Issue 12 | October 19, 2020

This issue is marks the official launch of the EFI-RCN NEON Ecological Forecast Challenge. I encourage you all to read more below about the details of the challenge and to share this with colleagues, but most important I encourage you to participate in this first "beta" round of the forecast challenge, either individually or as part of a team. Be aware that if you don't have time to participate in the Forecast Challenge this round (2021) that there will be opportunities to join in later years, and folks are also welcome to join late if it takes a while to get models set up (e.g. classes at Boston University, Virginia Tech, and UC Berkeley will be participating this spring, but may not have things running till later in the spring). To that point, this challenge is not restricted to ecologists -- feel encouraged to invite statisticians, data scientists, hydrologists, epidemiologists, etc. -- and folks can choose to participate in one challenge, multiple challenges, or all five of them.

I also want to take this opportunity to thank all of the members of all of the EFI Working Groups that have been working hard over many months to make this challenge a reality. The NEON Challenge Design Teams in particular have been busy crafting the rules and protocols as well as prepping datasets for model development and scoring, and extra thanks goes out to all the Team leads, who are all early career scientists. The thematic Working Groups have also played important roles finalizing the EFI standards, thinking about how we can increase diversity and build partnerships across the Challenge, organizing educational materials and technical info about workflows and methods, and working through how we can use the results to advance forecasting theory. The EFI RCN steering committee and our partners at NEON have worked hard to coordinate all of this. In particular, I want to call attention to the hard work of RCN PI Quinn Thomas, who has been devoting almost a full time effort to this recently, not only as the lead organizer but also deep in the trenches with Carl Boettiger working on setting up the cyberinfrastructure that is supporting the forecast challenge (many thanks to Carl as well!). Finally, as always, many thanks to EFI project manager Jody Peters, who has kept all of us organized and on task.

​Mike Dietze EFI Founding Director

NEON Ecological Forecast Challenge Launch

We are pleased to announce the launch of the inaugural NEON Ecological Forecast Challenge hosted by the EFI RCN! As a , we are excited to learn more about the predictability of ecological processes by forecasting NEON data prior to its release. What modeling frameworks, mechanistic processes, and statistical approaches best capture community, , and dynamics? These questions are answerable by a community generating a diverse array of forecasts. The challenge is open to any individual or team that wants to submit forecasts and includes categories for different career stages. Individuals or team contacts can register to submit forecasts HERE.

There are five themes in the Challenge that span aquatic and terrestrial systems, and population, community, and ecosystem processes across a broad range of ecoregions. The design of the challenge is the result of contributions of over 200 participants in the May 2020 virtual EFI-RCN meeting, including partner organizations, and the hard work from the Design Teams that have developed the protocols for each of the themes.

Challenges Themes: 1. Aquatic - Daily forecasts for 7 days into the future of dissolved oxygen and water temperature from a NEON lake and a river site. Forecast submissions are accepted once a month, May 31-August 31, 2021 2. Terrestrial Carbon and Water Fluxes - Half hour and daily forecasts for 35 days into the future of net ecosystem exchange of CO2, evapotranspiration, and soil moisture at four terrestrial NEON sites that differ in water availability. Forecast submissions are accepted once a month, January 31-December 31, 2021 3. Beetle Communities - Weekly forecasts for 20 months in the future of beetle and forecasts at 47 terrestrial NEON sites. Forecasts submissions are accepted one a month, starting June 30-December 31, 2021 4. Tick Abundance - Weekly forecasts for 34 weeks into the future of Amblyomma americanum and Ixodes scapularis nymphal tick abundance at seven NEON sites. Forecast submissions are accepted once a month, March 31-October 31, 2021 5. Phenology - Daily forecasts for 35 days into the future of plant greenness at seven deciduous broadleaf forest NEON sites as measured by Phenocams. Forecast submissions are accepted daily, February 1-July 1, 2021 (spring) with a second round being run for the autumn.

Forecasts may be submitted after the start date for each theme. Evaluations will occur throughout the year and are intended to result in a journal special issue highlighting the different approaches and lessons learned.

With this launch, we are sharing an overview of the themes, how to participate, and forecast evaluation descriptions on the Challenge webpage to help individuals, lab groups, and course instructors think about participating in the first round of the NEON Ecological Forecast Challenges. We will provide additional information about the Challenge in future Newsletters, on the Challenge webpage, and at the December 9, AGU EFI Town Hall as the final details come together prior to the start of each Challenge theme. There are Slack channels and GitHub repositories for each theme where registered participants can discuss issues and shared challenges. These repositories will include a “null” forecast workflow for each challenge that teams can build off of to develop more interesting forecasts.

In the model of many successful model-intercomparison projects in , we aim to support a collegial, supportive environment focused on advancing the discipline and building community, and where the is friendly and motivating, not negative. We encourage you to participate and as Mike mentioned above, share this announcement widely with a range of colleagues outside of ecology.

Forecast Challenge Advances Forecast Cyberinfrastructure

The backbone of the forecasting challenge is new state-of-the-art cyberinfrastructure led by Carl Boettiger (University of California, Berkeley) and Quinn Thomas (RCN PI, Virginia Tech). The cyberinfrastructure provides a server, https://data.ecoforecast.org/, that automates the NEON data download, processing, null model generation, scoring, and visualization of results through the use of Docker containers. It is designed to be reusable for other forecasting projects and run on a diversity of architectures like CyVerse Atmosphere and NSF's Jetstream. The cyberinfrastructure also provides real-time NOAA ensemble forecasts for each NEON site. The code underlying these tools is public on the EFI Github, https://github.com/eco4cast, as a collection of “neon4cast” repositories and we welcome community contributions and code reuse. We are partnering with CyVerse for the deployment of the cyberinfrastructure.

Additionally, Carl Boettiger has led the development of a new R package for downloading and reading NEON data (neonstore; available on CRAN). The new package provides a persistent local store of NEON data and a relational database interface to speed up data access. It uses the NEON API to only download NEON data that isn’t already in the local store.

Save the Date! November 19 EFI Conversations on Diversity and Data

The Diversity, Equity, and Inclusion Working Group is hosting a 4 part virtual seminar series to foster conversations and actions for increasing diversity in ecological forecasting.

Our initial call will be on November 19 at 2pm US eastern time focusing on What Diverse Students Need to Thrive in Data- and Computer-Heavy Settings. We will hear from three panelists followed by breakout discussions for smaller group conversations and a plenary Q&A. The formal portion of the call will last one hour with an optional 30 minutes for unstructured, casual discussions.

Register HERE for the Workshop to receive the Zoom link.

Panelists: Antoinette Abeyta is an Assistant Professor in the Mathematics, Physical and Natural Sciences Division at the University of New Mexico, Gallup. UNM-Gallup is a 2 year Minority Serving community college whose goals are to prepare students to transfer to 4-year STEM programs and specialize in helping under-served students get the help they need to succeed in college.

Nievita Bueno Watts is the Director of the Indian Natural Science & Engineering Program (INRSEP) + Diversity at Humboldt State University which provides academic and research support to first generation, low income, and historically underrepresented students in STEM disciplines. INRSEP's mission is to improve STEM fields by empowering students to become leaders who give back to their communities, society, and future generations while strengthening connections with their heritage and culture.

John Zobitz is a Mathematics professor at Augsburg University, an institution that put in place initiatives to increase diversity and in 10 years went from 25% students of color in 2009 to 53% students of color in 2019.

2020 ESA Forecasting Outstanding Publication Award

Congratulations to Paige Howell (USGS) and co- authors! Paige was awarded the 2020 ESA Forecasting Outstanding Publication Award for Howell et al. 2019. A statistical forecasting approach to viability analysis. Ecological Applications 30:e02038. ​The award panel said of this paper, "We believe that Howell et al (2019) provides a template for significant improvement in the way that population viability analyses are conducted. Their spatial occupancy model accounts for many of the uncertainties common to, but often ignored in, PVA projections. The case study forecast of Chiricahua leopard frogs provides an excellent example of the value of forecasts in this setting and guidance for others to use in other PVAs. The writing in Howell et al is clear and compelling, and we think it will motivate important improvements in the way that PVAs are carried out."

Forecast Spotlights - PROGNOS and WATExR

We are highlighting operational forecasts in conjunction with the release of Newsletters for our series called "Forecast Spotlights". The goal is to highlight operational forecasts conducted by EFI members, how they got into forecasting, and lessons learned. You can see all the project examples shared on the EFI Projects webpage. The second post in our series focuses on the PROGNOS water quality and WATExR fish phenology and water level forecasts that Elvira de Eyto works on with her collaborators Andrew French, Eleanor Jennings, and Tadgh Moore. One key lesson the group learned was to think specifically about uncertainties all along the workflow and the importance of making those uncertainties visible along the process when communicating results of forecasts to end users. We look forward to seeing the WATExR fish phenology forecast for a catchment in Ireland which will soon be submitted for publication and its subsequent application to the North Atlantic.

See the full blog post for more details about the forecasts, stakeholders, lessons learned, and challenges of working on these two forecasting projects.

3 Question Survey Request

Nine EFI Student Association (EFISA) members are writing a Plos Computational Biology manuscript titled “Ten simple rules for training yourself in an emerging field” based on their experiences as students in the emerging field of ecological forecasting. In order to illustrate the various ways one might join an emerging field, the group would like to document how the broader EFI community found out about the Ecological Forecasting Initiative. Help these students by taking less than 1 minute to fill out this 3 question survey.

New EFI Members Webpage Format

In another effort led by members of the EFI Student Association (EFISA), we now have a new format for our EFI Members webpage! In addition to seeing who the EFI Members are and their forecasting interests, you can now see where Members are located.

If you are an EFI Member, take a minute to check out your profile and email us if updates are needed.

If you would like to become an EFI Member, you can find more information about joining the group on our Members page.

American Geophysical Union 2020

EFI is hosting the "Ecological Forecasting in the Earth System" Session at AGU this year on December 16 at 7am Eastern time. The two invited speakers in our session will be Leslie Ott and Paige Howell (winner of the 2020 ESA Forecasting Outstanding Publication Award).

This year EFI will also be hosting a Town Hall "Ecological Forecasting Initiative: NEON Forecasting Challenge" on December 9 at 1:30pm Eastern time to provide the community with more information about EFI, its activities, and the RCN NEON Forecasting Challenge.

Working Group Calls and Summaries

The Working Groups are open for anyone to join at any time. Email EFI to be added to the mailing lists or Slack channels for these groups. Schedule of Calls. All times are US Eastern Time. Theory - November 18, December 16 12pm Methods/Cyberinfrastructure - October 20, November 24, December 15 at 12pm Forecasting Standards - November 24, December 15 at 1pm Partners - October 22, November 19, December 17 at 12pm Social Science - October 20, November 17, December 8 at 1pm Education - November 16, December 14 at 2pm Diversity & Inclusion - October 23, November 20, December 18 at 1pm Student Association(EFISA) - November 20, December 18 at 1pm

Theory & Synthesis Abby Lewis (Virginia Tech) and Amanda Gallinat (Utah State University) are the new co- chairs for the Theory Working Group. The group continues to discuss overarching theories of ecological forecasting such as transferability in terms of model structure vs in terms of model structure. The RCN NEON Forecasting Challenge themes are providing a way for the group to think about general patterns of temporal and spatial scale and uncertainty across multiple forecasts. The group has been examining these ideas with the Phenology Challenge and then will move to the other Challenge themes. Reflecting back on the group conversations for more than a year, the Theory group has started the outline for a manuscript that uses the context of ecological forecasting to discuss predictability and how it relates to spatiotemporal variability, what limits predictability across multiple scales, the limits of transferability, and how forecasts can inform ecological theory.

Methods & Tools and Cyberinfrastructure These two Working Groups are continuing to meet jointly. Over the past two months, the groups have made progress on developing two new Task Views to add to the EFI Task Views webpage to provide an annotated reference for commonly used tools and resources for 1) Uncertainty Quantification & Propagation and Modeling & Stats and 2) Visualization, Decision Support, and User Interface for ecological forecasting. The Visualization, Decision Support, and User Interface Task View is being developed with input from the Social Science Working group. There have also been a number of cyberinfrastructure development development of scripts, repositories, and dockers that are rolling out with the RCN NEON Forecasting Challenges.

Forecasting Standards The Forecasting Standards Working Group has been diligently working on community standards for common formatting and archiving of ecological forecasts that applies to output files, output metadata, and archiving. An alpha version (v0.3) of the standard has just been released; the eco4cast/EFIstandards Github repository summarizes the standards and provides vignettes and an EML validator. The Standards will be used with the Forecasting Challenge, but are applicable for forecasts in general. This is a community driven standard and repository. If you find areas where the Standards can be improved share them on the #forecasting_standards Slack channel or the GitHub repository.

Partners & Knowledge Transfer The Partners Working Group is developing a work plan for tasks related to the core functions of their Terms of Reference: (1) foster a collaborative community, (2) promote the co-development and uses of resources and tools, and (3) transition forecasts from research to operations. In particular, the group has focused on core function 1. In future calls they will work to develop concrete ways for match making between individuals or groups developing forecasts to decision makers and managers that want to apply or make decisions using forecasts. The Partners and Social Science groups have also separately talked about finding times for intermittent joint calls to discuss actionable or usable science to inform government, business, and other public efforts.

Social Science On recent calls, the Social Science Working Group, has been discussing ideas for the Visualization, Decision Support and User Interface Task View and thinking about different tools used for static and dynamic visualizations and the need for user input for decision support resources. The group will continue to provide input for the Task View as it is developed. Thinking about visualizations in another context, the Social Science group has also been asked to provide input for a vignette to create effective visualizations from forecasts output and metadata formatted and archived using the Forecasting Standards.

Education Over the past couple of meetings the Education Working group's discussions have focused on providing input on a number of topics including the manuscript comparing definitions of forecast and prediction led by Anna Sjodin (University of Idaho) and Gretchen Stokes (University of Florida), plans for using the summer 2021 EFI RCN workshop to develop concrete plans for creating educational materials from the NEON Forecasting Challenges, and the effort Alyssa Willson (University of Notre Dame) is leading to compile online forecasting related educational resources to provide a list of these resources on the EFI webpage as well as identifying where there are gaps and new online resources are needed.

Diversity and Inclusion The Diversity, Equity, and Inclusion (DEI) Working group spent much of the last call focusing on brainstorming ideas for a four part virtual seminar series focusing on conversations on diversity and data. The goal of each call will be to have 3-4 panelists share their perspective on a topic followed by smaller breakout discussions and plenary Q&A talks to promote conversations and community around equity and inclusion topics pertaining to ecological forecasting. Potential topics for the series include: What diverse students to thrive in data- and computer-heavy settings What culturally competent data science training looks like What community colleges need to support student to transfer into data-driven 4-year programs What kind of online tools are useful and work well for remote learning

Ecological Forecasting Initiative Student Association (EFISA) During the past two calls, students shared updates and frustrations on ongoing projects, as well as what has been new in student collaborations and across EFI. Toryn Schafer (Cornell University), Ben Toh (University of Florida), Libby Mohr (Montana State University), and others have deployed the EFI Explorer RShiny app; A ‘Ten Simple Rules’ manuscript effort led by Whitney Woelmer (Virginia Tech) is well under way, and Alyssa Wilson (University of Notre Dame), Whitney, and Ben helped put together a collection of education resources. Libby Mohr and Ryan McClure (Virginia Tech) have provided flash talks on nitrogen flux modeling work involving mesocosm experiments to tune a model of microbe community metabolism and the predictability of methane emissions from freshwater ecosystems, respectively.

Reading Groups

In September the EFI DEI group finished the first round of a book club, reading The Years That Matter Most, by Paul Tough. Focusing on privilege in higher education, the group discussed how we as individuals and members of EFI can make academia (and EFI) accessible to a more diverse student body. We agreed that understanding the history of privilege, whether it be racial, economic, or geographic, would help inform action items moving forward. For this reason, we have selected Caste, by Isabel Wilkerson, as our next read. DEI book club round two will begin in December, with date and time TBD. Everyone is welcome to join, regardless of EFI membership, and limited financial help is available to those who need assistance acquiring the book. Email EFI for more info or to be included on book club emails.​

On the Methods side, there is a group working through "Spatio-Temporal Statistics with R" by Christopher K. Wikle, Andrew Zammit-Mangion, and Noel Cressie. We meet Thursdays at 1pm ET and are about 1/3 of the way through the book. If you're interested in participating join the #spacetimer channel in the EFI Slack.

New EFI Members

Helen Scott - BBN Technology Ben Tupper - Bigelow Laboratory for Ocean Alex Baecher - University of Florida Sciences Grant Foster - Louisiana State University Kyle Oliveira - Bigelow Laboratory for Emelia Obodum Kusi - Virginia Ocean Sciences Commonwealth University Aabid Hussain Mir - Community of Libby Mohr - Montana State University Education, Research and Development Julia Stepanuk - Stony Brook University Foundation, J&K India/University of Kashmir Johnathan Evanilla - Bigelow Laboratory Alexey N Shiklomanov - NASA Goddard for Ocean Sciences Space Flight Center Whitney Woelmer - Virginia Tech

New Zotero Library

We have created this Zotero library with a bibliography of forecasting papers. You can use the Filter Tags section in the lower left hand corner of this library to search for papers provided on our EFI Diversity and Inclusion webpage "EFI DEI Paper", papers posted to Slack "EFI Slack Paper", and papers produced by the group "EFI Publication".

EFI Logos

​The EFI logos are available for people to use in presentations.

Slack Channel

The Slack channels provide an outlet for the group to share ideas and conversations quickly, which we expect will be especially important as the Working Groups' activities continue to ramp up. Join the EFI Slack with this link or email EFI to be added. If you have joined Slack, be sure to go to the Channel Browser to see if there are additional channels you want to join.

Membership and Project Profiles

As a reminder, EFI membership is free. If you are not already a member you can sign up here. The same form can be used to add your forecasting projects to our listing of project profiles to provide examples of ecological forecasts to the community. As an added bonus, new members will get a free EFI mug. (Mike apologizes for being slow on getting mugs out).

Calendar Summary

October 26-27, 2020: "Forecasting Social, Biological, and Physical Systems", Royal Society Meeting, London, UK [POSTPONED]

November 9-14: Canadian Ecological Forecasting Initiative CIEE Fall working group meeting

November 19, 2020: EFI Conversations on Diversity and Data

December 1-17, 2020: Virtual American Geophysical Union

Dec 9: EFI Town Hall, 10:30-11:30am PT, 1:30-2:30pm ET Dec 16: EFI session "Ecological Forecasting in the Earth System" Oral Session 4-5am PT, 7-8am ET Poster Session all day

February 17-18, 2021: NCEAS Workshop "The Future of Synthesis in Ecology and Environmental Science" [RESCHEDULED from Sept]

May 30 - June 4, 2021: Gordon Conference on Predictive Ecology

July 2021: " Science for Ecological Forecasting" British Ecological Society workshop, exact date TBD

Summer 2021: EFI Research Coordination Network Meeting, exact date TBD

ecoforecast.org @eco4cast