Workshop: Vector spatial data in R [Wednesday February 10]

Next week’s event will be a workshop, not a roundtable. The workshop will be led by Casey O’ Hara at NCEAS. We will have facilities for remote participation for those who’d like and/or if we run out of space at the NCEAS conference room.
Please RSVP to attend and get follow-up emails.
Vector spatial data in R

GIS is a useful tool for viewing spatial data and creating maps, but R can do a lot of the heavy lifting when it comes to analyzing your spatial data.  We will focus on vector spatial data in this workshop (polygons, lines, points) but also touch on raster spatial data, building upon the raster workshop led by Jamie last fall.  Please RSVP by filling out this google form, so we can send you a follow up e-mail with further instructions to set up your laptop.  Newbies and experts are all welcome.

Some things we will look at; if you have specific questions please feel free to send them in advance (e-mail or on the RSVP form):

  • reading and writing vector spatial data (shapefiles and geodatabases)
  • projecting and displaying vector spatial data (incl. mapping in ggplot)
  • understanding the structure of R spatial polygon objects so we can take them apart, analyze them, modify them, and put them back together again.
  • using basic geoprocessing tools in R to manipulate geometry, e.g. intersect, difference, area, buffer, etc.
  • working with polygons and rasters together
  • checking and repairing geometries (beware of orphan holes!)

Please bring a laptop if you can, so we can work through the examples together.  You can find the materials (scripts, data, and workshop notes) here:  Clone or fork the repository (if you’re a GitHub person) or download the zip file (button on right, above the list of files).

We’ll send a followup e-mail to attendees with a to-do list of things to set up ahead of time, including software and R packages you might need to install or update.  Please make sure to RSVP!

Hunting in the tropics: examining hunter rationality [Wed, Feb 3]

Excessive hunting pressure is a major threat to tropical vertebrates. Research on hunters has broadly assumed that hunters are rational economic agents, willing to switch to more attractive alternative activities. However, my study in Southwest China demonstrates that villagers may be highly unwilling to stop hunting, despite low expected catch rates and stiff penalties for hunting and gun ownership. I will primarily discuss a project that used quantitative and qualitative interviews to elucidate the behavior of hunters, as well as the application of novel techniques to analyze these data. I will also discuss ongoing research that combines field data with theoretical models to explore how resilient prey may subsidize the continued harvest of rare game species. I am eager to receive feedback and share ideas with audience members.

Charlotte Chang
PhD candidate | Ecology and Evolutionary Biology
Princeton University


Barriers to Diversity in Higher Education and the Promise of Diverse Scientific Teams [Wednesday, Jan 27]

This Wednesday’s roundtable will be led by Dr. Barbara Endemaño Walker and Professor Kyle Lewis from UCSB.

The Center for Research, Excellence and Diversity in Team Science (CREDITS) at UCSB is an integrated research and training program to increase and enhance the capacity and effectiveness of transdisciplinary scientific teams in California.  Diversity on teams is known to have positive effects on creativity, innovation, and productivity.  Apart from its contribution to scientific breakthroughs and grand challenge problems, collaborative transdisciplinary science – “Team Science” – has beneficial impacts on individual research careers.  Team Science projects garner more funding, and yield greater publication productivity and higher impact publications.  Despite the benefits of diversity to teams, women and URM scientists are less likely to participate in team science collaborations, and their participation in these networks develops later in their careers.  In this presentation we will provide an overview of key interventions to increase the broader participation of women and URM faculty in higher education, and summarize the research on diversity and collective intelligence.

Kyle Lewis Pic
Kyle Lewis
Professor of Technology Management
College of Engineering, UCSB

Barbara Endemaño Walker
Special Assistant to the Executive Vice Chancellor for Diversity Initiatives /
Director of Research Development for the Social Sciences, Humanities and Fine Arts
Office of Research, UCSB


Kyle Lewis is Professor of Technology Management in the College of Engineering. She holds a PhD in Organizational Behavior from the R.H. Smith School of Business at the University of Maryland, an MS in Industrial Administration (MBA) from Carnegie-Mellon University, and degrees in Mathematics and Computer Science from Duke University. She joined the faculty of UCSB in the Fall of 2014. Prior to joining UCSB, Dr. Lewis was a tenured professor at the McCombs School of Business at the University of Texas at Austin. Dr. Lewis’ research examines how organizations leverage individual and collective knowledge. She examines the performance of teams, especially those teams engaged in knowledge work such as professional services, new product development, and project-based tasks. She has published articles in the top journals in the field of Management, including Academy of Management Review, Academy of Management Journal, Organization Science, Organizational Behavior and Human Decision Processes, Management Science, Journal of Management, Journal of Applied Psychology, and Group Dynamics. Dr. Lewis served as Division Chair in the Academy of Management (Managerial and Organization Cognition Division) and was a past senior editor for Organization Science.


Barbara Louise Endemaño Walker is the Special Assistant to the Executive Vice Chancellor for Diversity Initiatives, and the Director of Research Development for the Social Sciences, Humanities and Fine Arts in the Office of Research at UC Santa Barbara. Walker’s research on the gendered political ecology of marine resources in Ghana, French Polynesia, and California has been funded by the National Science Foundation, the MacArthur Foundation, and NOAA Sea Grant, among others. Her current research programs examine a) the intersections of team science and broadening participation in STEM and higher education, and b) alternative food networks among US fishing communities. Her work has been published in the Professional Geographer; Gender Place and Culture; Society and Natural Resources; PLOS ONE; and the Journal of Geography and Higher Education among others. She has a Ph.D. and M.A. in Geography from UC Berkeley and a B.A. in Anthropology and African Studies from UCLA.


A primer on natural history collection digitization and data sharing.

Natural history collections contain both historical and contemporary
information about the ecology of our natural and urban areas. The
research and instructive potential of these data are rapidly becoming
more relevant as more and more collections become digitized.

I managed the digitization of over 3 million plant and insect
specimens for the National Science Foundation Tri-Trophic Thematic
Collection Network project from 2011 until 2015. The focus of this
high-throughput digitization effort was on the hemipteran herbivorous
insects (aphids, scales, hoppers, cicadas, and true bugs), their host
plants, and related parasitoids.  At this NCEAS roundtable, I plan to
present to review of contemporary standards in natural history
collection digitization, highlight some of the exciting derivative
research, and outline many of the ongoing challenges natural history
collection digitization still faces.

Katja Seltmann, PhD
Katherine Esau Director / Entomology Curator
Cheadle Center for Biodiversity & Ecological Restoration (CCBER)


Development at NCEAS, Fundraising for Ecology [Jan 13, 2016]

This round-table will be led by Jeanne Kearns who is the new Director of Development at NCEAS. Jeanne will be discussing what development is, in the context of NCEAS and how the NCEAS community can contribute to its development. In particular, Jeanne will present on:

1) Who I am and why I do what I do?
2) What is Development and What does Development look like at UCSB?
3) How does NCEAS fit into this picture?
and then answer any questions and hopefully have a fruitful discussion!
Jeanne Kearns

Director of Development

National Center for Ecological Analysis and Synthesis

University of California Santa Barbara

735 State Street, Suite 300
Santa Barbara, CA 93101
JSK blazer

Synthetic ecology across scales: a follow-up discussion on hurdles to synthesis

This will be a follow-up to a round-table last July on hurdles to synthesis (here). Look forward to an informal discussion on the process of data synthesis, based on a poster presentation by the GoA group at the CERF meeting last November in Portland, OR. A list of questions for discussion will be posted before the round-table on Wed, Jan 6th.

Here’s a link to the full poster (pdf): CERF 2015_Poster_Large

Large-scale ecological syntheses are increasingly important to understanding patterns, processes, and effects at an ecosystem scale.  However, conducting such syntheses requires lots of data which frequently is considered either large data (large-scale, designed to identify broad patterns not mechanisms, often many investigators or organizational) or small data (intensive, designed to identify mechanisms, often single/few investigators).  We explored a case where we integrated large and small data to examine questions across spatial and temporal scales in the Gulf of Alaska, focusing on the impacts of the Exxon Valdez oil spill.  However, for this discussion we will be focusing on the process of synthesizing disparate datasets rather than the actual data themselves.  Key to integrating data for synthetic analyses is the availability of informative documentation of the data.  We used Ecological Metadata Language (EML), online code sharing (GitHub), and an online data repository (DataONE) to document the data we used and to aid in transparency of these analyses.  Some of the hurdles encountered included a wide variety of poorly documented data formats, and fragmented research (through space and time).  Potential solutions include standardization of data formatting and storage across organizations, and better integration of research efforts by large organizations (government agencies, academia, etc.).  We hope to foster a discussion about these hurdles and potential solutions to synthesizing ecological data across scales.

Rachael Blake, NCEAS Post Doc
Jessica Couture, NCEAS Research Associate
Colette Ward, NCEAS Post Doc

Open Science with the Ocean Health Index [Nov 18, 2015]

The Ocean Health Index (OHI) is a framework to assess the state of our marine systems. With a definition of ‘healthy’ that includes sustainable human use, the OHI scores locations from 0-100 depending on how sustainably their waters provide a suite of benefits to people. The OHI framework was first used to assess all coastal nations globally, and was published in 2012 (Halpern et al. 2012, Nature).
Following the 2012 publication, the OHI framework has been used to assess smaller-scale locations, most often states or provinces within a single nation. These smaller spatial scales often have information that better represents local characteristics of marine systems and are also often the scale at which policy decisions are made.
To date, eleven assessments using the OHI framework have been completed at global, national, and regional scales, four of which have been led by independent academic or government groups. To facilitate these assessments, we have developed a suite of open-source tools and instruction. The OHI Toolbox provides structure for data organization and storage, with data processing and goal modeling done in the programming language R and RStudio for reproducibility and repeatability. The OHI Toolbox is stored on the open-source online platform GitHub, which allows for transparency and collaboration and also houses websites to display and communicate methods and results with interactive visualizations. More information can be found at (currently under a major restructuring and improvement, stay tuned!).
Julia Stewart Lowndes, PhD
Project Scientist, Ocean Health Index
National Center for Ecological Analysis and Synthesis (NCEAS)
University of California, Santa Barbara (UCSB)
735 State Street, Suite 300
Santa Barbara, CA, 93101, USA
ohi • ohi-science • github • twitter

Climate change, plant ecology and conservation: a case study of the SF Bay Area [Thurs, Nov 5]

Climate change is expected to profoundly impact terrestrial vegetation, and the mechanisms, rate and extent of change will influence biodiversity conservation and the ecological functions of natural ecosystems. The San Francisco Bay Area has steep climate gradients and rugged topography, supporting a wide range of natural habitats. Using a novel application of multinomial logistic regression, we have modeled the projected impacts of climate change on Bay Area vegetation. Model projections are evaluated over a wide range of possible future climates, allowing us to evaluate sensitivity of vegetation to changing climate, without choosing specific future climate scenarios. Sensitivity is highly variable across the Bay Area. Perhaps surprisingly, sensitivity to climate change is modeled to be greater on north-facing slopes and cooler locations. The model projections are best interpreted as the long-term equilibrium response to a particular degree of climate change, but they do not provide insight into how fast this equilibrium will be achieved or the transient states that may occur in response to rapid climate change. We combine model results with a discussion of the ecological mechanisms of vegetation change to better understand the challenges raised by disequilibrium dynamics and the implications for conservation biology in coming decades.

Dr. David D. Ackerly
Department of Integrative Biology
University of California, Berkeley


A Network Approach to Assessing Social-Ecological Systems in the Cook Islands (Nov 10)

A social-ecological system approach emphasizes the connectivity that exists between natural and human systems. This coupling is evident at a local scale, with people accessing natural resources for food provisioning and economic gain, and ecosystems providing services such as storm protection and food security. At a larger scale, institutions, and regional and global ecological processes influence how systems function. I present findings from research in Colombia and the Solomon Islands where social networks, institutions, livelihoods, and local ecological knowledge were analyzed to determine the factors that influence an individual’s motivation to comply with marine resource management and to withstand large-scale ecological disturbances. Finally, I propose a network-based approach to quantify social-ecological system interaction and assess the drivers of resilience in the Cook Islands.

Dr. Jaime Matera
Anthropology Program
California State University Channel Islands

Matera Pic

Progress towards developing a fisheries management strategy for data-limited species in Peru (Nov 3)

A majority of fisheries around the world lack the data and/or capacity to be scientifically assessed and managed. Scientifically assessed fish stocks are in better shape than those that are not, with small-scale, unassessed fisheries in worse shape with declining trends. While most of the assessment and management practices have been developed for large-scale, data-rich fisheries, there are many emerging options available for data and capacity limited fisheries. However, there is a challenge in navigating all of the available options, given their differences in data requirements, outputs, costs, and meeting different objectives. To address this, the SNAP Data-limited Fisheries working group is nearing completion of a Decision Support System (DSS) for data- and capacity-limited fisheries. The DSS is a process oriented approach to selecting the three components of a management strategy: 1) a monitoring plan; 2) assessment of the status of the resource; and 3) management decision rules. The DSS allows users to characterize the unique attributes of their fishery through a series of questions, which narrows down the management strategy options to those most cost-effective and relevant to the fishery.

In this round-table, I will present our progress towards applying this framework for a set of data-limited fisheries in Peru: 1) the Lorna Drum (Sciaena deliciosa) fishery; and 2) the Chita (Anisotremus scapularis) fishery. The project will be presented in the context of the Peruvian case study, but I hope this will stimulate discussion around the broader application of this framework and the use of decision support systems.

– – – – –
Dawn Dougherty
NCEAS Data-limited Fisheries SNAP Working Group