Article
Fisheries
Kira Lancker, Rudi Voss, Fabian Zimmermann, Martin F. Quaas
Summary: Reliable stock assessments are crucial for successful fisheries management. Traditional methods are expensive and not widely used, especially in developing regions. The BESA approach proposed in this study, which incorporates price data, provides reliable estimates for both biological and economic parameters, thus enhancing stock assessment accuracy and informing advanced fisheries management.
FISH AND FISHERIES
(2023)
Article
Fisheries
Olav Nikolai Breivik, Anders Nielsen, Casper W. Berg
Summary: The state-space assessment model (SAM) was extended by allowing a functional relationship between observation variance and prediction, which led to significant improvements in the official assessments of North East Arctic cod and haddock.
ICES JOURNAL OF MARINE SCIENCE
(2021)
Article
Behavioral Sciences
Ladan Shams, Ulrik Beierholm
Summary: The theory of Bayesian causal inference is a powerful and versatile theory that can explain human behavior and brain function, making it highly significant in neuroscience research.
NEUROSCIENCE AND BIOBEHAVIORAL REVIEWS
(2022)
Article
Biochemical Research Methods
Hana Susak, Laura Serra-Saurina, German Demidov, Raquel Rabionet, Laura Domenech, Mattia Bosio, Francesc Muyas, Xavier Estivill, Georgia Escaramis, Stephan Ossowski
Summary: Complex diseases are influenced by genetic and environmental factors, with rare variants playing a crucial role in explaining disease mechanisms. A new Bayesian rare variant Association Test using Integrated Nested Laplace Approximation (BATI) was developed, outperforming established methods and achieving high power even when variants explain a small fraction of phenotypic variance.BATI was integrated into the 'Rare Variant Genome Wide Association Study' (rvGWAS) framework, allowing for comprehensive analysis of rare variants in whole-exome or whole genome sequencing data.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Engineering, Civil
Pinghe Ni, Qiang Han, Xiuli Du, Xiaowei Cheng, Hongyuan Zhou
Summary: This paper presents a data-driven approach for post-earthquake reliability assessments of civil structures. It updates the probability density functions of random variables using measured vibration data, and generates the posterior probability density functions of structural parameters using two approximate Bayesian computation techniques. The updated probability density functions are then used for reliability assessments, and numerical studies verify the accuracy and efficiency of the proposed techniques.
ENGINEERING STRUCTURES
(2022)
Article
Fisheries
Daniel Ovando, Christopher M. Free, Olaf P. Jensen, Ray Hilborn
Summary: Understanding the status of fish stocks is crucial for ecological and economic sustainability of marine ecosystems. However, a lack of formal stock assessments in many global fisheries, combined with reliance on catch data, has led to imprecise and biased estimates of stock status in new data-limited fisheries when using catch-only models.
FISH AND FISHERIES
(2022)
Article
Health Care Sciences & Services
Zhenxun Wang, Lifeng Lin, James S. Hodges, Richard MacLehose, Haitao Chu
Summary: Network meta-analysis combines direct and indirect evidence in systematic reviews of multiple treatments for better estimation. The article introduces a variance shrinkage method assuming different treatment variances share a common prior with unknown hyperparameters. This method improves estimation by shrinking the variances in a data-dependent way.
STATISTICAL METHODS IN MEDICAL RESEARCH
(2021)
Article
Biochemical Research Methods
Aimin Chen, Tianshou Zhou, Tianhai Tian
Summary: This article introduces effective methods for the inference of gene regulatory networks and advocates the development of ensemble methods that combine multiple approaches.
CURRENT BIOINFORMATICS
(2022)
Article
Robotics
Michele Ginesi, Paolo Fiorini
Summary: This paper proposes two generalizations of the ARHMM, one with a more general AR dynamics in Cartesian space and the other with linear dynamics in unit quaternion space to describe orientations. These extensions allow for the description of more complex dynamics of the observed state.
IEEE ROBOTICS AND AUTOMATION LETTERS
(2023)
Review
Environmental Sciences
Nasrin Taghavi, Robert K. Niven, David J. Paull, Matthias Kramer
Summary: This article provides a comprehensive review of modern groundwater vulnerability assessment methods, focusing on statistical methods and hybrid methods. It concludes that Bayesian inference offers many advantages compared to other methods, as it combines theory and data, provides posterior probabilities, and can be continually updated with new data.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Computer Science, Theory & Methods
Lisa Gaedke-Merzhaeuser, Janet van Niekerk, Olaf Schenk, Havard Rue
Summary: This work presents parallelization strategies for the methodology of integrated nested Laplace approximations (INLA) to meet the growing demand of larger-scale Bayesian inference tasks. The introduced approach leverages nested thread-level parallelism, robust regression and state-of-the-art sparse linear solver PARDISO, resulting in significant speedups in various real-world applications. The improved parallelization scheme is already integrated into the open-source R-INLA package for convenient use.
STATISTICS AND COMPUTING
(2023)
Article
Mathematics
Virgilio Gomez-Rubio, Roger S. Bivand, Havard Rue
Summary: The integrated nested Laplace approximation (INLA) offers a fast and effective method for marginal inference in Bayesian hierarchical models, implemented in the R-INLA package. This paper outlines the implementation and application of a new class of latent models through R-INLA, particularly in spatial econometrics.
Article
Statistics & Probability
Rui Gao, Yaqiong Li, Yanfei Bai
Summary: In this paper, the pricing problem of exchange option with correlated and imperfectly liquid underlying stocks is investigated. An explicit pricing formula for the exchange option is obtained using Esscher measure transformation. A Bayesian statistical method is proposed for estimating the unknown parameters, considering the prior information and correlation of market data. The method combines a Markov chain Monte Carlo algorithm for posterior inference on the exchange option price. Empirical analysis shows the significant effect of stock liquidity on the exchange option price.
COMMUNICATIONS IN STATISTICS-THEORY AND METHODS
(2022)
Review
Psychology, Mathematical
Johnny van Doorn, Don van den Bergh, Udo Bohm, Fabian Dablander, Koen Derks, Tim Draws, Alexander Etz, Nathan J. Evans, Quentin F. Gronau, Julia M. Haaf, Max Hinne, Simon Kucharsky, Alexander Ly, Maarten Marsman, Dora Matzke, Akash R. Komarlu Narendra Gupta, Alexandra Sarafoglou, Angelika Stefan, Jan G. Voelkel, Eric-Jan Wagenmakers
Summary: Although there is a lack of practical guidelines on how to apply Bayesian procedures and interpret results in empirical research, this study offers specific guidance for four stages of Bayesian statistical reasoning in a research setting: planning the analysis, executing the analysis, interpreting the results, and reporting the results. Each stage's guidelines are illustrated with a running example, primarily focusing on analyses performed with the open-source statistical software JASP, but with applicability to Bayesian inference in general.
PSYCHONOMIC BULLETIN & REVIEW
(2021)
Article
Mathematics, Applied
Ruanui Nicholson, Noemi Petra, Umberto Villa, Jari P. Kaipio
Summary: To reduce computational costs in solving large-scale inverse problems governed by PDEs, a linear approximation can be used instead of a nonlinear parameter-to-observable mapping. However, this linear surrogate model may give misleading results if the model approximation error is not considered. In this paper, the Bayesian approximation error (BAE) approach is utilized to account for the errors, and it is proven that the (approximate) posterior measure obtained from a linear approximation is independent of the specific choice of linear approximation.
Article
Fisheries
Ji X. He, James R. Bence, Charles P. Madenjian, Steven A. Pothoven, Norine E. Dobiesz, David G. Fielder, James E. Johnson, Mark P. Ebener, R. Adam Cottrill, Lloyd C. Mohr, Scott R. Koproski
CANADIAN JOURNAL OF FISHERIES AND AQUATIC SCIENCES
(2015)
Article
Fisheries
Travis O. Brenden, Kim T. Scribner, James R. Bence, Iyob Tsehaye, Jeannette Kanefsky, Christopher S. Vandergoot, David G. Fielder
NORTH AMERICAN JOURNAL OF FISHERIES MANAGEMENT
(2015)
Article
Ecology
Travis O. Brenden, James R. Bence, Weihai Liu, Iyob Tsehaye, Kim T. Scribner
METHODS IN ECOLOGY AND EVOLUTION
(2015)
Article
Fisheries
Ji X. He, James R. Bence, Edward F. Roseman, David G. Fielder, Mark P. Ebener
CANADIAN JOURNAL OF FISHERIES AND AQUATIC SCIENCES
(2016)
Editorial Material
Fisheries
James R. Bence, Charles P. Madenjian, Ji X. He, David G. Fielder, Steven A. Pothoven, Norine E. Dobiesz, James E. Johnson, Mark P. Ebener, R. Adam Cottrill, Lloyd C. Mohr, Scott R. Koproski
CANADIAN JOURNAL OF FISHERIES AND AQUATIC SCIENCES
(2016)
Article
Fisheries
Iyob Tsehaye, Travis O. Brenden, James R. Bence, Weihai Liu, Kim T. Scribner, Jeannette Kanefsky, Kristin Bott, Robert F. Elliott
FISHERIES RESEARCH
(2016)
Article
Fisheries
David G. Fielder, Michael L. Jones, James R. Bence
NORTH AMERICAN JOURNAL OF FISHERIES MANAGEMENT
(2016)
Article
Fisheries
Yang Li, James R. Bence, Travis O. Brenden
NORTH AMERICAN JOURNAL OF FISHERIES MANAGEMENT
(2016)
Article
Fisheries
Richard D. Clark, James R. Bence, Randall M. Claramunt, James E. Johnson, David Gonder, Nicholas D. Legler, Steve R. Robillard, Ben D. Dickinson
NORTH AMERICAN JOURNAL OF FISHERIES MANAGEMENT
(2016)
Article
Fisheries
Iyob Tsehaye, Michael L. Jones, James R. Bence, Travis O. Brenden, Charles P. Madenjian, David M. Warner
CANADIAN JOURNAL OF FISHERIES AND AQUATIC SCIENCES
(2014)
Article
Fisheries
Tyler Wagner, Brian J. Irwin, James R. Bence, Daniel B. Hayes
Article
Fisheries
Yang Li, James R. Bence, Travis O. Brenden
ICES JOURNAL OF MARINE SCIENCE
(2015)
Article
Environmental Sciences
Carson G. Prichard, James R. Bence
JOURNAL OF GREAT LAKES RESEARCH
(2013)
Article
Fisheries
David G. Fielder, James R. Bence
NORTH AMERICAN JOURNAL OF FISHERIES MANAGEMENT
(2014)
Article
Fisheries
Iyob Tsehaye, Michael L. Jones, Travis O. Brenden, James R. Bence, Randall M. Claramunt
TRANSACTIONS OF THE AMERICAN FISHERIES SOCIETY
(2014)
Article
Fisheries
Miguel Petrere Jr, Davi Butturi-Gomes
Summary: This short communication aims to raise awareness about the misuse of confidence intervals in Ecology and Fisheries statistical models that ignore the lack of independence.
FISHERIES RESEARCH
(2024)
Article
Fisheries
Peter-John F. Hulson, Benjamin C. Williams
Summary: This study evaluates the impact of considering ageing error and growth variability on the determination of input sample size (ISS) in statistical catch-at-age assessment models. The results show that including these sources of uncertainty decreases the ISS determined through bootstrap methods. This indicates that there is more variability in age composition and conditional age-at-length data than previously accounted for. Including these sources of uncertainty improves the estimation of ISS and subsequently improves the quality of stock assessment models.
FISHERIES RESEARCH
(2024)
Article
Fisheries
Jason M. Cope
Summary: Fishery resource assessment is a complex and challenging task, but with the use of different analysis methods and tools, effective management guidance can be provided even with limited data and resources.
FISHERIES RESEARCH
(2024)
Article
Fisheries
Regina L. Cunha, Joana I. Robalo, Sara M. Francisco, Ines Farias, Rita Castilho, Ivone Figueiredo
Summary: Recent advances in genomics have greatly contributed to the assessment of fish stocks by providing precise identification of genetic boundaries. This study used a genotyping-by-sequencing approach to reveal the existence of an additional genetic cluster of blackspot seabream in the northeast Atlantic, which was not previously identified. Factors such as ocean circulation patterns and local upwelling may play a role in the genetic differentiation observed in this study.
FISHERIES RESEARCH
(2024)
Article
Fisheries
Huihua Lee, Mark N. Maunder, Kevin R. Piner
Summary: Estimating growth is important for fish population assessment. Integrated assessment models and the influence of misfitting size composition data have renewed interest in how growth is modeled. The available data types control how the length-at-age relationship is estimated. Estimating length-at-age is complex due to multiple sources of biological variability and difficulties in obtaining representative samples.
FISHERIES RESEARCH
(2024)
Article
Fisheries
A. Ladino, I. Perez-Arjona, V. Espinosa, M. Chillaron, V. Vidal, L. M. Godinho, G. Moreno, G. Boyra
Summary: This study examines the acoustic properties of skipjack tuna and Atlantic mackerel, both bladderless pelagic fish species, and explains the significant differences observed. The research shows that the differences in material properties of their tissues predict a more than 10 dB greater reduced target strength in skipjack compared to mackerel at certain frequencies.
FISHERIES RESEARCH
(2024)
Article
Fisheries
Nelly Pena-Cutimbo, Cristel Cordero-Maldonado, Clara Ortiz-Alvarez, Joanna Alfaro-Shigueto, Jeffrey C. Mangel
Summary: Bycatch is a global problem for marine megafauna. This study assessed the bycatch interactions of the Peruvian artisanal purse-seine fishery in 2019 and found that all taxa groups were affected by bycatch. Dusky dolphins, guanay cormorants, and eagle rays were the most frequently reported bycatch species.
FISHERIES RESEARCH
(2024)
Article
Fisheries
Jen-Ming Liu, Po-Yuk So
Summary: The set-net fishery is an environmentally friendly fishery posing little risk to the marine ecosystem. This study identified ocean temperature, sea surface factors, and climatic factors as the main factors affecting the installation of set-nets.
FISHERIES RESEARCH
(2024)
Article
Fisheries
Josie L. Palmer, Carina Armstrong, Hasan D. Akbora, Damla Beton, Cigdem Caglar, Brendan J. Godley, Kristian Metcalfe, Meryem Ozkan, Robin T. E. Snape, Annette C. Broderick
Summary: Small-scale fisheries are vital for global food security and cultural heritage, but the lack of information hampers effective management and mitigation of ecological impacts. This study provides the first comprehensive overview of the small-scale fishery fleet in Northern Cyprus. The fleet operates mainly over the continental shelf, using static and demersal gear types, and catches a diverse range of species, some of which are threatened. The findings can be used to improve fisheries management and conservation measures.
FISHERIES RESEARCH
(2024)