The Delta Science Program’s Synthesis Working Group with the National Center for Ecological Analysis


The Delta Science Program partnered with the National Center for Ecological Analysis and Synthesis (NCEAS) in the summer and fall of 2021 and 2023 to lead two collaborative synthesis working groups. The synthesis working groups delivered high-quality training in synthetic data science, and statistical techniques and provided a focused opportunity for enhanced collaboration between scientists from federal and State agencies as well as academic scientists.

Working group participants convened for three weeks of training and collaboration facilitated by experts from NCEAS. Following this working group event, participants analyzed and synthesized data using their newly developed skills to address questions important to Bay-Delta management. Outputs from the effort include multiple publications, reproducible workflows, R functions, and derived data.

Why a synthesis working group is important

Ecological synthesis is a critical component of ecosystem-based management and informed decision-making. NCEAS’s emphasis on open science principles and techniques promotes transparency and data sharing through reproducible data, software, and workflows. The need for increased capacity, dedicated time, and coordinated synthesis is recognized and included as an action in the Delta Science Plan, Science Action Agenda, and Interagency Ecological Program Science Strategy.


The working group consisted of 16 participants from nine agencies and universities interested in bringing together environmental and social data to solve problems at the human-environment interface in the San Francisco Estuary. Affiliations of participants include:

  • Bureau of Ocean Energy Management (BOEM)
  • California Department of Fish and Wildlife (CDFW)
  • California Department of Water Resources (DWR)
  • California Office of Environmental Health Hazard Assessment (OEHHA)
  • California State Water Resources Control Board (SWRCB)
  • Delta Stewardship Council (DSC)
  • San Francisco Estuary Partnership (SFEP)
  • University of California Davis (UCD)
  • University of California Merced (UCM)


Synthesis leverages disparate datasets and advances the information available to address complex management issues. With this effort, we aim to provide innovative data science and statistics training with immediate opportunities to use those newly acquired skills to synthesize available data and produce relevant research. This working group will focus on expanding multi-benefit approaches to managing the Delta as a social-ecological system and investigate the integration of human dimension data into research and management decision-making. This may include the development of integrated frameworks, data visualization tools, and models of social-ecological systems that evaluate, for example,

  1. how ecosystem restoration projects benefit and burden human communities, with an emphasis on environmental justice,
  2. Evaluate the social economic, and ecological costs and benefits of levee infrastructure within the Delta, and
  3. the sensitivity of social metrics to different socio-political or environmental scales.


A graphic representing California’s coequal goals for the Sacramento-San Joaquin Delta: A reliable statewide water supply and a resilient ecosystem. The coequal goals are to be achieved in a manner that protects and enhances the Delta as a place where people live, work, and recreate.

The training event began in June of 2023, and in the summer months, participants focused on data publications. Training events continued in fall 2023, with an emphasis on interdisciplinary analysis techniques, such as human subject research considerations within reproducible workflows, spatially explicitly modeling using Census data, and text analysis. The products from this effort will build and integrate knowledge of the social processes and behaviors of Delta communities to support effective and equitable natural resource management. This effort will address complex information needs with peer-reviewed articles, presentations, and briefings. Targeted management briefings are also possible and will be determined by the synthesis findings.


Next steps

The products from this working group are anticipated to be released by December 2024 and will offer strong scientific support in expanding multi-benefit approaches to managing the Delta as a social-ecological system (addressing Science Action Agenda, Management Need 3).

Learn more

Item Link Progress
Publication of ‘multi-benefit approaches to managing the Delta as a social-ecological system’ relevant datasets See the working group’s latest progress on GitHub: Repositories beginning with “swg-23-“
Week 1 curriculum RStudio Server Setup
Week 1 curriculum & Git and GitHub Setup & Introduction to Git and GitHub
Week 1 curriculum Literate Analysis with Quarto
Week 1 curriculum Data Management Lens for Publishing and Accessing Data
Week 1 curriculum Logic Model
Week 1 curriculum Data Modeling Essentials
Week 1 curriculum FAIR and CARE principles
Week 1 curriculum Reproducible Data Access
Week 1 curriculum Cleaning and Wrangling Data
Week 1 curriculum Creating Functions in R
Week 1 curriculum Creating R Packages
Week 1 curriculum Reproducibility & Provenance
Week 2 curriculum Collaborating using Git and GitHub & Merge Conflicts
Week 2 curriculum Publishing your analysis to the web with GitHub Pages
Week 2 curriculum Data Visualization
Week 2 curriculum R Practice: Collaborating on, Wrangling & Visualizing Data
Week 2 curriculum Thinking Preferences
Week 2 curriculum Social Aspects of Collaborations
Week 2 curriculum Group Work: Developing Authorship Guidelines & Data Policy
Week 2 curriculum Using SF for Spatial Data & Intro to Making Maps
Week 2 curriculum Working with US Census Data
Week 2 curriculum Working with Text Data in R
Week 2 curriculum Reproducible Surveys
Week 2 curriculum Shiny in R
Week 3 curriculum Mapping Census Data
Week 3 curriculum Communicating your Science
Week 3 curriculum Flex dashboard
Week 3 curriculum Shiny Review
Week 3 curriculum Practice Session: Shiny and Flexdashboard
Week 3 curriculum Reproducible Workflows Using Targets
Week 3 curriculum Parallel Processing
Week 3 curriculum Publishing Data
Week 3 curriculum Git Workflows


The working group consisted of 18 participants from nine agencies and universities interested in synthesis projects involving primary productivity, contaminants, connectivity, climate change, growth, floodplains, zooplankton, food web linkages, forecasting, hydrodynamics, and more. Affiliations of participants include:

  • California Department of Fish and Wildlife (CDFW)
  • California Department of Water Resources (DWR)
  • Delta Stewardship Council, Delta Science Program (DSP)
  • National Oceanic and Atmospheric Administration (NOAA)
  • University of California Berkeley (UCB)
  • University of California Davis (UCD)
  • University of California Santa Cruz (UCSC)
  • U.S. Bureau of Reclamation (USBR)
  • U.S. Fish and Wildlife Service (USFWS)
  • U.S. Geological Survey (USGS)


The working group is leveraging the fall 2021 training and the collaborative setting to analyze drivers of the estuarine aquatic food supply. Products from this working group will offer strong scientific support to inform decision-making for restoration, protection of endangered species, and management of flow actions. The focus on food webs serves broad interagency goals, such as ecosystem function, resilience, and sustainability. Furthermore, comprehensive, spatially explicit, food-web modeling that is tied to environmental driving forces and conditions is a recommendation in the Independent Science Board's review of The Science of Non-native Species in a Dynamic Delta.


The diagram illustrates the synthesis required to evaluate key environmental drivers in aquatic systems and inform ecosystem-based management.

In the summer of 2021, the Delta Science Program worked with a data wrangling and publication expert from the NCEAS in the integration and publication of ‘estuarine food supply' relevant datasets from the Interagency Ecological Program and working group participants. The Delta Science Program sees this as an opportunity to make select datasets that previously had limited accessibility more available. The three-week synthesis, collaboration, and statistics training was held in September, October, and November 2021. Delta Science Program project leads presented results at the January 2023 Delta Stewardship Council meeting.


Next steps

The participants were divided into two distinct subgroups focusing on the following:

  1. The effect of flood management on estuary health.
  2. Identifying the drivers of food web dynamics on an estuary scale.

In March 2022, both subgroups presented preliminary results at the Delta Independent Science Board meeting (beginning at 2:05) and Interagency Ecological Program (IEP) Annual Workshop (beginning at 20:53). Recent products include two new R packages, deltafish and inundation, as well as the Environmental Monitoring Program’s benthic invertebrate monitoring data publication (Wells and IEP 2021), Sacramento-San Joaquin Delta genus and community level classification maps (Shruti Khanna, Susan Ustin, Erin Hestir, et al. 2022), fish abundance in the San Francisco Estuary (1959-2021), an integration of 9 monitoring surveys (Bashevkin et al., 2022), daily water temperature (C) in the Yolo Bypass and Sacramento River, 1998-2019 (Goertler and Pien, 2022), modeled daily Yolo Bypass inundation (Goertler, 2022) data from "evaluating top-down, bottom-up, and environmental drivers of pelagic food web dynamics along an estuarine gradient" (Mitchell et al., 2023), data from “floodplain inundation and lateral connectivity promote productivity in the river ecosystem” (Pien et al., 2023 ) and zooplankton energy densities from literature (Dudley et al., 2022).

The R code for the above data sets are publicly available through GitHub. These include Connectivity synthesis, food web synthesis, meta-analysis, chlorophyll integration, phytoplankton enumeration synthesis, and Delta smelt diet integration.

Each subgroup will produce one or two peer-reviewed journal submissions, R functions, and derived data, along with communication materials for a manager-level and general audience. Manuscripts from the 2021 workshop: Evaluating top-down, bottom-up, and environmental drivers of pelagic food web dynamics along an estuarine gradient.

Learn more

The following table provides the curricula for the synthesis working group, as well as interim data and code products, and will be updated as more products are available. To learn more, please visit the links in the table below.

Item Link Progress
Publication of ‘estuarine food supply' relevant datasets See the working group’s latest progress on GitHub: Repositories beginning with “swg-21-“
Pre-workshop curriculum An introduction to RMarkdown
Pre-workshop curriculum Guide to setting up RStudio and GitHub
Week 1 curriculum Reproducible papers with RMarkdown
Week 1 curriculum Git and GitHub
Week 1 curriculum & Cleaning and manipulating data
Week 1 curriculum Functions and packages
Week 1 curriculum & Collaboration, logic models, and synthesis development
Week 1 curriculum & & Meta-analysis and systematic review
Week 2 curriculum Git conflicts
Week 2 curriculum & & Bayesian models and informative priors
Week 2 curriculum Missing data and Markov Chain Monte Carlo
Week 3 curriculum Time series and forecasting
Week 3 curriculum & Web-based data archival and reproducible data
Week 3 curriculum Comparing models to data and simulation models
Week 3 curriculum Shiny
Week 3 curriculum Reproducible workflows
Week 3 curriculum Communicating research
One-day workshop Spatial vector analysis using SF


Delta Science Program. National Center for Ecological Analysis and Synthesis.