Showcasing EcoDiet, a novel hierarchical model to combine stomach, biotracer and literature data into diet matrix estimation: simulated and in situ trophic data

Date 2021-06
Author(s) Hernvann Pierre-YvesORCID1, 2, 3, 4, Gascuel DidierORCID2, Kopp DorotheeORCID1, Robert MarianneORCID1, Rivot EtienneORCID2
Affiliation(s) 1 : Ifremer, STH, F-56100, Lorient, France
2 : ESE, Ecology and Ecosystem Health, Institut Agro, INRAE, 35042 Rennes, France
3 : Institute of Marine Sciences, University of California, Santa Cruz, Santa Cruz, CA, United States
4 : Northwest Fisheries Science Center, National Marine Fisheries Service, NOAA, Seattle, WA, United States
DOI 10.17882/81075
Publisher SEANOE
Keyword(s) Ecosystem modeling, Trophic ecology, Food-web topology, Stomach content analyzes, Stable isotope analyzes, Biotracers, Diet matrix, Bayesian integrated model, Mixing Model
Abstract

Quantifying trophic interactions is a critical path to understanding and forecasting ecosystem functioning, but fitting trophic models to field data remains challenging. It requires flexible statistical tools to combine different sources of information from the literature and fieldwork samples. In an article published in Ecological Applications, we present EcoDiet, a hierarchical Bayesian modeling framework to simultaneously estimate food-web topology and diet composition of all consumers in the food web, by combining (i) a priori knowledge from the literature on both food-web topology and diet proportions; (ii) stomach content analyses (SCA), with frequencies of prey occurrence used as the primary source of data to update the prior knowledge on the topological food-web structure; (iii) and biotracers data, notably stable isotope analyses (SIA), through a mixing model. Inferences are derived in a Bayesian probabilistic rationale that quantifies the uncertainty around both the topological structure of the food web and the diet proportions. The present SEANOE dataset makes available the trophic and literature data to which EcoDiet was applied in this publication to assess its performance and demonstrate its ability to deal with real case-studies. On the one hand, it includes the diet matrix and the associated topology matrix describing a simplified but realistic food web, and the SCA and SIA data simulated from these matrices. On the other hand, it displays real in situ SCA and SIA data for most trophic groups of the Celtic Sea food web (collected during EVHOE surveys, EATME project) and a priori topology and diet matrices issued of a bibliographic search (with associated scores characterizing the reliability of the literature information). This SEANOE dataset allows to reproduce the runs of the EcoDiet model conducted as part of the Ecological Applications article.

Licence CC-BY-NC-ND
Acknowledgements This work was part of a PhD funded by IFREMER and Région Bretagne. The EATME project, from which was issued the Celtic Sea in situ trophic data, was supported by France Filière Pêche and Région Bretagne. We thank Guillaume Allanic, Margaux Denamiel, and Dominique Huteau for their help onboard the R/V Thalassa and/or in the laboratory. We thank the Stable Isotopes in Nature Laboratory (SINLAB, New Brunswick, Canada) for having realized stable isotope analyses.
Sensor metadata

The EcoDiet model used in Hernvann et al. (2021) was run in R under the Version 1.0.0.0. It can be directly downloaded from the R CRAN repository (https://CRAN.R-project.org/package=EcoDiet) or downloaded from GitHub, where the code is made available (https://github.com/pyhernvann/EcoDiet). To facilitate the run of the model on the data used in (Hernvann et al. 2021), we chose to directly provide it as .RData files. Moreover, two separate .html files are provided to guide step-by-step the application of EcoDiet to simulated and real in situ data.

Simplified food web and simulated trophic data:

  • readme_simplified_foodweb.html - helps applying EcoDiet to the datasets in simulated_data.RData
  • true_data.RData - contains:
    • Topo_true: the true topology matrix of the simplified food web
    • Diets_true: the true diet matrix of the simplified food web
  • simulated_data.RData - contains:
    • SCA_data: 10 replicates of simulated stomach content analyzes (occurrences) datasets for the trophic groups of the simplified food web
    • SIA_data: one dataset of simulated stable isotope analyzes (carbon and nitrogen) for the trophic groups of the simplified food web

Real in situ and literature information:

  • readme_Celtic_Sea_data.html - helps applying EcoDiet to the datasets in CelticSea_data.RData
  • Celtic_Sea_data.RData - contains:
    • SCA_CelticSea: stomach content analyzes (occurrences) for troophic groups of the Celtic Sea food web
    • SIA_CelticSea: stable isotope analyzes (carbon and nitrogen) for trophic groups of the Celtic Sea food web
    • Literature_CelticSea: diet matrix issued of the bibliographic search on the diets of Celtic Sea species
Data
File Size Format Processing Access
true_data 2 KB .RData Processed data Open access
simulated_data 100 KB .RData Processed data Open access
Celtic_Sea_data 59 KB .RData Processed data Open access
readme_simplified_foodweb 738 KB .html Open access
readme_Celtic_Sea_data 2 MB .html Open access
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How to cite 

Hernvann Pierre-Yves, Gascuel Didier, Kopp Dorothee, Robert Marianne, Rivot Etienne (2021). Showcasing EcoDiet, a novel hierarchical model to combine stomach, biotracer and literature data into diet matrix estimation: simulated and in situ trophic data. SEANOE. https://doi.org/10.17882/81075