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Gowen, R. J., Collos, Y., Tett, P., Scherer, C., Bec, B., Abadie, E., et al. (2015). Response of diatom and dinoflagellate lifeforms to reduced phosphorus loading: A case study in the Thau lagoon, France. Estuarine, Coastal and Shelf Science, , 45–52.
Résumé: The basin of Thau in southern France is a shallow, weakly flushed lagoon which is an important location for oyster cultivation. Phytoplankton analyses were carried out in 1975–1976 and then (almost) continuously since 1987. We report an investigation of ‘the balance of organisms’ in phytoplankton in relation to reductions in phosphorus loading, using two new tools based on phytoplankton lifeforms: the Plankton Index for Phytoplankton (PIp); Euclidean distance in statespace. Our results show the utility of the tools for analysing changes in the ‘balance of organisms’ at the level of functional groups (in our study diatoms and dinoflagellates), but also illustrate the difficulties in demonstrating the reversal of human impacts resulting from eutrophication. The comparison between 1987–89 and 1976 showed the expected ‘deeutrophication’ due to the reduction in dissolved inorganic phosphate (DIP), with a decrease in dinoflagellate abundance. Since 1989, yeartoyear variation in annual mean concentrations of DIP may have contributed to interannual variability in the balance of the two lifeforms, but the data suggest that the system has remained in a dynamically stable regime because: (1) there was no longterm trend in Euclidean distance from the reference; and (2) there was no increase in interannual variability about the timeseries mean Euclidean distance suggesting there has been no decrease in resilience which might signal a regime change. Integrated management of human activities will be required to manage (and reduce) total P in the system. Monitoring phytoplankton and nutrients concentrations to determine how primary production and the balance of species respond to further changes in the nutrient status of the lagoon should be an integral part of any management programme.
MotsClés: Euclidean distance; eutrophication; lifeform; phosphorus; statespace; Thau lagoon

Robert, M., Faraj, A., McAllister, M. K., & Rivot, E. (2010). Bayesian statespace modelling of the De Lury depletion model : strengths and limitations of the method, and application to the Moroccan octopus fishery. Ices Journal of Marine Science, 67, 1272–1290.
Résumé: The strengths and limitations of a Bayesian statespace modelling framework are investigated for a De Lury depletion model that accommodates two recruitment pulses per year. The framework was applied to the Moroccan fishery for common octopus ( Octopus vulgaris) between 1982 and 2002. To allow identifiability, natural mortality ( M) and the recruitment rhythm were fixed, and the variance of both process and observation errors were assumed to be equal. A simulationestimation ( SE) approach was derived to test the performance of the method. If the data showed responses to harvest, the estimates of the most important figures, i.e. the initial abundance and the second recruitment pulse, were accurate, with relatively small bias. Results confirm that greater depletion yields smaller bias and uncertainty and that inferences are sensitive to the misspecification of M. The 21 depletion series in the Moroccan dataset were jointly treated in a hierarchical model including random walk to capture the systematic fluctuations in estimates of catchability and initial abundance. The model provides estimates of the annual recruitment and monthly octopus population size. The recruitment estimates could be used to investigate the link between recruitment variability and the coastal North African upwelling regime to improve understanding of the dynamics and management of octopus stocks.
MotsClés: Bayesian; De; depletion; hierarchical; Lury; Mcmc; model; modelling; octopus; recruitment; statespace

Walker, E., & Bez, N. (2010). A pioneer validation of a statespace model of vessel trajectories (VMS) with observers' data. Ecological Modelling, 221, 2008–2017.
Résumé: In the context of the expansion of animal tracking and biologging, statespace models have been developed with the objective to characterise animals' trajectories and to understand the factors controlling their behaviour. In the fisheries community, the electronic tagging of vessels commonly designated by Vessel Monitoring Systems (VMS) is developing and provides a new insight for the understanding, the analysis and the modelling of the trajectories of vessels and their prospecting behaviour. VMS data are thus a clue for the proper definition of fishing effort which remains a fundamental parameter of tuna stock assessments. In this context, we used the VMS (recording of hourly positions) of the French tropical tuna purseseiners operating in the Indian Ocean to characterise three types of movement (states) on the VMS trajectories (stillness, tracking, and cruising). Based on empirical evidences, and on the regular frequency of VMS acquisition, this was achieved by the development of a Bayesian Hidden Markov model for the speeds and turning angles derived from the hourly steps of the trajectories. In a second phase, states were related to activities disentangling stillness into fishing or stop at sea. Finally the quality of the model performances was rigorously quantified thanks to observers' data. Confronting model prediction and true activities allowed estimating that 10% of the hourly steps were misclassified. The assumptions and model' choices are discussed, highlighting the fact that VMS data and observers' data having different time resolutions, the effective use of validating data was troublesome. However, without validation, these analyses remain speculative. The validation part of this work represents an important step for the operational use of statespace models in ecology in the broad sense (predators' tracking data, e.g. birds or mammals trajectories).
MotsClés: Bayes; data; Markov; model; Monitoring; Observers'; purseseiners; statespace; Systems; Trajectory; Tropical; tuna; Validation; Vessel; (Vms)
