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Registros recuperados: 94
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A bootstrap method for estimating bias and variance in statistical fisheries modelling frameworks using highly disparate datasets ArchiMer
Elvarsson, B. P.; Taylor, L.; Trenkel, Verena; Kupca, V.; Stefansson, G..
Statistical models of marine ecosystems use a variety of data sources to estimate parameters using composite or weighted likelihood functions with associated weighting issues and questions on how to obtain variance estimates. Regardless of the method used to obtain point estimates, a method is required for variance estimation. A bootstrap technique is introduced for the evaluation of uncertainty in such models, taking into account inherent spatial and temporal correlations in the datasets, which are commonly transferred as assumptions from a likelihood estimation procedure into Hessian-based variance estimation procedures. The technique is demonstrated on a real dataset and the effects of the number of bootstrap samples on estimation bias and variance...
Tipo: Text Palavras-chave: Bootstrapping; Correlated data; Fish population dynamics; Non-linear models.
Ano: 2014 URL: http://archimer.ifremer.fr/doc/00193/30459/29913.pdf
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A certain stability in topics and a highly connected community. Text mining of acoustic symposia abstracts ArchiMer
Trenkel, Verena.
In this poster I will present the results from text mining analyses of the abstracts of the current and previous ICES acoustic symposia as well as WGFAST working group reports. By creating and comparing lists of the most common words in each symposium and WGFAST reports it will be possible to measure the overall change in breadth and possible shifts in focus in the field of marine ecosystem acoustics. The same analysis will also identify the contribution of WGFAST to the progress in the field. An analysis of the authors will provide means to characterize the structure of the research fellow communities participating in ICES acoustic symposia and WGFAST meetings.
Tipo: Text
Ano: 2015 URL: https://archimer.ifremer.fr/doc/00598/71042/69352.pdf
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A fisheries acoustic multi-frequency indicator to inform on large scale spatial patterns of aquatic pelagic ecosystems ArchiMer
Trenkel, Verena; Berger, Laurent.
Fisheries acoustic instruments provide information on four major groups in aquatic ecosystems: fish with and without swim bladder (tertiary and quaternary consumers), fluidlike zooplankton (secondary consumers) and small gas bearing organisms such as larval fish and phytoplankton (predominantly primary producers). We entertain that this information is useable to describe the spatial structure of organism groups in pelagic ecosystems. The proposal we make is based on a multi-frequency indicator that synthesises in a single metric the shape of the acoustic frequency response of different organism groups, i.e. the dependence of received acoustic backscattered energy on emitting echosounder frequency. We demonstrate the development and interpretation of the...
Tipo: Text Palavras-chave: Acoustics; Frequency response curve; Monitoring; EOF; Ecosystem state.
Ano: 2013 URL: http://archimer.ifremer.fr/doc/00128/23886/21848.pdf
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A framework for evaluating management plans comprehensively ArchiMer
Trenkel, Verena; Rochet, Marie-joelle; Rice, Jake C..
We present a framework for evaluating fisheries management plans comprehensively, both rebuilding plans and others. The framework includes a first rapid appraisal of the likelihood that the plan will result in management meeting its objectives, and guides subsequent quantitative analyses of potential weaknesses in the proposed plan. The framework includes four steps: (i) evaluating if a set of management objectives, if achieved, would result in a sustainable fishery, (ii) using qualitative analysis of a bio-economic model to evaluate whether the set of stock management tactics might be capable of achieving the specified fisheries objectives, (iii) using empirical criteria derived from the literature to evaluate if other management measures in the plan...
Tipo: Text Palavras-chave: Loop analysis; Management strategy; Management strategy evaluation; Qualitative modelling; Stock rebuilding; Sustainability.
Ano: 2015 URL: http://archimer.ifremer.fr/doc/00198/30931/29363.pdf
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A framework for qualitatively evaluating management plans in a results-based perspective ArchiMer
Rochet, Marie-joelle; Trenkel, Verena; Rice, Jake.
Currently many multi-year management plans are being developed either for rebuilding depleted stocks or for avoiding difficult negotiations when management decisions must be revisited on a regular basis. Management plans are commonly evaluated by intensive model simulations that describe the ecological and economic dynamics, and the management loop. Under the results-based management paradigm, the fishing industry or particular fishing sectors will develop their own management plans, potentially leading to a huge number of plans to be evaluated. Guidelines for evaluating the plans on a qualitative level before launching quantitative evaluations will be essential. Here we propose a framework for evaluating management strategies in a qualitative way. A...
Tipo: Text
Ano: 2010 URL: http://archimer.ifremer.fr/doc/00029/13988/11166.pdf
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A future for marine fisheries in Europe (Manifesto of the Association Francaise d'Halieumetrie) ArchiMer
Gascuel, D.; Bez, Nicolas; Forest, Andre; Guillotreau, P.; Laloe, F.; Lobry, Jeremy; Mahevas, Stephanie; Mesnil, Benoit; Rivot, Etienne; Rochette, S.; Trenkel, Verena.
We, members of the Association Francaise d'Halieumetrie, share the conviction that European fisheries have a future. It is time to get off the wrong track. Radical change is required to embark on the path of sustainable development and truly implement the ecosystem approach to fisheries. Today, high fishing pressure is deployed to catch a rare resource, which in return is responsible for the rarity. We must reverse the situation: an abundant resource that affords high catches applying moderate fishing pressure. All management tools and especially all actors must be mobilized. The transition is not simple, and European solidarity must accompany the changes. It is well worth the effort. By reducing fishing pressure, it will be possible in the medium term to...
Tipo: Text Palavras-chave: Access regulation; Ecosystem approach to fisheries; European Common Fishery Policy; ITQ; MPA; MSY; Management plan; Overcapacity; Subsidies.
Ano: 2011 URL: http://archimer.ifremer.fr/doc/00035/14598/11947.pdf
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A method for reducing uncertainty in estimates of fish-school frequency response using data from multifrequency and multibeam echosounders ArchiMer
Berger, Laurent; Poncelet, Cyrille; Trenkel, Verena.
Fish schools can be insonified simultaneously with multifrequency echosounders (e.g. Simrad EK60s) and a multibeam echosounder (e.g. Simrad ME70). This paper presents a method for combining these data to improve estimates of the relative frequency response r(f) of fish schools. Values of r(f) are now commonly used to classify echoes in fishery surveys. The data from the roll- and pitch-stabilized, high-resolution ME70 are used to correct beam-width effects in the multifrequency EK60 data. First, knowing the exact position and orientation of the transducers and the position of the vessel, the echoes are placed into a common geographic coordinate system. Then, the EK60 data are rejected if they do not include a significant percentage of the fish school...
Tipo: Text Palavras-chave: Species identification; Scomber scombrus; Sardina pilchardus; Pelagic fish; Acoustics.
Ano: 2009 URL: http://archimer.ifremer.fr/doc/2009/publication-6590.pdf
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A new class of predator prey models with interactions described by thresholds ArchiMer
Trenkel, Verena; Rochet, Marie-joelle; Sari, Tewfik.
There exists an urgent need in fisheries science for simple models for assessing the impact of fishing on the dynamics of fish communities. We present a new class of predator prey models that describe the relationship between predators and their prey by piecewise-linear differential equations. Interactions are governed by threshold values for population abundances. The simplest model has four distinct cases with different asymptotic stable states. The model allows for fishing mortality on both predator and prey. If fishing mortality on either the predator, the prey or both are varied, the system might move to new stable states. The threshold values act as reference points for fishing exploitation, as they indicate a structural change in the predator-prey...
Tipo: Text Palavras-chave: Predator-prey model; Reference points; Differential equations.
Ano: 2004 URL: http://archimer.ifremer.fr/doc/00453/56511/58207.pdf
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A new compilation of stomach content data for commercially-important pelagic fish species in the Northeast Atlantic ArchiMer
Pinnegar, J. K.; Goni, N.; Trenkel, Verena; Arrizabalaga, H.; Melle, W.; Keating, J.; Oskarsson, G..
There is increasing demand for information on predator-prey interactions in the ocean as a result of legislative commitments aimed at achieving sustainable exploitation. However, comprehensive datasets are lacking for many fish species and this has hampered development of multispecies fisheries models and the formulation of effective food-web indicators. This work describes a new compilation of stomach content data for five pelagic fish species (herring, blue whiting, mackerel, albacore and bluefin tuna) sampled across the northeast Atlantic and submitted to the PANGAEA open-access data portal (www.pangaea.de). We provide detailed descriptions of sample origin and of the corresponding database structures. We describe the main results in terms of diet...
Tipo: Text
Ano: 2015 URL: http://archimer.ifremer.fr/doc/00195/30641/29096.pdf
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A random effects population dynamics model based on proportions-at-age and removal data for estimating total mortality ArchiMer
Trenkel, Verena; Bravington, Mark V.; Lorance, Pascal.
Catch curves are widely used to estimate total mortality for exploited marine populations. The usual population dynamics model assumes constant recruitment across years and constant total mortality. We extend this to include annual recruitment and annual total mortality. Recruitment is treated as an uncorrelated random effect, while total mortality is modelled by a random walk. Data requirements are minimal as only proportions-at-age and total catches are needed. We obtain the effective sample size for aggregated proportion-at-age data based on fitting Dirichlet-multinomial distributions to the raw sampling data. Parameter estimation is carried out by approximate likelihood. We use simulations to study parameter estimability and estimation bias of four...
Tipo: Text
Ano: 2012 URL: http://archimer.ifremer.fr/doc/00130/24168/22506.pdf
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A review of fishery-independent assessment models, and initial evaluation based on simulated data ArchiMer
Mesnil, Benoit; Cotter, John; Fryer, Rob J.; Needle, Coby L.; Trenkel, Verena.
Large uncertainties in catch data (officially-reported landings and discards) are undermining the ability of scientific organisations to provide valid management advice based on the conventional approach of analytical stock assessments. There is thus an urgent need to consider alternative tools that do not depend on long series of precise age-structured catch data. This paper presents four fishery-independent assessment models developed under the EU project FISBOAT (Fishery Independent Survey Based Operational Assessment Tools). It also reports on rudimentary tests based on simulated data, using the same data sets and protocol as an evaluation study conducted by the US National Research Council in 1997. The survey-based assessment models at hand are able...
Tipo: Text Palavras-chave: Survey indices; Fishery independent assessment methods (F I methods); Catch free models; Fish stock assessment.
Ano: 2009 URL: http://archimer.ifremer.fr/doc/2009/publication-6902.pdf
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A two-stage biomass random effects model for stock assessment without catches: What can be estimated using only biomass survey indices? ArchiMer
Trenkel, Verena.
A simple two-stage biomass random effects population dynamics model is presented for carrying out fish stock assessments based on survey indices using no commercial catch information. Recruitment and biomass growth are modelled as random effects, reducing the number of model parameters while maintaining model flexibility. No assumptions regarding natural mortality rates are required. The performance of the method was evaluated using simulated data with emphasis on identifying parameter redundancy, which showed that the variance of the biomass growth random effect might only be estimable if large (> 0.2). The full and two nested models were fitted to European anchovy (Engraulis encrasicolus) in the Bay of Biscay using two survey series. The best-fitting...
Tipo: Text Palavras-chave: Survey based assessment; Population state; Random effects.
Ano: 2008 URL: http://archimer.ifremer.fr/doc/2008/publication-4565.pdf
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Analysis of species associations in deep-sea fisheries off the British Isles from an industry haul-by-haul database ArchiMer
Baulier, Loic; Pawlowski, Lionel; Lorance, Pascal; Trenkel, Verena.
Tipo: Text
Ano: 2010 URL: http://archimer.ifremer.fr/doc/00018/12951/9926.pdf
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Assessment of impacts from human activities on ecosystem components in the Bay of Biscay in the early 1990s ArchiMer
Lorance, Pascal; Bertrand, Jacques; Brind'Amour, Anik; Rochet, Marie-joelle; Trenkel, Verena.
The ecosystem-based approach to fisheries management and, more specifically, the European Marine Strategy Framework Directive require the assessment of the state and dynamics of an ecosystem in order to determine suitable management strategies. This paper takes an analytical approach to assess the state of the Bay of Biscay ecosystem in the early 1990s, chosen as a period of reference because key monitoring data series have been collected since then. To assess the state of the ecosystem, the pressures exerted by six broad categories of human activities were examined. A literature review of the ecosystem components was made and a component tree was tailored according to data availability. Data rich components were subdivided into subcomponents for their...
Tipo: Text Palavras-chave: Reference state; Ecosystem based management; Human pressure; Inventory; Atlantic Ocean.
Ano: 2009 URL: http://archimer.ifremer.fr/doc/00000/11164/7520.pdf
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Capacity management, not stock status or economics, drives fleet dynamics in the Bay of Biscay ecosystem on a decadal time scale ArchiMer
Rochet, Marie-joelle; Daures, Fabienne; Trenkel, Verena.
This paper introduces a semiqualitative approach to analyse the joint dynamics of fleets and stocks in a multispecies, multifleet fishery. We ask whether changes in fleets affect resource dynamics and whether trends in resource influence fleet dynamics more than external drivers do. External drivers include vessel buyback, fuel price, and fish prices, as well as environmental fluctuations. Resource status is measured by abundance and length metrics; fleet capacity is measured by total horse power, and economic metrics such as profitability and earnings are examined as well. A maximum likelihood approach is used to identify the combined metric trends with the largest support in the data. The approach is applied to the French Bay of Biscay fisheries in...
Tipo: Text
Ano: 2012 URL: http://archimer.ifremer.fr/doc/00076/18730/16336.pdf
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Censored catch data in fisheries stock assessment ArchiMer
Hammond, T; Trenkel, Verena.
Landings statistics can be lower than true catches because many fish are discarded or landed illegally. Since many discards do not survive, treating landings as true catches can lead to biased stock assessments. This paper proposes treating catch as censored by bounding it below by the landings, L, and above by cL (for scalar c > 1), We demonstrate the approach with a simulation study, using a Schaefer surplus production model. Parameters were estimated in a Bayesian framework with BUGS software using two sets of priors. Both the traditional true-catch method and a survey-and-effort method (which was landings free) performed worse on average than the censored approach, as measured by the Bayes risk associated with estimates of maximum sustainable yield...
Tipo: Text Palavras-chave: Stock assessment; Misreporting; Discarding; Censored data.
Ano: 2005 URL: http://archimer.ifremer.fr/doc/2005/publication-641.pdf
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Changes in Brain Monoamines Underlie Behavioural Disruptions after Zebrafish Diet Exposure to Polycyclic Aromatic Hydrocarbons Environmental Mixtures ArchiMer
Vignet, Caroline; Trenkel, Verena; Vouillarmet, Annick; Bricca, Giampiero; Begout, Marie-laure; Cousin, Xavier.
Zebrafish were exposed through diet to two environmentally relevant polycyclic aromatic hydrocarbons (PAHs) mixtures of contrasted compositions, one of pyrolytic (PY) origin and one from light crude oil (LO). Monoamine concentrations were quantified in the brains of the fish after six month of exposure. A significant decrease in noradrenaline (NA) was observed in fish exposed to both mixtures, while a decrease in serotonin (5HT) and dopamine (DA) was observed only in LO-exposed fish. A decrease in metabolites of 5HT and DA was observed in fish exposed to both mixtures. Several behavioural disruptions were observed that depended on mixtures, and parallels were made with changes in monoamine concentrations. Indeed, we observed an increase in anxiety in fish...
Tipo: Text Palavras-chave: Monoamine; Polycyclic aromatic hydrocarbons; Behaviour; Anxiety; Swimming activity; Zebrafish.
Ano: 2017 URL: https://archimer.ifremer.fr/doc/00375/48578/48900.pdf
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Choosing survey time series for populations as part of an ecosystem approach to fishery management ArchiMer
Trenkel, Verena; Cotter, John.
Ecosystem assessments of fisheries based only on survey data will often have to use surveys that were designed historically for special purposes, e. g. for assessing abundances of two or three target species, or for tuning VPAs. An important question then is whether the previously collected data can provide informative time series of abundance indices and other state indicators for a wider range of target and non-target species. Some potential shortcomings of existing data series are treated in this paper leading to four questions which can guide the user to determine the suitability of an existing time series: did the survey cover the stock of each species adequately? Did survey catchability vary significantly between length or age classes? Did survey...
Tipo: Text Palavras-chave: Bias; Survey based methods; Indicators.
Ano: 2009 URL: http://archimer.ifremer.fr/doc/2009/publication-6900.pdf
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Cluster analysis of linear model coefficients under contiguity constraints for identifying spatial and temporal fishing effort patterns ArchiMer
Mahevas, Stephanie; Bellanger, Lise; Trenkel, Verena.
For fisheries management purposes, it is essential to take into account spatial and seasonal characteristics of fishing activities to allow a reliable assessment of fishing impact on resource. This paper presents a novel technique for describing spatial and temporal patterns in fishing effort. The spatial and seasonal fishing activity patterns of the French trawler fleet in the Celtic Sea during the period 1991–1998 were analysed by modelling fishing effort (fishing time) with generalised linear models. The linear model for fishing effort included fixed effects for both spatial (statistical rectangles) and temporal units (months). In addition, spatial correlations in any given month were modelled by an exponentially decreasing function. Temporal...
Tipo: Text Palavras-chave: Fleet dynamics; Allocation of Fishing effort; Spatial and seasonal pattern; Statistics for spatial data; Cluster analysis under contiguity constraints; Generalised linear model.
Ano: 2008 URL: http://archimer.ifremer.fr/doc/2008/publication-4302.pdf
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Combining indicator trends to assess ongoing changes in exploited fish communities: diagnostic of communities off the coasts of France ArchiMer
Rochet, Marie-joelle; Trenkel, Verena; Bellail, Robert; Coppin, Franck; Le Pape, Olivier; Mahe, Jean-claude; Morin, Jocelyne; Poulard, Jean-charles; Schlaich, Ivan; Souplet, Arnauld; Verin, Yves; Bertrand, Jacques.
We present a method for combining individual indicator results into a comprehensive diagnostic of fishing impacts on fish populations and communities. A conceptual framework for interpreting combined trends in a set of simple indicators is proposed, relying beforehand on qualitative expectations anchored in ecological theory. The initial state of the community is first assessed using published information. Which combinations of trends are acceptable or undesirable is decided, depending on the initial status. The indicators are then calculated from a time-series and their time trends are estimated as the slopes of linear models. Finally, the test results are combined within the predefined framework, providing a diagnostic on the dynamics of fishing impacts...
Tipo: Text Palavras-chave: Scientific surveys; Multispecies fisheries; Indicators; Ecosystem approach to fisheries management.
Ano: 2005 URL: http://archimer.ifremer.fr/doc/2005/publication-773.pdf
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