The new R-package Bfiat (Soetaert and Beauchard, 2024), developed by NIOZ, includes a mechanistic model that predicts the state of benthic species during and following trawling disturbance. Trawling disturbance is described as an instantaneous reduction of species density, the extent of which depends on the overlap of the species living depth with the gear. Subsequent recovery is predicted according to the logistic population growth model, the recovery rate estimated from the species’ age at maturity. The observed species densities in a region are used to estimate the species carrying capacity.
Model applications combine existing data sets on organism densities with organism functional traits and fishing parameters.
To install the R-package Bfiat, one needs the Btrait R-package (Soetaert and Beauchard, 2023), previously published in the frame of EMODnet Biology Phase V. Together these two packages also contain several datasets (from EMODnet and other sources, e.g. Beauchard et al., 2021) that serve to exemplify the use of the modelling tools.
The new R-package is fully accessible through the EMODnet github repository (https://github.com/EMODnet/Bfiat) from where one can download the software, and that contains information on how to install the R-package.
A github webpage is at (https://emodnet.github.io/Bfiat), where users can inspect the functions that are included in the R-package and where a number of tutorials (so-called package vignettes) can be downloaded. The main tutorial (https://emodnet.github.io/Bfiat/articles/Bfiat) explains how to use the many functions of the new R-package, together with the functions of the R-package Btrait. Two other tutorials provide a real-life application from the Dutch continental waters, estimating the impact of trawling on the macrofauna density (https://emodnet.github.io/Bfiat/articles/MWTL.html), and on ecosystem functioning (https://emodnet.github.io/Bfiat/articles/MWTL_EF.html).
The set of tools in the two R-packages (Btrait and Bfiat) provide an opportunity to use the EMODnet Biology datasets to explore anthropogenic impacts (i.c. bottom trawling) on benthic life. The EMODnet repository, rich in benthos data, will therefore greatly facilitate the use of the new tools for research, policy, and management applications.
References:
Karline Soetaert, Olivier Beauchard (2023). R-package Btrait: Working with Biological density, taxonomy, and trait composition data. Data product created under the European Marine Observation Data Network (EMODnet) Biology Phase IV. https://github.com/EMODnet/Btrait
Karline Soetaert, Olivier Beauchard (2024). R-package Bfiat: Tools for estimating the impact of bottom disturbance on sediment ecosystems. Data product created under the European Marine Observation Data Network (EMODnet) Biology Phase V, and under the NECCTON project (New Copernicus Capability for Trophic Ocean Networks).
Olivier Beauchard, Kari Elsa Ellingsen, Murray S.A. Thompson, Gerjan Piet, Pascal Laffargue, Karline Soetaert, 2023. Assessing sea floor functional diversity and vulnerability. Marine Ecology Progress Series, 708, 21-43. DOI: https://doi.org/10.3354/meps14270, DOI:10.3354/meps14270
“The EMODnet repository, rich in benthos data, will greatly facilitate the use of the new toolbox for research, policy, and management applications”.
Dr. pr. Karline Soetaert, Head of department, NIOZ Royal Netherlands Institute for Sea Research