailand, Aug 28, 2019    
  • Gregory F Albery, Evan A Eskew, Noam Ross and Kevin J Olival (2019, preprint) Predicting the global mammalian viral sharing network using phylogeography. doi:10.1101/732255  
  • Epidemiological Modeling: From Basics to Artificial Intelligence, Department of Homeland Security Biosurveillance Presentation Series, Jun 19, 2019  
  • Simulating Epidemiological Models with R, EcoHealth Net Workshop, George Mason University, Fairfax, Virgina, Jun 4, 2019    
  • Noam Ross, Evan Eskew and Nicolas Ray (2019) citesdb: An R package to support analysis of CITES Trade Database shipment-level data. doi:10.21105/joss.01483
  • Generalized Additive Models in R: A Free Interactive Course, (online), May 30, 2019    
  • Eric J. Pedersen, David L. Miller, Gavin L. Simpson and Noam Ross (2019) Hierarchical generalized additive models in ecology: an introduction with mgcv. doi:10.7717/peerj.6876