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A Geostatistical Definition of Hotspots for Fish Spatial Distributions ArchiMer
Petitgas, Pierre; Woillez, Mathieu; Doray, Mathieu; Rivoirard, Jacques.
Research surveys at sea are undertaken yearly to monitor the distribution and abundance of fish stocks. In the survey data, a small number of high fish concentration values are often encountered, which denote hotspots of interest. But statistically, they are responsible for important uncertainty in the estimation. Thus understanding their spatial predictability given their surroundings is expected to reduce such uncertainty. Indicator variograms and cross-variograms allow to understand the spatial relationship between values above a cutoff and the rest of the distribution under that cutoff. Using these tools, a “top” cutoff can be evidenced above which values are spatially uncorrelated with their lower surroundings. Spatially, the geometric set...
Tipo: Text Palavras-chave: Hotspots; Indicators; Non-linear geostatistics; Multivariate geostatistics; Anchovy; Biscay.
Ano: 2016 URL: http://archimer.ifremer.fr/doc/00273/38380/36734.pdf
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A geostatistical method for assessing biomass of tuna aggregations around moored fish aggregating devices with star acoustic surveys ArchiMer
Doray, Mathieu; Petitgas, Pierre; Josse, E.
Universal kriging was used to model the spatio-temporal variability in the acoustic density of tuna aggregations recorded during star echosounding surveys around moored fish aggregating devices (FADs) in Martinique (Lesser Antilles). The large-scale deterministic drift in the tuna spatial distribution was modeled using an advection-diffusion equation applied to animal grouping. Residuals from the drift were modeled as a random component with small-scale spatial correlation. An estimation variance formula was derived from this deterministic-statistical mixed model to assess the mean precision of density estimates of daytime tuna aggregation. The mean relative error obtained with our star design for daytime surveys was 24%. The methodology was applied to...
Tipo: Text Palavras-chave: Acoustic survey precision; Advection diffusion model; Moored fish aggregating devices; Tuna; Geostatistics.
Ano: 2008 URL: http://archimer.ifremer.fr/doc/2008/publication-4559.pdf
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A method for controlled target strength measurements of pelagic fish, with application to European anchovy ( Engraulis encrasicolus ) ArchiMer
Doray, Mathieu; Berger, Laurent; Le Bouffant, Naig; Coail, Jean-yves; Vacherot, Jean-philippe; De La Bernardie, Xavier; Moriniere, Pierre; Lys, Elisabeth; Schwab, Romain; Petitgas, Pierre.
Measuring fish target strength (TS) in the wild is challenging because: (i) TS varies versus physical (orientation relative to the incident sound wave, size, and depth) and physiological fish attributes (maturity and condition), (ii) the target species and its aforementioned attributes are difficult to assess in near real time, and (iii) in the case of packed fish schools, accepted echoes may originate from multiple unresolved targets. We propose a method for controlled TS measurements of densely packed small pelagic fish during daytime, based on the joint use of a Remotely Operated Towed Vehicle, “EROC”, with a pelagic trawl fitted with a codend opening system, “ENROL”. EROC, equipped with a 70-kHz split-beam echosounder (Simrad EK60) and a low-light...
Tipo: Text Palavras-chave: Acoustics; Deformed cylinder model; Engraulis encrasicolus; Remotely operated vehicle; Target strength; Video.
Ano: 2016 URL: http://archimer.ifremer.fr/doc/00346/45693/45623.pdf
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Acoustic characterisation of pelagic fish aggregations around moored fish aggregating devices in Martinique (Lesser Antilles) ArchiMer
Doray, Mathieu; Josse, Erwan; Gervain, Paul; Reynal, Lionel; Chantrel, Josselin.
Sea cruises were conducted for 57 days over 16 months to characterise pelagic fish aggregations around 2 moored fish aggregating devices (FADs) in Martinique (Lesser Antilles). Echosounder surveys run in a star pattern were used in conjunction with obliquely beamed sonar observations. An echo-integration-by-shoal algorithm was implemented to isolate pelagic fish shoals from sound scattering layers and to compute mean morphometric, positional and density parameters. Tree regressions were used to select and classify pelagic fish Target Strengths (TS), with reference to their spatial and temporal characteristics. The main type of pelagic fish aggregation was a large sub-surface aggregation. It was observed during all daytime periods within a radius of 400 m...
Tipo: Text Palavras-chave: Lesser Antilles; Tuna; Large pelagic fish; Aggregative behaviour; Shoal density; Target Strength; Acoustics; Fish Aggregating Device.
Ano: 2006 URL: http://archimer.ifremer.fr/doc/2006/publication-1734.pdf
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Age and growth of blackfin tuna (Thunnus atianticus) caught under moored fish aggregating devices, around Martinique Island ArchiMer
Doray, Mathieu; Stequert, Bernard; Taquet, Marc.
Daily growth increments measured in the otolith of Thunnus atlanticus were used to estimate the age and growth of individuals. which were sampled from an artisanal fishery operating around fish aggregating devices (FADs) moored off Martinique Island. In this study, 76 otoliths were analysed for fish ranging from 20 to 68 cm fork lengths (FL). The fish were caught using trolling lines at depths ranging from 0 to 10 m. Counts were made, under a light microscope, on the external part of the transverse section of the sagittae, from the primordium to the ventral edge. The mean coefficient of variation of the age reading was 2.4%. To validate readings, the number of increments for 11 individuals was counted using both optic and scanning electron microscopes. The...
Tipo: Text Palavras-chave: Thunnus atlanticus; Daily increment; Otolith; Age.
Ano: 2004 URL: http://archimer.ifremer.fr/doc/2004/publication-396.pdf
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Caractérisation de la réponse acoustique individuelle des clupéidés du golfe de Gascogne: le projet TOMOFISH ArchiMer
Le Cornec, Gilles; Doray, Mathieu.
The TOMOFISH project aims at modelling the acoustic Target Strength of Biscay anchovy and sardine, based on 3D swimbladder morphologies obtained by micro-tomography. This report presents the methods and results of the biological sampling conducted during the PELGAS2014 cruise.
Tipo: Text
Ano: 2014 URL: http://archimer.ifremer.fr/doc/00210/32128/30584.pdf
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Characterization of sound scattering layers in the Bay of Biscay using broadband acoustics, nets and video ArchiMer
Blanluet, Arthur; Doray, Mathieu; Berger, Laurent; Romagnan, Jean-baptiste; Le Bouffant, Naig; Lehuta, Sigrid; Petitgas, Pierre.
Sound scattering layers (SSLs) are observed over a broad range of spatio-temporal scales and geographical areas. SSLs represent a large biomass, likely involved in the biological carbon pump and the structure of marine trophic webs. Yet, the taxonomic composition remains largely unknown for many SSLs. To investigate the challenges of SSL sampling, we performed a survey in a small study area in the Northern Bay of Biscay (France) by combining broadband and narrowband acoustics, net sampling, imagery and video recordings. In order to identify organisms contributing to the observed SSLs, we compared measured frequency spectra to forward predicted spectra derived from biological data. Furthermore, to assess the confidence in SSL characterization, we evaluated...
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Ano: 2019 URL: https://archimer.ifremer.fr/doc/00588/70035/67955.pdf
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Converting RAW data into HAC format using HERMES. Tutorial ArchiMer
Berger, Laurent; Doray, Mathieu.
In this tutorial, you will learn how to convert hydro-acoustic data in Simrad .raw format into HAC international format (McQuinn et al., 2005).
Tipo: Text
Ano: 2019 URL: https://archimer.ifremer.fr/doc/00487/59837/62982.pdf
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Data products for fish stocks and ecosystem assessment:the PELGAS survey example ArchiMer
Doray, Mathieu; Petitgas, Pierre; Romagnan, Jean-baptiste; Huret, Martin; Duhamel, Erwan; Dupuy, Christine; Spitz, Jérôme; Berger, Laurent; Dorémus, Ghislain; Bourriau, Paul; Grellier, Patrick; Massé, Jacques; Sanchez, Florence.
The initial objective of the PELGAS integrated survey was to assess the biomass of small pelagic fish in the Bay of Biscay in spring. Sampling has been extended to study the spatial structure and dynamics of the pelagic ecosystem in springtime. The PELGAS survey has produced since 2000 long-term time-series of spatially-explicit data and indices, describing the main pelagic ecosystem components: hydrology, phytoplankton, mesozooplankton, fish and megafauna. In addition to small pelagic fish biomass estimates used for fish stock assessment, the survey now delivers two types of ecosystem products: standard gridded maps of ecosystem parameters, and a time series dataset of indicators of the Bay of Biscay pelagic ecosystem state. The evolution of the PELGAS...
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Ano: 2018 URL: http://archimer.ifremer.fr/doc/00457/56844/58693.pdf
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Decadal stability in top predator habitat preferences in the Bay of Biscay ArchiMer
Lambert, C.; Authier, M.; Doray, Mathieu; Doremus, G.; Spitz, J.; Ridoux, V..
Most oceanographic systems, especially shelf ecosystems, are characterised by interannual variability in the timing, extent and intensity of their seasonal patterns. Such interannual variations have important consequences on top predator habitat preferences. Capitalising on oceanographic surveys performed every spring since 2004 in the Bay of Biscay (BoB), this study explored interannual variations in habitat preferences exhibited by five mobile top predator species: bottlenose and common dolphins, auks, fulmars and northern gannets. We expected to find species with similar habitat preferences every year or species exhibiting important variability in their habitat preferences. First, we identified with a Principal Component Analysis (PCA) three different...
Tipo: Text Palavras-chave: Habitat preference; Temporal variability; Cetaceans; Seabirds; North Atlantic; Bay of Biscay.
Ano: 2018 URL: https://archimer.ifremer.fr/doc/00431/54226/55549.pdf
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Direct assessment of small pelagic fish by the PELGAS13 acoustic survey ArchiMer
Duhamel, Erwan; Doray, Mathieu; Huret, Martin; Doremus, Ghislain; Pengrech, Alexis.
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Ano: 2013 URL: http://archimer.ifremer.fr/doc/00157/26825/24937.pdf
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Direct assessment of small pelagic fish by the PELGAS14 acoustic survey ArchiMer
Duhamel, Erwan; Doray, Mathieu; Huret, Martin; Authier, Matthieu; Gestin, Thomas.
Acoustic surveys are carried out every year in the Bay of Biscay in spring onboard the French research vessel Thalassa. The objective of PELGAS surveys is to study the abundance and distribution of pelagic fish in the Bay of Biscay. The main target species are anchovy and sardine but they are considered in a multi-specific context and within an ecosystemic approach as they are located in the centre of pelagic ecosystem.
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Ano: 2014 URL: http://archimer.ifremer.fr/doc/00209/32018/30455.pdf
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Direct assessment of small pelagic fish by the PELGAS15 acoustic survey ArchiMer
Duhamel, Erwan; Doray, Mathieu; Huret, Martin; Sanchez, Florence; Authier, Matthieu; Bergot, Patricia.
The Pelgas15 acoustic survey has been carried out with globally good weather conditions (regular low wind, medium temperatures) for the whole area, from the South of the bay of Biscay to the west of Brittany. The help of commercial vessels (two pairs of pelagic trawlers and a single one) during 18 days provided about 130 valid identification hauls instead of about 50 before 2007 when Thalassa was alone to identify echotraces. Their participation increased the precision of identification of echoes and some double hauls permitted to confirm that results provided by the two types of vessels (R/V and Fishing boats) were comparable and usable for biomass estimate purposes. These commercial vessels participated to the PELGAS survey in a very good spirit of...
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Ano: 2015 URL: http://archimer.ifremer.fr/doc/00278/38972/37513.pdf
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Direct assessment of small pelagic fish by the PELGAS16 acoustic survey ArchiMer
Duhamel, Erwan; Doray, Mathieu; Huret, Martin; Sanchez, Florence; Lespagnol, Patrick; Doremus, Ghislain; Lemerre, Charlotte.
The Pelgas16 acoustic survey has been carried out with very good weather conditions (regular low wind, medium temperatures) for the whole area, from the South of the bay of Biscay to the west of Brittany. The help of commercial vessels (two pairs of pelagic trawlers and a single one) during 18 days provided about 120 valid identification hauls instead of about 60 before 2007 when Thalassa was alone to identify echotraces. Their participation increased the precision of identification of echoes and some double hauls permitted to confirm that results provided by the two types of vessels (R/V and Fishing boats) were comparable and usable for biomass estimate purposes. These commercial vessels participated to the PELGAS survey in a very good spirit of...
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Ano: 2016 URL: http://archimer.ifremer.fr/doc/00344/45546/45157.pdf
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Direct assessment of small pelagic fish by the PELGAS17 acoustic survey ArchiMer
Duhamel, Erwan; Doray, Mathieu; Huret, Martin; Sanchez, Florence; Lespagnol, Patrick; Doremus, Gislain; Le Bourdonnec, Pierre.
An acoustic survey (PELGAS) is carried out every year in the Bay of Biscay in spring onboard the French research vessel Thalassa. The objective of PELGAS survey is to study the abundance and distribution of pelagic fish in the Bay of Biscay. The main target species are anchovy and sardine but they are considered in a multi-specific context and within an ecosystemic approach as they are located in the centre of pelagic ecosystem. The Pelgas17 acoustic survey has been carried out with medium weather conditions (regular wind, low atmospheric temperatures) for the whole area, from the South of the bay of Biscay to the west of Brittany. The help of commercial vessels (two pairs of pelagic trawlers and a single one) during 18 days provided about 110 valid...
Tipo: Text
Ano: 2017 URL: http://archimer.ifremer.fr/doc/00398/50903/51674.pdf
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Direct assessment of small pelagic fish by the PELGAS18 acoustic survey ArchiMer
Duhamel, Erwan; Doray, Mathieu; Huret, Martin; Sanchez, Florence; Marie-lepoittevin, Theodore; Peltier, Hélène; Autthier, Matthieu.
An acoustic survey (PELGAS) is carried out every year in the Bay of Biscay in spring onboard the French research vessel Thalassa. The objective of PELGAS survey is to study the abundance and distribution of pelagic fish in the Bay of Biscay. The main target species are anchovy and sardine but they are considered in a multi-specific context and within an ecosystemic approach as they are located in the centre of pelagic ecosystem.
Tipo: Text
Ano: 2018 URL: https://archimer.ifremer.fr/doc/00465/57653/59845.pdf
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EchoR package tutorial ArchiMer
Doray, Mathieu.
EchoR is a R statistical software package aiming at: i) handling pre-processed fisheries acoustics data collected during sea surveys, and ii) computing standard ec(h)osystemic indicators based on those fisheries acoustics data. This tutorial gives examples of EchoR capacities.
Tipo: Text
Ano: 2013 URL: http://archimer.ifremer.fr/doc/00128/23879/21814.pdf
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Ecosystem spatial structure revealed by integrated survey data ArchiMer
Petitgas, Pierre; Huret, Martin; Dupuy, Christine; Spitz, Jerome; Authier, Matthieu; Romagnan, Jean-baptiste; Doray, Mathieu.
Integrated marine survey series such as PELGAS provide comprehensive geo-referenced data over large sea areas in major ecosystem components with defined biological resolution and spatio-temporal sampling scale. These data enable to develop product at different levels of biological organization and spatial scale that are useful for ecosystem integrated assessments. Using the PELGAS integrated data series, we applied a generic procedure made of several steps to identify and map ecologically coherent ecosystem spatial units in the Bay of Biscay. First, the data were interpolated on a common spatial grid and organized as a time series of matrices containing at each time the variables as columns and the grid cell values as rows. The multi-table analysis method...
Tipo: Text Palavras-chave: Integrated surveys; Ecosystems; Spatial structure; Multi-factor analysis; Bay of Biscay; Pelagic.
Ano: 2018 URL: https://archimer.ifremer.fr/doc/00403/51402/51977.pdf
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Effect of Target Strength equation selection on PELGAS anchovy and sardine biomass estimates ArchiMer
Doray, Mathieu.
Knowledge of the acoustic response of single fish (or Target Strength: TS) is of prime importance for acoustic target classification and abundance estimation. This report investigates the effect of TS~length equation selection on the anchovy and sardine biomass estimates derived from PELGAS acoustic and fishing survey data. We aim at assessing the respective effects of b20 and depth correction terms on anchovy biomass acoustic estimates derived from the PELGAS survey, in order to evaluate the magnitude of a potential non linear effect of fish depth on acoustic biomass estimates. The PELGAS 2012, 2014, 2015 and 2016 survey data are re-analysed using several TS equations with different b20 values and/or depth correction terms to assess the respective effects...
Tipo: Text
Ano: 2016 URL: https://archimer.ifremer.fr/doc/00377/48839/49265.pdf
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Estimating gear efficiency in a combined acoustic and trawl survey, with reference to the spatial distribution of demersal fish ArchiMer
Doray, Mathieu; Mahevas, Stephanie; Trenkel, Verena.
Few analyses have been performed to estimate the efficiency of trawls targeting demersal fish using the ratio of catches and acoustic densities. In summer 2006, acoustic and fishing data were collected simultaneously over 3 d by three fishing vessels equipped with identical pelagic trawls in the Bay of Biscay. Variography identified moderate spatial autocorrelation in the acoustic backscatter at a mean scale of 3 km, a scale slightly smaller than the mean haul length (3.5 km), indicating that fish horizontal availability did not influence trawl efficiency. Acoustic backscattering densities expressed as nautical area scattering coefficients (NASCs) recorded in the trawled layer were compared with equivalent NASC (ENASC) values calculated from the species...
Tipo: Text Palavras-chave: Availability; Bay of Biscay; Catchability; Generalized linear model; Geostatistics; Hake; Vulnerability.
Ano: 2010 URL: http://archimer.ifremer.fr/doc/00002/11372/7980.pdf
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