Article
Fisheries
James T. Thorson, Cole C. Monnahan, Peter-John F. Hulson
Summary: Integrated stock assessments specify distributions for multiple data types and control the relative leverage of each datum. Unresolved questions include modeling age and length data, handling correlated residuals, efficiently communicating information between sampling and assessment teams, and addressing alternative hypotheses. This study proposes a categorization of assessment errors and offers practical recommendations for mitigating bias and imprecision in the assessment models.
FISHERIES RESEARCH
(2023)
Article
Fisheries
Ismail K. Saglam, James Hobbs, Randall Baxter, Levi S. Lewis, Alyssa Benjamin, Amanda J. Finger
Summary: The southernmost stock of longfin smelt in the San Francisco Estuary is nearing extinction, but genetic structure, diversity, and gene flow patterns are poorly understood. The study found high genetic structure between major estuaries, fine-scale structure within the Fraser River, and low levels of structure within the San Francisco Estuary. Furthermore, there were signatures of local adaptation within the Fraser River and the Skeena River estuaries.
CANADIAN JOURNAL OF FISHERIES AND AQUATIC SCIENCES
(2021)
Article
Engineering, Civil
Shun Taguchi, Takayoshi Yoshimura
Summary: This study proposes a data assimilation method using a state space neural network for predicting non-recurring traffic congestion. The results show that the method achieves higher prediction accuracy for predicting unknown traffic congestion and is more robust against data sparsity.
IEEE TRANSACTIONS ON INTELLIGENT TRANSPORTATION SYSTEMS
(2022)
Article
Ecology
Edward Gross, Wim Kimmerer, Josh Korman, Levi Lewis, Scott Burdick, Lenny Grimaldo
Summary: The distribution of larval fishes is influenced by where they hatch and their movements after hatching. Human interventions may contribute to the decline of the longfin smelt species. Research results suggest that the longfin smelt may hatch closer to the seaward than previously believed, and losses due to freshwater diversions are relatively small.
MARINE ECOLOGY PROGRESS SERIES
(2022)
Article
Computer Science, Interdisciplinary Applications
Pin Wu, Xuting Chang, Wenyan Yuan, Junwu Sun, Wenjie Zhang, Rossella Arcucci, Yike Guo
Summary: This paper introduces a fast data assimilation (FDA) method based on machine learning, which greatly reduces the time of the data assimilation process.
JOURNAL OF COMPUTATIONAL SCIENCE
(2021)
Article
Mathematics, Applied
Georg A. Gottwald, Sebastian Reich
Summary: The research combines machine-learning algorithms and data assimilation to achieve enhanced forecasting capabilities. By incorporating data-driven methods as forecast models within data assimilation procedures, the obtained forecast model shows remarkably good skill.
PHYSICA D-NONLINEAR PHENOMENA
(2021)
Article
Environmental Sciences
Dorota Jozwicki, Puneet Sharma, Ingrid Mann, Ulf-Peter Hoppe
Summary: This paper presents an approach to segment Polar Mesospheric Summer Echoes (PMSE) from datasets obtained from EISCAT VHF radar data. The method involves manual labeling of data into different categories and using random forests algorithm to segment the PMSE. The results show that random forests can effectively segment the PMSE and the weighted-down labels technique improves the performance.
Correction
Mathematics, Applied
Tomas Caraballo, Renato Colucci, Javier Lopez-de-la-Cruz, Alain Rapaport
Summary: The corrigendum corrects an error in the original paper regarding modeling real noisy perturbations with bounded realizations using the Ornstein-Uhlenbeck process. The corrected formula ensures the boundedness property to be satisfied with probability one, which was not the case in the original paper despite observed in simulations.
COMMUNICATIONS IN NONLINEAR SCIENCE AND NUMERICAL SIMULATION
(2021)
Article
Ecology
Jaclyn R. Aliperti, Kimberly Jenderseck, Dirk H. Van Vuren
Summary: Investigating individual-based habitat settlement decisions is a central theme in ecology. This study focused on golden-mantled ground squirrels and quantified their habitat selection and how it may be influenced by density or linked to fitness outcomes. The study found that squirrels preferred dry meadow over other habitat types and that the lack of visual obstruction in dry meadow may drive their habitat selection. Surprisingly, the study also found that squirrels maintained their preference for dry meadow even as density increased, leading to reduced survival rates. This study contributes to our understanding of the causes and consequences of changes in habitat use.
ECOLOGY AND EVOLUTION
(2022)
Article
Computer Science, Interdisciplinary Applications
Edoardo Saredi, Nikhilesh Tumuluru Ramesh, Andrea Sciacchitano, Fulvio Scarano
Summary: State observer techniques are used to assimilate three-dimensional velocity measurements into computational fluid dynamics simulations to reduce the mismatch between simulation and reference data. Two different approaches for the forcing term are considered and the effects of forcing density on the simulation are studied, showing that the integral term is more effective than the proportional term.
COMPUTERS & FLUIDS
(2021)
Article
Computer Science, Artificial Intelligence
Fateme Nateghi Haredasht, Celine Vens
Summary: This article explores the potential of including unlabeled data instances in survival analysis, proposing three approaches to handle this novel scenario and empirically demonstrating that all approaches can significantly improve predictive performance for survival times.
Article
Geosciences, Multidisciplinary
Seunghee Lee, Seohui Park, Myong-In Lee, Ganghan Kim, Jungho Im, Chang-Keun Song
Summary: This study used a machine learning algorithm to estimate ground-level particulate matter (PM) and applied it to a weather forecasting model. Initializing the model with the new analysis data significantly reduced analysis error and improved forecast skill. The synergistic use of data assimilation and machine learning can maximize the effectiveness of satellite-based air quality forecasts at the ground.
GEOPHYSICAL RESEARCH LETTERS
(2022)
Article
Meteorology & Atmospheric Sciences
Yihao Chen, Zheqi Shen, Youmin Tang
Summary: This study investigates the influence of model state errors at the initial time of assimilation on the quality of an ensemble-based data assimilation system for a complex fully coupled general circulation model. Two strategies are applied to alleviate the initial state errors and a reliable assimilation system is developed. The assimilation of observation-derived climatological data is found to be an effective approach to reduce initial state errors and improve the performance of the assimilation system.
JOURNAL OF ADVANCES IN MODELING EARTH SYSTEMS
(2022)
Article
Environmental Sciences
Duoduo Li, Xuhua Zhou, Kai Li
Summary: GNSS real-time applications benefit greatly from the International GNSS Service's (IGS) real-time service (RTS). This paper discusses the GPS real-time orbit and clock corrections provided by 11 analysis centers (ACs) from days 144 to 153 of 2022, evaluating them from the perspectives of integrity, continuity, and accuracy. The study concludes that CNE, ESA, and GMV perform better in terms of integrity and continuity, while CNE, ESA, and WHU are the most accurate in terms of satellite orbit and clock corrections.
Article
Engineering, Civil
Su Jiang, Louis J. Durlofsky
Summary: Subsurface flow models are imperfect and model error can lead to unreliable predictions. This study introduces a method to handle model error in a data-space inversion framework, showing that the coupled model error treatment provides highly accurate results.
JOURNAL OF HYDROLOGY
(2021)
Article
Environmental Sciences
Cleridy E. Lennert-Cody, Mark N. Maunder, Marlon H. Roman, Haikun Xu, Mihoko Minami, Jon Lopez
ENVIRONMENTAL AND ECOLOGICAL STATISTICS
(2020)
Article
Fisheries
Mark N. Maunder, James T. Thorson, Haikun Xu, Ricardo Oliveros-Ramos, Simon D. Hoyle, Laura Tremblay-Boyer, Hui Hua Lee, Mikihiko Kai, Shui-Kai Chang, Toshihide Kitakado, Christoffer M. Albertsen, Carolina V. Minte-Vera, Cleridy E. Lennert-Cody, Alexandre M. Aires-da-Silva, Kevin R. Piner
FISHERIES RESEARCH
(2020)
Article
Fisheries
James T. Thorson, Mark N. Maunder, E. Punt
FISHERIES RESEARCH
(2020)
Article
Fisheries
Andre E. Punt, Alistair Dunn, Bjarki Por Elvarsson, John Hampton, Simon D. Hoyle, Mark N. Maunder, Richard D. Methot, Anders Nielsen
FISHERIES RESEARCH
(2020)
Article
Fisheries
Andre E. Punt, Claudio Castillo-Jordan, Owen S. Hamel, Jason M. Cope, Mark N. Maunder, James N. Ianelli
Summary: Natural mortality (M) is a crucial parameter in fish stock assessment, but estimating it accurately can be challenging and errors can impact management decisions. Using feedback management strategies can mitigate the effects of errors in M, but achieving management objectives may be compromised when errors are present.
FISHERIES RESEARCH
(2021)
Article
Fisheries
Felipe Carvalho, Henning Winker, Dean Courtney, Maia Kapur, Laurence Kell, Massimiliano Cardinale, Michael Schirripa, Toshihide Kitakado, Dawit Yemane, Kevin R. Piner, Mark N. Maunder, Ian Taylor, Chantel R. Wetzel, Kathryn Doering, Kelli F. Johnson, Richard D. Methot
Summary: Integrated analysis is increasingly popular for stock assessments worldwide, requiring a variety of decisions to be made. This study offers practical guidelines for analysts to identify and address model issues using diagnostic tools, as well as a general process for model development and selection. The objective criteria proposed could significantly benefit the stock assessment community by improving the inclusion of diagnostic tests in future assessment models.
FISHERIES RESEARCH
(2021)
Article
Fisheries
Simon D. Hoyle, Mark N. Maunder, Andre E. Punt, Pamela M. Mace, Jennifer A. Devine, Z. Teresa A'mar
FISHERIES RESEARCH
(2022)
Article
Fisheries
Keisuke Satoh, Haikun Xu, Carolina V. Minte-Vera, Mark N. Maunder, Toshihide Kitakado
Summary: This study revealed the size-specific spatiotemporal dynamics of bigeye tuna in the eastern Pacific Ocean, showing spatial segregation by size and different distribution patterns for adult, intermediate size, and juvenile fish. The study also observed spatial restructuring by size in response to El Nino and La Nina events, highlighting the impact of oceanographic conditions on fish distribution and movement.
FISHERIES RESEARCH
(2021)
Review
Fisheries
Carolina V. Minte-Vera, Mark N. Maunder, Alexandre M. Aires-da-Silva
Summary: The study demonstrates the use of auxiliary diagnostic analyses to identify and understand model misspecification, with various tools revealing consistency in information about population abundance from different data sets. The analyses highlight the importance of considering various components of data in stock assessment models, to better estimate biological and fishery processes.
ICES JOURNAL OF MARINE SCIENCE
(2021)
Article
Fisheries
Mark N. Maunder
Summary: The Ricker and Beverton-Holt stock recruitment relationships show that changes in adult abundance can strongly influence juvenile survival even at low biomass levels. This suggests that factors other than resource limitation, such as changes in predation risk, control density dependence. A simple habitat limitation model and a generalized logistic survival stock-recruitment model are proposed to explain these relationships. The findings have important implications for fisheries management and understanding the population dynamics of different species.
FISHERIES RESEARCH
(2022)
Article
Fisheries
Cleridy E. Lennert-Cody, Marti McCracken, Salvador Siu, Ricardo Oliveros-Ramos, Mark N. Maunder, Alexandre Aires-da-Silva, Jose Miguel Carvajal-Rodriguez, Jean D. Opsomer, Pedro de Barros
Summary: Sampling designs are needed for collection of shark size composition data in order to manage shark fisheries in Central America. Tailored designs for multi-species fisheries with structured landings are necessary to minimize impact on catch landing process. Simulation results suggest that a single sampling design can be implemented for obtaining size composition estimates of common shark and non-shark species in landings with sharks.
FISHERIES RESEARCH
(2022)
Article
Fisheries
Simon D. Hoyle, Ashley J. Williams, Carolina V. Minte-Vera, Mark N. Maunder
Summary: The values of natural mortality (M) play a significant role in stock assessment models and have a strong impact on model outcomes and management advice. Estimating natural mortality is challenging, and there is often limited information available. In this study, we review the evidence used to estimate natural mortality at different ages for the four main stocks of yellowfin tuna. We discuss important factors influencing the estimation, such as age-related variations linked to size, maturity state, or senescence, and identify information gaps. We also assess the historical values of natural mortality used in stock assessments and propose a range of estimates based on approaches discussed in a recent meeting. Furthermore, we recommend future research to improve the estimation of natural mortality.
FISHERIES RESEARCH
(2023)
Review
Fisheries
Mark N. Maunder, Owen S. Hamel, Hui-Hua Lee, Kevin R. Piner, Jason M. Cope, Andre E. Punt, James N. Ianelli, Claudio Castillo-Jordan, Maia S. Kapur, Richard D. Methot
Summary: Natural mortality (M), an important parameter in fisheries stock assessment and management, is difficult to estimate and uncertain. This paper reviews various methods to estimate M and suggests that directly estimating M using data and assigning a prior based on empirical methods is the most effective approach.
FISHERIES RESEARCH
(2023)
Article
Fisheries
Cleridy E. Lennert-Cody, Jon Lopez, Mark N. Maunder
Summary: The study developed annual set type classification algorithms for the tropical tuna purse-seine fishery in the eastern Pacific Ocean using random forests. The results showed that different set types can be reliably distinguished based on operational characteristics and catch and bycatch information. The algorithms had low misclassification error rates and could be used to validate set type determinations based on other criteria.
FISHERIES RESEARCH
(2023)
Editorial Material
Fisheries
Owen S. Hamel, James N. Ianelli, Mark N. Maunder, Andre E. Punt
FISHERIES RESEARCH
(2023)
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)