October 2017 MAINE COASTAL NEWS Page 13. Commercial Fishing News


lowed with a similar moratorium in federal waters.


Leveling Up: Improving EBFM with Rpath, an R Implementation of Ecopath with Ecosim (EwE)


Scientists from the Northeast Fisheries Science Center (NEFSC) and others helped organize and facilitate a 2017 American Fisheries Society (AFS) symposium on advancing fi sheries management strategy evaluation (MSE). Sean Lucey, fi sheries biologist at NEFSC, presented his collab- orative work on linking multiple Ecopath models using Rpath at the symposium. This feature story is an extension of his presenta- tion for AFS participants and those involved in fi sheries science and natural resource management.


Reproducibility, the ability to repeat


another scientist’s research and get the same results, is at the core of science. It gives scientists confi dence in research fi ndings and allows them to build off of each other’s work, advancing both science and society. Scientists at the Northeast Fisheries Sci- ence Center (NEFSC) and Alaska Fisheries Science Center (AFSC) are making repro- ducibility, transparency, and full reporting easier for ecosystem scientists with Rpath, an R implementation of Ecopath with Eco- sim (EwE).


Building a new open source tool About 20 years ago Sarah Gaichas and


Kerim Aydin, fi sheries scientists at NOAA’s Alaska Fisheries Science Center began working on ecosystem model simulations to address management questions. They started with the Windows-based ecosystem simulation software EwE, but found it limiting saying, “the problem was that the Ecosim graphical user interface is a kind of black box where you can’t eff ectively control what simulations were going on.” To gain that control, Aydin fi rst developed an in-house version in Visual Basic, and from there they moved it into C++, a powerful and fairly technical computer programming language. There were complications with the C++ version. “The way it was designed worked for us, but was kind of awful to try to share with other scientists. It had all these other scripts [commands] to do graphics and it was just gigantic and unwieldy.” Desiring a more fl exible and familiar computing framework, the team saw the potential of R and soon began working with Sean Lucey,


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fi sheries biologist at NEFSC to develop Rpath. Rpath builds on the open source nature of Ecopath by allowing users more customization, as well as cross-platform support (Windows, Linux, Macs). Rpath helps solve the reproducibility problem with ecosystem models by containing all steps in a single fi le or script. Lucey and the team re-coded the source code from EwE using a combination of R and C++, allowing users to build and run their models, analyze outputs, and create publication quality graphics without switching programs. “R is much stronger for reproducibility because everything is captured in a script so you can see what changes you’ve made and you can annotate why you made those changes. Those aren’t things you can necessarily do in the EwE graphic user interface (GUI) where you’re just clicking buttons,” says Lucey. This re-coding and development of Rpath was partially funded by NOAA’s Inte- grated Ecosystem Assessment, a program supporting Ecosystem-Based Management by providing the tools that help transfer scientifi c knowledge to management. Connecting the dots With Gaichas now at NEFSC, the


team is currently customizing ecosystem simulation models to address management questions by improving capabilities like modeling diff erent fi sheries simultaneously. Rpath allows the team to see how a scallop management action might aff ect the yellow- tail fl ounder fi shery. “You can see these other connections that you might not see if you’re focused on a single species approach,” says Lucey. Another new area the team is explor- ing with Rpath is testing place-based man- agement strategies. “What ecosystem-based fi sheries management (EBFM) looks to do is be more place-based, meaning we’re managing Georges Bank, not Georges Bank cod. We’re managing Georges Bank based on many of the characteristics of Georges Bank like predator-prey interactions and the production of the area - primary production or prey fi elds - to make a more holistic view of what’s going on in that area rather than by species,” says Lucey. Leveling up Fish and many other marine species


move around and with their movement go a whole host of factors that can aff ect the function and sustainability of a region. “One of the things this particular project does is linking these ecological production


units – regions -- together. Fish don’t care about where you draw lines. So the point is to build a model where you can have biomass leave Georges Bank and go to the Gulf of Maine and vice versa. You need to be able to account for that in the model, especially if you want to test single-species strategies against ecosystem strategies because if you just test for a single-species strategy, you might be doing it for its whole range rather than just one region. You need to account for that biomass at all times,” says Lucey. “That’s the big trick that I’m doing right now, to allow the biomass to fl ow using migration terms in this model.” Biomass transfers between regions will


be relatively small given the annual time step of the model, but it allows the team to see creeps related to global warming over longer periods of time. Distribution shifts result when species move and inhabit areas that they either historically haven’t been found in or haven’t been as abundant in. Recent research by NEFSC scientists and collaborators highlight the projected northward migration of lobster and other species related to thermal habitat. While Lucey can’t directly input environmental factors like water temperature at this time, he can input an attractiveness rating for how “attractive” (e.g., lots of food, great habitat, cooler water temperatures, etc.) or “repul-


sive” (e.g., little food, little habitat, warmer water temperatures, etc.) a place would be for marine species. This rating will allow the team to see the immigration (movement in) and emigration (movement out) of biomass not related to the production and mortality of marine species. “I can’t think of a single Ecopath model that uses immigration and


Continued on Page 20.


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