Shiny is a web application framework for the R programming language. At SFG, we do the majority of our modeling and analysis in R, and Shiny provides a powerful platform for sharing our research. By combining the computational power of R with the interactivity of modern web applications, Shiny allows our collaborators and clients to explore results, test assumptions, and download custom datasets and figures. See the link below for an example of our Shiny applications:
Interactive Kobe plot of results from Costello et al. (2016) - https://sfg-ucsb.shinyapps.io/gfr-kobe/
SFG is firmly committed to open and reproducible science. For this reason, we use GitHub, which allows anyone to access our data, check our code, run our models, and validate our results.
For those who are not familiar with GitHub or its companion program, Git, it provides storage space (similar to Dropbox) and includes track-changes capabilities (similar to Microsoft Word). But it also contains other unique features that make it a particularly valuable resource to scientists and researchers. GitHub allows users to host, track, edit, and share scientific content and software code, making it easy for research groups, like ours, to ensure their science is open and reproducible.
If you’re new to Git or GitHub and would like to learn more, there are several helpful tutorials available online. We highly recommend Jenny Bryan’s Happy Git with R website.
As part of our ongoing effort to transfer technical capacity, we have developed a tutorial for using the programming language R for basic fisheries analysis. This tutorial walks users through the process of installing R and points to helpful resources and packages. Furthermore, it teaches users how to manipulate and analyze fisheries data in R, outlining important data management and quality control steps, how to calculate basis statistics like catch-per-unit-effort, and how to make visualizations such as length-frequency histograms and trends in catch.
Nearly 80% of global catch comes from unassessed fisheries. We know very little about these unassessed fisheries, and this lack of information makes it difficult to implement the kinds of science-based management strategies that are needed to ensure the long-term sustainability of fisheries. The data inputs required for conducting traditional stock assessments are commonly unavailable in small-scale fisheries, meaning the majority of these fisheries are unassessed and risk incurring significant ecological, economic, and social losses over time.
Reducing the risk these fisheries face is a big challenge, but SFG is working to close the sustainability gap between the world’s unassessed and assessed fisheries by developing innovative management tools that require fewer data inputs than traditional stock assessments. One such tool is the Adaptive Fisheries Assessment and Management Toolkit (AFAM), a comprehensive decision-support toolkit that combines many of the most common and effective data-limited assessment methods. Each method included in AFAM creatively use different types of data to assess the health of a fishery. The tool itself is a modular, color-coded Microsoft Excel workbook that managers and stakeholders can use to analyze data from their fishery. Users can explore the different techniques built into the tool, and all methods are tied together with a comprehensive framework that guides stakeholders in interpreting results and adaptively implementing tailored fisheries management controls to recover their fishery. SFG has been piloting the toolkit in Belize, Philippines, Indonesia, Brazil, and Mozambique.
Bioeconomic modeling is SFG’s primary tool for forecasting the likely impacts of fisheries and marine conservation management interventions. This forecasting framework combines a biological model of a fish population with an economic model of the fishing fleet that harvests that population. By simulating the characteristics of a fishery, bioeconomic models allow us to predict the likely impacts over time of different management interventions on key outcome indicators like fish abundance in the water, catch, and fishing profits. This type of analysis can be used to evaluate targeted investment strategies (link “targeted investment strategies” to our project page for Forecasting the Impacts of the Vibrant Ocean Initiative), inform the design of more effective management interventions, guide the development of sustainable financing mechanisms for these interventions, and produce global analyses of the likely impacts of large-scale fisheries management reform.
SFG is working with partners from Fish Forever to create TURF-Reserves, which include spatial fishing rights called TURFs (Territorial User Rights Fisheries), and no-take zones (reserves) inside or adjacent to the TURF. Providing exclusive access to coastal fisheries through TURFs is critical; it ensures that local fishermen reap the rewards of being responsible guardians of the sea. Additionally, reserves boost fish productivity while protecting biodiversity. The coupled TURF-Reserve system overcomes the limitations that these approaches face when used in isolation. Because communities have direct ownership over TURFs, they can capture the spillover benefits of well-enforced reserves. These benefits incentivize enforcement and compliance with no-take restrictions. Exclusive access can also be seen as a reward for establishing or enforcing a reserve, creating a clear benefits exchange. This has been demonstrated in many TURFs around the world where fishermen have elected to create reserves within their own TURF. In short, well-designed TURF-Reserve systems help to recover and sustain fish populations, providing conservation, economic, and food security benefits.
With support from Fish Forever partners, including the Sustainable Fisheries Group, students at the University of California, Santa Barbara developed a TURF-reserve design tool, TURFtools, to support TURF-reserve design in small-scale fisheries. TURFtools was developed for data-limited, coastal fisheries, and this easy-to-use tool allows resource managers and communities to compare the expected biological and economic performance of proposed TURF-reserve designs. By forecasting the expected outcomes of a TURF-reserve, communities can make more informed decisions about the optimal size and placement of TURFs and marine reserves.
TURFtools was created in Microsoft Excel, a software program that is familiar to many managers, and can be used offline. The tool was piloted in the Philippines and Brazil, and it will soon be used across all Fish Forever (link “Fish Forever” to Fish Forever project page) sites. TURFtools is a simple mechanism for visualizing TURF-reserve design options, and it provides a way for fishers and communities to be engaged in the spatial planning process. Ultimately, fishing communities can use TURFtools to increase their catch, conserve habitats, and ensure the long-term sustainability of their fisheries.