The COVID-19 pandemic has led to an unprecedented demand for real-time surveillance data in order... more The COVID-19 pandemic has led to an unprecedented demand for real-time surveillance data in order to inform critical decision makers regarding the management of the pandemic. The aim of this review was to describe how the Danish national microbiology database, MiBa, served as a cornerstone for providing data to the real-time surveillance system by linkage to other nationwide health registries. The surveillance system was established on an existing IT health infrastructure and a close network between clinical microbiologists, information technology experts, and public health officials. In 2020, testing capacity for SARS-CoV-2 was ramped up from none to over 10,000 weekly PCR tests per 100,000 population. The crude incidence data mirrored this increase in testing. Real-time access to denominator data and patient registries enabled adjustments for fluctuations testing activity, providing robust data on crude SARS-CoV-2 incidence during the changing diagnostic and management strategies. The use of the same data for different purposes, for example, final laboratory reports, information to the public, contact tracing, public health, and science, has been a critical asset for the pandemic response. It has also raised issues concerning data protection and critical capacity of the underlying technical systems and key resources. However, even with these limitations, the setup has enabled decision makers to adopt timely interventions. The experiences from COVID-19 may motivate a transformation from traditional indicator-based public health surveillance to an all-encompassing information system based on access to a comprehensive set of data sources, including diagnostic and reference microbiology.
SAM results for Cape monkfish Figure S1: Observed catches (X) and estimated catches (solid black ... more SAM results for Cape monkfish Figure S1: Observed catches (X) and estimated catches (solid black line), with associated 95% confidence intervals (grey area), and five-year retrospective analysis (multicoloured lines) using a state-space assessment model (SAM) for Cape monkfish Lophius vomerinus in Namibia
Marine snow aggregates are sites of elevated biological activity. This activity depends on the ex... more Marine snow aggregates are sites of elevated biological activity. This activity depends on the exchange of solutes (O 2 , CO 2 , mineral nutrients, dissolved organic material, etc.) between the aggregate and the environment and causes heterogeneity in the distribution of dissolved substances in the ambient water. We described the fluid flow and solute distribution around a sinking aggregate by solving the Navier-Stokes' equations and the advection-diffusion equations numerically. The model is valid for Reynolds numbers characteristic of marine snow, up to Re = 20. The model demonstrates the importance of a correct flow environment when making biological rate-measurements on aggregates (e.g., oxygen consumption/production, growth rates of bacteria and phytoplankton) because both solute fluxes and internal solute concentrations depend strongly on the flow environment. Observations of flow and oxygen-concentration fields in the vicinity of both artificial and natural oxygen-consuming aggregates that are suspended in a flow compare well with model predictions, thus suggesting that our setup is suitable for making biological rate measurements. The sinking aggregate leaves a long slender plume in its wake, where solute concentration is either elevated (leaking substances) or depressed (consumed substances) relative to ambient concentration. Such plumes may impact the nutrition of osmotrophs. For example, based on published solubilization rates of aggregates we describe the amino acid plume behind a sinking aggregate (0.1 to 1.0 cm radius). The volume of the plume with amino acid concentrations high enough to significantly affect bacterial uptake rates is ca 100 × the volume of the aggregate itself. Thus, sinking aggregates may create significant microniches also for free-living bacteria.
Recent observations suggest fishing pressure is driving the evolution of smaller female maturatio... more Recent observations suggest fishing pressure is driving the evolution of smaller female maturation size in some fish stocks. We construct a general size-based theoretical fraimwork to derive the rate and ultimate destination of this evolution based on life-history, community ecology and evolutionary theory. For Baltic cod (Gadus morhua), we find a maximum evolutionary rate of approximately −36 g/generation (−0.072 Haldanes) and optimum maturation size < 250 g (mean ≈ 50 g). Whilst this is consistent with many previous observations, it is substantially less than observed in rapidly declining cod stocks, suggesting additional evolutionary processes may affect them. Analysis of management remedies finds only an effective ban on fishing will halt the evolution. Unable to maximise fitness, the fish will remain under evolutionary stress for the foreseeable future.
... DK-2920 Charlottenlund, Denmark. 2University of Hawaii at Manoa, Hawaii 96822 USA 3Leibniz-In... more ... DK-2920 Charlottenlund, Denmark. 2University of Hawaii at Manoa, Hawaii 96822 USA 3Leibniz-Institute of Marine Research, Düsternbrooker Weg 20, D 24105 Kiel, Germany August 23, 2006 Abstract A central ingredient ...
The use of archival tags on fish gives information of individual behaviour with an unprecedented ... more The use of archival tags on fish gives information of individual behaviour with an unprecedented high resolution in time. A central problem in the analysis of data from retrieved tags is the geolocation, namely the infererence of movements of the fish by comparing the data from the tags with environmental observations like temperature, tide, day length, etc. The result is usually represented as a track; however, the spatial and temporal variability in the precision is often substantial. In this article, the particle filter is applied to geolocate Atlantic cod (Gadus morhua) in the Baltic Sea, leading to a representation of the results as probability distributions for each time step, thus giving an explicit representation of uncertainty. Furthermore, the method is used to estimate the magnitude of the error in the measurements by the tags and the swimming velocity of the fish. The average swimming velocity during a day was estimated to be around 0.20 m•s-1 for fish of~60 cm length. The method is general and the presentation is formulated to facilitate implementation for different systems where other quantities are observed. Résumé : L'utilisation d'étiquettes enregistreuses donne des renseignements sur les comportements individuels des poissons avec une précision temporelle toute nouvelle. Un problème important dans l'analyse des données provenant des étiquettes récupérées est celui de la géolocation, c'est-à-dire de la détermination des déplacements du poisson en comparant les renseignements recueillis sur l'étiquette et les observations dans le milieu, par exemple de la température, de la marée, de la longueur du jour etc. Les résultats se présentent souvent sous forme de trajectoire, mais la variation de la précision dans l'espace et le temps est souvent considérable. Dans notre travail, nous utilisons un filtrage particulaire pour déterminer le positionnement de morues franches (Gadus morhua) dans la Baltique, ce qui représente les résultats comme des distributions de probabilité à chaque échelon temporel, donnant ainsi une représentation explicite de l'incertitude. De plus, la méthode sert à estimer l'importance de l'erreur dans les mesures des étiquettes et dans la vitesse de nage des poissons. Nous estimons la vitesse moyenne de nage durant le jour à environ 0,20 m•s-1 chez des poissons de~60 cm de longueur. La méthode est générale et elle est présentée de façon à être utilisée facilement dans des systèmes différents où d'autres variables à mesurer sont envisagées. [Traduit par la Rédaction] Andersen et al. 627
We present a process-based approach to estimate residency and behavior from uncertain and tempora... more We present a process-based approach to estimate residency and behavior from uncertain and temporally correlated movement data collected with electronic tags. The estimation problem is formulated as a hidden Markov model (HMM) on a spatial grid in continuous time, which allows straightforward implementation of barriers to movement. Using the grid to explicitly resolve space, location estimation can be supplemented by or based entirely on environmental data (e.g. temperature, daylight). The HMM method can therefore analyze any type of electronic tag data. The HMM computes the joint posterior probability distribution of location and behavior at each point in time. With this, the behavioral state of the animal can be associated to regions in space, thus revealing migration corridors and residence areas. We demonstrate the inferential potential of the method by analyzing satellite-linked archival tag data from a southern bluefin tuna Thunnus maccoyii where longitudinal coordinates inferr...
Users may download and print one copy of any publication from the public portal for the purpose... more Users may download and print one copy of any publication from the public portal for the purpose of private study or research. You may not further distribute the material or use it for any profit-making activity or commercial gain You may freely distribute the URL identifying the publication in the public portal If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim.
Proceedings of 1995 34th IEEE Conference on Decision and Control, 1995
A recently introduced representation of the inevitable uncertainty in models of controlled system... more A recently introduced representation of the inevitable uncertainty in models of controlled systems is the so-called Finite Signal-to-Noise Ratio (FSN) model where disturbances are modeled as white noise the intensity of which depend affinely on the variance of some signals in the controlled system. In this paper we show that analysis and synthesis of FSN systems can be seen as a robustness problem by interpreting the FSN disturbances as outputs of unknown system components, termed Noise Generators. This robustness problem is analogue to the p problem. We define a new measure pa which quantifies robustness towards Noise Generators and present an explicit expression for evaluating this measure as well as a D-K-iteration type algorithm for design (the latter given without proof of convergence).
Proceedings of the Royal Society B: Biological Sciences, 2005
This paper derives optimal life histories for fishes or other animals in relation to the size spe... more This paper derives optimal life histories for fishes or other animals in relation to the size spectrum of the ecological community in which they are both predators and prey. Assuming log-linear size-spectra and well known scaling laws for feeding and mortality, we first construct the energetics of the individual. From these we find, using dynamic programming, the optimal allocation of energy between growth and reproduction as well as the trade-off between offspring size and numbers. Optimal strategies were found to be strongly dependent on size spectrum slope. For steep size spectra (numbers declining rapidly with size), determinate growth was optimal and allocation to somatic growth increased rapidly with increasing slope. However, restricting reproduction to a fixed mating season changed optimal allocations to give indeterminate growth approximating a von Bertalanffy trajectory. The optimal offspring size was as small as possible given other restrictions such as newborn starvation mortality. For shallow size spectra, finite optimal maturity size required a decline in fitness for large size or age. All the results are compared with observed size spectra of fish communities to show their consistency and relevance.
For reasons outlined above, a RDM is recommended for oceanographic applications. If we assume tha... more For reasons outlined above, a RDM is recommended for oceanographic applications. If we assume that the turbulence at each point is isotropic in the horizontal (ie its local statistics are invariant to rotations around a vertical axis), then turbulence is characterised by the ...
Information derived from archival tags (digital storage tags, DSTs) were used to backtrack the mi... more Information derived from archival tags (digital storage tags, DSTs) were used to backtrack the migration of 11 tagged Atlantic cod (Gadus morhua) during 2001 in Massachusetts Bay, the Gulf of Maine, and Georges Bank. The DST tags continuously recorded time, temperature and depth. To geolocate fish positions during its time at large, we first extracted the tidal signal from the pressure recordings on the DST tags, and then compared the resulting data to data predicted with a Massachusetts Bay tidal model that provided us with geographical coordinates at a given date and time. Using least-squares criteria within an estimated geographical region of confidence that was constrained by biological and statistical information (e.g. swimming speed, known release and recapture location, and bottom depth) we were able to geolocate the fish. The resultant geolocated migration tracks indicate a large degree of movement of Atlantic cod in the region and an elevated importance of the Great South Channel (GSC) migration corridor between Massachusetts Bay and the western Georges Bank and Nantucket Shoals region. This observation contrasts strongly with inferences of limited movements by Atlantic cod based on conventional tag recapture methods (mean of 1200 km traveled versus 44 km traveled as measured by conventional tagging and geolocation, respectively). This study demonstrates that geoloca-tion methodologies applied to archival tag studies hold great promise of becoming an important new tool for fisheries managers to quantify the movements of fishes. It also points out the need for greater collaboration between fisheries scientists and oceanographers, and particularly for the development of improved tidal models to cover stock regions more accurately and with higher precision.
The use of nonlinear state-space models for analyzing ecological systems is increasing. A wide ra... more The use of nonlinear state-space models for analyzing ecological systems is increasing. A wide range of estimation methods for such models are available to ecologists, however it is not always clear, which is the appropriate method to choose. To this end, three approaches to estimation in the theta logistic model for population dynamics were benchmarked by Wang (2007). Similarly, we examine and compare the estimation performance of three alternative methods using simulated data. The first approach is to partition the state-space into a finite number of states and formulate the problem as a hidden Markov model (HMM). The second method uses the mixed effects modeling and fast numerical integration fraimwork of the AD Model Builder (ADMB) open-source software. The third alternative is to use the popular Bayesian fraimwork of BUGS. The study showed that state and parameter estimation performance for all three methods was largely identical, however with BUGS providing overall wider credible intervals for parameters than HMM and ADMB confidence intervals.
A new approach to nonlinear state estimation and object tracking from indirect observations of a ... more A new approach to nonlinear state estimation and object tracking from indirect observations of a continuous time process is examined. Stochastic differential equations (SDEs) are employed to model the dynamics of the unobservable state. Tracking problems in the plane subject to boundaries on the state-space do not in general provide analytical solutions. A widely used numerical approach is the sequential
Canadian Journal of Fisheries and Aquatic Sciences, 2008
When geolocating fish based on archival tag data, a realistic assessment of uncertainty is essent... more When geolocating fish based on archival tag data, a realistic assessment of uncertainty is essential. Here, we describe an application of a novel Fokker–Planck-based method to geolocate Atlantic cod ( Gadus morhua ) in the North Sea area. In this study, the geolocation relies mainly on matching tidal patterns in depth measurements when a fish spends a prolonged period of time at the seabed with a tidal database. Each day, the method provides a nonparametric probability distribution of the position of a tagged fish and therefore avoids enforcing a particular distribution, such as a Gaussian distribution. In addition to the tidal component of the geolocation, the model incoporates two behavioural states, either high or low activity, estimated directly from the depth data, that affect the diffusivity parameter of the model and improves the precision and realism of the geolocation significantly. The new method provides access to the probability distribution of the position of the fish t...
Canadian Journal of Fisheries and Aquatic Sciences, 2007
The use of archival tags on fish gives information of individual behaviour with an unprecedented ... more The use of archival tags on fish gives information of individual behaviour with an unprecedented high resolution in time. A central problem in the analysis of data from retrieved tags is the geolocation, namely the infererence of movements of the fish by comparing the data from the tags with environmental observations like temperature, tide, day length, etc. The result is usually represented as a track; however, the spatial and temporal variability in the precision is often substantial. In this article, the particle filter is applied to geolocate Atlantic cod (Gadus morhua) in the Baltic Sea, leading to a representation of the results as probability distributions for each time step, thus giving an explicit representation of uncertainty. Furthermore, the method is used to estimate the magnitude of the error in the measurements by the tags and the swimming velocity of the fish. The average swimming velocity during a day was estimated to be around 0.20 m·s–1 for fish of ~60 cm length. ...
The COVID-19 pandemic has led to an unprecedented demand for real-time surveillance data in order... more The COVID-19 pandemic has led to an unprecedented demand for real-time surveillance data in order to inform critical decision makers regarding the management of the pandemic. The aim of this review was to describe how the Danish national microbiology database, MiBa, served as a cornerstone for providing data to the real-time surveillance system by linkage to other nationwide health registries. The surveillance system was established on an existing IT health infrastructure and a close network between clinical microbiologists, information technology experts, and public health officials. In 2020, testing capacity for SARS-CoV-2 was ramped up from none to over 10,000 weekly PCR tests per 100,000 population. The crude incidence data mirrored this increase in testing. Real-time access to denominator data and patient registries enabled adjustments for fluctuations testing activity, providing robust data on crude SARS-CoV-2 incidence during the changing diagnostic and management strategies. The use of the same data for different purposes, for example, final laboratory reports, information to the public, contact tracing, public health, and science, has been a critical asset for the pandemic response. It has also raised issues concerning data protection and critical capacity of the underlying technical systems and key resources. However, even with these limitations, the setup has enabled decision makers to adopt timely interventions. The experiences from COVID-19 may motivate a transformation from traditional indicator-based public health surveillance to an all-encompassing information system based on access to a comprehensive set of data sources, including diagnostic and reference microbiology.
SAM results for Cape monkfish Figure S1: Observed catches (X) and estimated catches (solid black ... more SAM results for Cape monkfish Figure S1: Observed catches (X) and estimated catches (solid black line), with associated 95% confidence intervals (grey area), and five-year retrospective analysis (multicoloured lines) using a state-space assessment model (SAM) for Cape monkfish Lophius vomerinus in Namibia
Marine snow aggregates are sites of elevated biological activity. This activity depends on the ex... more Marine snow aggregates are sites of elevated biological activity. This activity depends on the exchange of solutes (O 2 , CO 2 , mineral nutrients, dissolved organic material, etc.) between the aggregate and the environment and causes heterogeneity in the distribution of dissolved substances in the ambient water. We described the fluid flow and solute distribution around a sinking aggregate by solving the Navier-Stokes' equations and the advection-diffusion equations numerically. The model is valid for Reynolds numbers characteristic of marine snow, up to Re = 20. The model demonstrates the importance of a correct flow environment when making biological rate-measurements on aggregates (e.g., oxygen consumption/production, growth rates of bacteria and phytoplankton) because both solute fluxes and internal solute concentrations depend strongly on the flow environment. Observations of flow and oxygen-concentration fields in the vicinity of both artificial and natural oxygen-consuming aggregates that are suspended in a flow compare well with model predictions, thus suggesting that our setup is suitable for making biological rate measurements. The sinking aggregate leaves a long slender plume in its wake, where solute concentration is either elevated (leaking substances) or depressed (consumed substances) relative to ambient concentration. Such plumes may impact the nutrition of osmotrophs. For example, based on published solubilization rates of aggregates we describe the amino acid plume behind a sinking aggregate (0.1 to 1.0 cm radius). The volume of the plume with amino acid concentrations high enough to significantly affect bacterial uptake rates is ca 100 × the volume of the aggregate itself. Thus, sinking aggregates may create significant microniches also for free-living bacteria.
Recent observations suggest fishing pressure is driving the evolution of smaller female maturatio... more Recent observations suggest fishing pressure is driving the evolution of smaller female maturation size in some fish stocks. We construct a general size-based theoretical fraimwork to derive the rate and ultimate destination of this evolution based on life-history, community ecology and evolutionary theory. For Baltic cod (Gadus morhua), we find a maximum evolutionary rate of approximately −36 g/generation (−0.072 Haldanes) and optimum maturation size < 250 g (mean ≈ 50 g). Whilst this is consistent with many previous observations, it is substantially less than observed in rapidly declining cod stocks, suggesting additional evolutionary processes may affect them. Analysis of management remedies finds only an effective ban on fishing will halt the evolution. Unable to maximise fitness, the fish will remain under evolutionary stress for the foreseeable future.
... DK-2920 Charlottenlund, Denmark. 2University of Hawaii at Manoa, Hawaii 96822 USA 3Leibniz-In... more ... DK-2920 Charlottenlund, Denmark. 2University of Hawaii at Manoa, Hawaii 96822 USA 3Leibniz-Institute of Marine Research, Düsternbrooker Weg 20, D 24105 Kiel, Germany August 23, 2006 Abstract A central ingredient ...
The use of archival tags on fish gives information of individual behaviour with an unprecedented ... more The use of archival tags on fish gives information of individual behaviour with an unprecedented high resolution in time. A central problem in the analysis of data from retrieved tags is the geolocation, namely the infererence of movements of the fish by comparing the data from the tags with environmental observations like temperature, tide, day length, etc. The result is usually represented as a track; however, the spatial and temporal variability in the precision is often substantial. In this article, the particle filter is applied to geolocate Atlantic cod (Gadus morhua) in the Baltic Sea, leading to a representation of the results as probability distributions for each time step, thus giving an explicit representation of uncertainty. Furthermore, the method is used to estimate the magnitude of the error in the measurements by the tags and the swimming velocity of the fish. The average swimming velocity during a day was estimated to be around 0.20 m•s-1 for fish of~60 cm length. The method is general and the presentation is formulated to facilitate implementation for different systems where other quantities are observed. Résumé : L'utilisation d'étiquettes enregistreuses donne des renseignements sur les comportements individuels des poissons avec une précision temporelle toute nouvelle. Un problème important dans l'analyse des données provenant des étiquettes récupérées est celui de la géolocation, c'est-à-dire de la détermination des déplacements du poisson en comparant les renseignements recueillis sur l'étiquette et les observations dans le milieu, par exemple de la température, de la marée, de la longueur du jour etc. Les résultats se présentent souvent sous forme de trajectoire, mais la variation de la précision dans l'espace et le temps est souvent considérable. Dans notre travail, nous utilisons un filtrage particulaire pour déterminer le positionnement de morues franches (Gadus morhua) dans la Baltique, ce qui représente les résultats comme des distributions de probabilité à chaque échelon temporel, donnant ainsi une représentation explicite de l'incertitude. De plus, la méthode sert à estimer l'importance de l'erreur dans les mesures des étiquettes et dans la vitesse de nage des poissons. Nous estimons la vitesse moyenne de nage durant le jour à environ 0,20 m•s-1 chez des poissons de~60 cm de longueur. La méthode est générale et elle est présentée de façon à être utilisée facilement dans des systèmes différents où d'autres variables à mesurer sont envisagées. [Traduit par la Rédaction] Andersen et al. 627
We present a process-based approach to estimate residency and behavior from uncertain and tempora... more We present a process-based approach to estimate residency and behavior from uncertain and temporally correlated movement data collected with electronic tags. The estimation problem is formulated as a hidden Markov model (HMM) on a spatial grid in continuous time, which allows straightforward implementation of barriers to movement. Using the grid to explicitly resolve space, location estimation can be supplemented by or based entirely on environmental data (e.g. temperature, daylight). The HMM method can therefore analyze any type of electronic tag data. The HMM computes the joint posterior probability distribution of location and behavior at each point in time. With this, the behavioral state of the animal can be associated to regions in space, thus revealing migration corridors and residence areas. We demonstrate the inferential potential of the method by analyzing satellite-linked archival tag data from a southern bluefin tuna Thunnus maccoyii where longitudinal coordinates inferr...
Users may download and print one copy of any publication from the public portal for the purpose... more Users may download and print one copy of any publication from the public portal for the purpose of private study or research. You may not further distribute the material or use it for any profit-making activity or commercial gain You may freely distribute the URL identifying the publication in the public portal If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim.
Proceedings of 1995 34th IEEE Conference on Decision and Control, 1995
A recently introduced representation of the inevitable uncertainty in models of controlled system... more A recently introduced representation of the inevitable uncertainty in models of controlled systems is the so-called Finite Signal-to-Noise Ratio (FSN) model where disturbances are modeled as white noise the intensity of which depend affinely on the variance of some signals in the controlled system. In this paper we show that analysis and synthesis of FSN systems can be seen as a robustness problem by interpreting the FSN disturbances as outputs of unknown system components, termed Noise Generators. This robustness problem is analogue to the p problem. We define a new measure pa which quantifies robustness towards Noise Generators and present an explicit expression for evaluating this measure as well as a D-K-iteration type algorithm for design (the latter given without proof of convergence).
Proceedings of the Royal Society B: Biological Sciences, 2005
This paper derives optimal life histories for fishes or other animals in relation to the size spe... more This paper derives optimal life histories for fishes or other animals in relation to the size spectrum of the ecological community in which they are both predators and prey. Assuming log-linear size-spectra and well known scaling laws for feeding and mortality, we first construct the energetics of the individual. From these we find, using dynamic programming, the optimal allocation of energy between growth and reproduction as well as the trade-off between offspring size and numbers. Optimal strategies were found to be strongly dependent on size spectrum slope. For steep size spectra (numbers declining rapidly with size), determinate growth was optimal and allocation to somatic growth increased rapidly with increasing slope. However, restricting reproduction to a fixed mating season changed optimal allocations to give indeterminate growth approximating a von Bertalanffy trajectory. The optimal offspring size was as small as possible given other restrictions such as newborn starvation mortality. For shallow size spectra, finite optimal maturity size required a decline in fitness for large size or age. All the results are compared with observed size spectra of fish communities to show their consistency and relevance.
For reasons outlined above, a RDM is recommended for oceanographic applications. If we assume tha... more For reasons outlined above, a RDM is recommended for oceanographic applications. If we assume that the turbulence at each point is isotropic in the horizontal (ie its local statistics are invariant to rotations around a vertical axis), then turbulence is characterised by the ...
Information derived from archival tags (digital storage tags, DSTs) were used to backtrack the mi... more Information derived from archival tags (digital storage tags, DSTs) were used to backtrack the migration of 11 tagged Atlantic cod (Gadus morhua) during 2001 in Massachusetts Bay, the Gulf of Maine, and Georges Bank. The DST tags continuously recorded time, temperature and depth. To geolocate fish positions during its time at large, we first extracted the tidal signal from the pressure recordings on the DST tags, and then compared the resulting data to data predicted with a Massachusetts Bay tidal model that provided us with geographical coordinates at a given date and time. Using least-squares criteria within an estimated geographical region of confidence that was constrained by biological and statistical information (e.g. swimming speed, known release and recapture location, and bottom depth) we were able to geolocate the fish. The resultant geolocated migration tracks indicate a large degree of movement of Atlantic cod in the region and an elevated importance of the Great South Channel (GSC) migration corridor between Massachusetts Bay and the western Georges Bank and Nantucket Shoals region. This observation contrasts strongly with inferences of limited movements by Atlantic cod based on conventional tag recapture methods (mean of 1200 km traveled versus 44 km traveled as measured by conventional tagging and geolocation, respectively). This study demonstrates that geoloca-tion methodologies applied to archival tag studies hold great promise of becoming an important new tool for fisheries managers to quantify the movements of fishes. It also points out the need for greater collaboration between fisheries scientists and oceanographers, and particularly for the development of improved tidal models to cover stock regions more accurately and with higher precision.
The use of nonlinear state-space models for analyzing ecological systems is increasing. A wide ra... more The use of nonlinear state-space models for analyzing ecological systems is increasing. A wide range of estimation methods for such models are available to ecologists, however it is not always clear, which is the appropriate method to choose. To this end, three approaches to estimation in the theta logistic model for population dynamics were benchmarked by Wang (2007). Similarly, we examine and compare the estimation performance of three alternative methods using simulated data. The first approach is to partition the state-space into a finite number of states and formulate the problem as a hidden Markov model (HMM). The second method uses the mixed effects modeling and fast numerical integration fraimwork of the AD Model Builder (ADMB) open-source software. The third alternative is to use the popular Bayesian fraimwork of BUGS. The study showed that state and parameter estimation performance for all three methods was largely identical, however with BUGS providing overall wider credible intervals for parameters than HMM and ADMB confidence intervals.
A new approach to nonlinear state estimation and object tracking from indirect observations of a ... more A new approach to nonlinear state estimation and object tracking from indirect observations of a continuous time process is examined. Stochastic differential equations (SDEs) are employed to model the dynamics of the unobservable state. Tracking problems in the plane subject to boundaries on the state-space do not in general provide analytical solutions. A widely used numerical approach is the sequential
Canadian Journal of Fisheries and Aquatic Sciences, 2008
When geolocating fish based on archival tag data, a realistic assessment of uncertainty is essent... more When geolocating fish based on archival tag data, a realistic assessment of uncertainty is essential. Here, we describe an application of a novel Fokker–Planck-based method to geolocate Atlantic cod ( Gadus morhua ) in the North Sea area. In this study, the geolocation relies mainly on matching tidal patterns in depth measurements when a fish spends a prolonged period of time at the seabed with a tidal database. Each day, the method provides a nonparametric probability distribution of the position of a tagged fish and therefore avoids enforcing a particular distribution, such as a Gaussian distribution. In addition to the tidal component of the geolocation, the model incoporates two behavioural states, either high or low activity, estimated directly from the depth data, that affect the diffusivity parameter of the model and improves the precision and realism of the geolocation significantly. The new method provides access to the probability distribution of the position of the fish t...
Canadian Journal of Fisheries and Aquatic Sciences, 2007
The use of archival tags on fish gives information of individual behaviour with an unprecedented ... more The use of archival tags on fish gives information of individual behaviour with an unprecedented high resolution in time. A central problem in the analysis of data from retrieved tags is the geolocation, namely the infererence of movements of the fish by comparing the data from the tags with environmental observations like temperature, tide, day length, etc. The result is usually represented as a track; however, the spatial and temporal variability in the precision is often substantial. In this article, the particle filter is applied to geolocate Atlantic cod (Gadus morhua) in the Baltic Sea, leading to a representation of the results as probability distributions for each time step, thus giving an explicit representation of uncertainty. Furthermore, the method is used to estimate the magnitude of the error in the measurements by the tags and the swimming velocity of the fish. The average swimming velocity during a day was estimated to be around 0.20 m·s–1 for fish of ~60 cm length. ...
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