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CEREO February 2017

Director of the Center for Water Policy, School of Freshwater Sciences, University of Wisconsin Milwaukee

Type: Administrative Leadership Appointment within UWM
Official Title: Director, Unspecified (9) or Academic Program Director
Preferred Start Date: August 21, 2017
Application Deadline: Open until filled, screening begins March 15, 2017
Applications must be electronically submitted at
Inquiries about this position can be directed to Sandra McLellan ( or Scott Graham (grahams@uwm.ed).

“Nitrogen: At the Nexus Between Food Security and Sustainability.”

This on-line, real time symposium will be held on March 8 & 9, 2017 from 9am-11:30am US Pacific Time; a detailed schedule and connection information is attached. The symposium is hosted by Michael Udvardi of the Samuel Roberts Noble Foundation, USA, and John Peters of Washington State University, USA.

Information and free registration:


Packrat Package – managing package versions

This week CEREO’s Stephanie Labou introduced us to the packrat package. Packrat is a relatively new package that assists collaboration and functionality of code by maintain and standardizing package versions used in a project. Depending on the level of experience, R users may not have ran into this issue before but it is a persistent problem with the R system. Due to the dynamic and open nature of the software, changes and improvements to packages can tweek the way that certain functions interact, making old code buggy or obsolete. Packrat is an attempt to control for this.

Packrat, in essence, creates a large zip file with all of the libraries and settings used for a project. Users then send this entire file to their collaborators and collaborators load packages and libraries from that zip file. This ensures that the versions of packages used are the same across all collaborators. Within packrat, each folder is essentially its own project, with its own packages – packrat folders are created within the working directory when the creation command is called.

The first step in using packrat is to create, or “bundle” your libraries. This is shown in the script below. In addition, the script below uses the “::” syntax to call commands. The double colon symbol is a way to specify exactly which packages commands are being used. This is because some packages have commands with the same name – whichever package is loaded last will overwrite the identically named commands from the other one. This is why people’s script may sometimes have notes about the loading order of packages.


Once the packrat package has bundled the libraries for a project, you can then send the entire file to a collaborator. To re-create this on your own computer open a brand new R session and then follow the script below, which will unbundle the packrat file created in the above script:


Once you are working within a packrat session there are some useful commands to know. One is sessionInfo() which shows what versions of things you have loaded. There is also a way to install older versions of packages – this is useful if you want to create a new packrat project but you realize your current packages are too new. Information on how to do that can be found here.

Additionally, the scripts provided by Stephanie do an excellent job of annotating, or commenting, on the code. This is especially important when working with collaborators, but is also important when working solo as it makes it easier to troubleshoot issues. Good annotations can help users determine if issues are code issues, are package related (and can therefore be addressed with packrat), or are (rarely) issues with versions of R. R version errors are harder to fix, and are not addressed by the packrat package. But! As Dr. Katz said during this session: “there is a long conversation to be had about strategies in programming for another time.”

Enjoy packrat!

Reflections, Transitions, & Solutions: Perspectives on the Past, Present & Future of Environmental Issues

Abstract submission deadline: March 10, 2017
The environment is more politicized than ever and creative approaches are required to understand and address the environmental issues that pervade everyday life.
Unfolding political realities, funding uncertainties and public confusion leave us in a
crucial position to take stock of environmental issues.
The conference will serve to forge or strengthen interdisciplinary ties as we critically reflect on the environment as a dynamic process of both physical conditions and social understandings. Together, we will explore pressing questions about how best to engage in meaningful interdisciplinary work to both recognize and respond to environmental realities.
Ideal papers will focus on case studies or cross-sectional analyses of (1) creative approaches to examine the past, present, or future of environmental issues
or (2) interdisciplinary efforts that seek to address or adapt to such problems
in local, regional, national, and/or international venues.
To submit abstracts please email
Conference date: April 1, 2017 at WSU


NW Climate Science Center Graduate Fellowships

Theme: Abrupt ecological transformations in the Northwest
SOI: Due Tuesday February 28, 2017
Full Proposal Deadline: April 1, 2017
Support offered: Partial or full stipend, benefits, and tuition for June 2017 to December 2019 (2.5 years), travel and networking support for participating in Climate Fellows Cohort activities.
Process: Advisor/student team submits a statement of intent (SOI), including only a draft title by email to Responses will follow within 14 days and may include suggestions via consultation. After this consultation, advisor-student team submits a proposal (see details below). NW CSC PI team (OSU, UI and UW) selects several advisor-student teams for funding (see selection criteria below). PIs send notification to advisor-student teams as soon as possible, but no later than April 15, 2017.


DataONE Summer Internship Projects Announced

Six different project opportunities through the DataONE Summer Internship Program.  Applications are being accepted from now until March 17th 2017. Project opportunities are:

  • Project 1: Markdown-based Semantic Annotation of Workflow Scripts
  • Project 2: DataONE Messaging: Creating Marketing for DataONE Stakeholder Communities
  • Project 3: Prospective and Retrospective Provenance Queries Using YesWorkflow, RDF, and SPARQL
  • Project 4: Exploration of Search Logs, Metadata Quality and Data Discovery
  • Project 5: Improving DataONE’s Search Capabilities Through Controlled Vocabularies
  • Project 6: Development of an Open Source Units of Measure Knowledge Graph

The DataONE Summer Internship Program runs from May through July for a period of 9 weeks and is open to undergraduate students, graduate students, and postgraduates who have received their degree within the past five years. The internship project can be conducted remotely and offers a stipend of $5000.

For full information and to apply, visit  You will also find a link to other internship opportunities offered by DataONE leadership and partners.