Applying Bayesian model selection to determine ecological covariates for recruitment and natural mortality in stock assessment

The highs and lows of herring: A meta‐analysis of patterns and factors in herring collapse and recovery

(2020) John T. Trochta et al.   FISH AND FISHERIES

The changing physical and ecological meanings of North Pacific Ocean climate indices

(2020) Michael A. Litzow et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Good practices for including environmental data to inform spawner-recruit dynamics in integrated stock assessments: Small pelagic species case study

(2019) Paul R. Crone et al.   FISHERIES RESEARCH

Nonstationary environmental and community relationships in the North Pacific Ocean

(2019) Michael A. Litzow et al.   ECOLOGY

Recruitment: Theory, estimation, and application in fishery stock assessment models

(2019) Rishi Sharma et al.   FISHERIES RESEARCH

Structure of winter groundfish feeding guilds in Pacific herring Clupea pallasii and walleye pollock Gadus chalcogrammus nursery fjords

(2019) Benjamin P. Gray et al.   JOURNAL OF FISH BIOLOGY

Do Gulf of Alaska fish and crustacean populations show synchronous non-stationary responses to climate?

(2019) Patricia Puerta et al.   PROGRESS IN OCEANOGRAPHY

Attending to spatial social–ecological sensitivities to improve trade‐off analysis in natural resource management

(2019) Daniel K. Okamoto et al.   FISH AND FISHERIES

Bayesian model selection for spatial capture–recapture models

(2019) Soumen Dey et al.   Ecology and Evolution

Performance evaluation of information criteria for estimating a shape parameter in a Bayesian state-space biomass dynamics model

(2019) Mikihiko Kai et al.   FISHERIES RESEARCH

The dream and the reality: meeting decision-making time frames while incorporating ecosystem and economic models into management strategy evaluation

(2018) Jonathan J. Deroba et al.   CANADIAN JOURNAL OF FISHERIES AND AQUATIC SCIENCES

Empirically based models of oceanographic and biological influences on Pacific Herring recruitment in Prince William Sound

(2018) Fletcher Sewall et al.   DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY

Seasonal presence and potential influence of humpback whales on wintering Pacific herring populations in the Gulf of Alaska

(2018) Janice M. Straley et al.   DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY

Migration patterns of post-spawning Pacific herring in a subarctic sound

(2018) Mary Anne Bishop et al.   DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY

Regional variation in the intensity of humpback whale predation on Pacific herring in the Gulf of Alaska

(2018) J.R. Moran et al.   DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY

Variability and stability in predation landscapes: A cross-ecosystem comparison on the potential for predator control in temperate marine ecosystems

(2018) Kiva L Oken et al.   FISH AND FISHERIES

Paulik revisited: Statistical framework and estimation performance of multistage recruitment functions

(2018) Elizabeth N. Brooks et al.   FISHERIES RESEARCH

No-U-turn sampling for fast Bayesian inference in ADMB and TMB: Introducing the adnuts and tmbstan R packages

(2018) Cole C. Monnahan et al.   PLoS One

Modeling temporal variation in recruitment in fisheries stock assessment: A review of theory and practice

(2018) Mark N. Maunder et al.   FISHERIES RESEARCH

Non-stationary climate–salmon relationships in the Gulf of Alaska

(2018) Michael A. Litzow et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Optimization of a Plaque Neutralization Test (PNT) to Identify the Exposure History of Pacific Herring to Viral Hemorrhagic Septicemia Virus (VHSV)

(2017) Lucas M. Hart et al.   JOURNAL OF AQUATIC ANIMAL HEALTH

Evaluating signals of oil spill impacts, climate, and species interactions in Pacific herring and Pacific salmon populations in Prince William Sound and Copper River, Alaska

(2017) Eric J. Ward et al.   PLoS One

Bayesian stock assessment of Pacific herring in Prince William Sound, Alaska

(2017) Melissa L. Muradian et al.   PLoS One

Reconsidering the impossible — linking environmental drivers to growth, mortality, and recruitment of fish

(2016) Pierre Pepin   CANADIAN JOURNAL OF FISHERIES AND AQUATIC SCIENCES

A state-space approach to incorporating environmental effects on recruitment in an age-structured assessment model with an application to southern New England yellowtail flounder

(2016) Timothy J. Miller et al.   CANADIAN JOURNAL OF FISHERIES AND AQUATIC SCIENCES

Effects of warm and cold climate conditions on capelin ( Mallotus villosus ) and Pacific herring ( Clupea pallasii ) in the eastern Bering Sea

(2016) Alexander G. Andrews et al.   DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY

Plankton indices explain interannual variability in Prince William Sound herring first year growth

(2016) S. D. Batten et al.   FISHERIES OCEANOGRAPHY

Comparison of Bayesian predictive methods for model selection

(2016) Juho Piironen et al.   STATISTICS AND COMPUTING

Practical Bayesian model evaluation using leave-one-out cross-validation and WAIC

(2016) Aki Vehtari et al.   STATISTICS AND COMPUTING

Faster estimation of Bayesian models in ecology using Hamiltonian Monte Carlo

(2016) Cole C. Monnahan et al.   Methods in Ecology and Evolution

When “data” are not data: the pitfalls of post hoc analyses that use stock assessment model output

(2015) Elizabeth N. Brooks et al.   CANADIAN JOURNAL OF FISHERIES AND AQUATIC SCIENCES

A guide to Bayesian model selection for ecologists

(2015) M. B. Hooten et al.   ECOLOGICAL MONOGRAPHS

Use of state-space population dynamics models in hypothesis testing: advantages over simple log-linear regressions for modeling survival, illustrated with application to longfin smelt (Spirinchus thaleichthys)

(2015) Mark N. Maunder et al.   FISHERIES RESEARCH

The parasiteIchthyophonussp. in Pacific herring from the coastal NE Pacific

(2015) P K Hershberger et al.   JOURNAL OF FISH DISEASES

Changing central Pacific El Niños reduce stability of North American salmon survival rates

(2015) D. Patrick Kilduff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

First time series of estimated humpback whale (Megaptera novaeangliae) abundance in Prince William Sound

(2014) Suzanne F. Teerlink et al.   ENVIRONMENTAL AND ECOLOGICAL STATISTICS

Examining common assumptions about recruitment: a meta-analysis of recruitment dynamics for worldwide marine fisheries

(2014) Cody S Szuwalski et al.   FISH AND FISHERIES

Where has all the recruitment research gone, long time passing?

(2014) Jake Rice et al.   ICES JOURNAL OF MARINE SCIENCE

Time-varying natural mortality in fisheries stock assessment models: identifying a default approach

(2014) K. F. Johnson et al.   ICES JOURNAL OF MARINE SCIENCE

The dynamics of fish populations at low abundance and prospects for rebuilding and recovery

(2014) R. Hilborn et al.   ICES JOURNAL OF MARINE SCIENCE

Performance of stock assessments with misspecified age- and time-varying natural mortality

(2013) Jonathan J. Deroba et al.   FISHERIES RESEARCH

Model selection for selectivity in fisheries stock assessments

(2013) André E. Punt et al.   FISHERIES RESEARCH

Understanding predictive information criteria for Bayesian models

(2013) Andrew Gelman et al.   STATISTICS AND COMPUTING

Can steepness of the stock–recruitment relationship be estimated in fishery stock assessment models?

(2012) Hui-Hua Lee et al.   FISHERIES RESEARCH

AD Model Builder: using automatic differentiation for statistical inference of highly parameterized complex nonlinear models

(2011) David A. Fournier et al.   OPTIMIZATION METHODS & SOFTWARE

Hypotheses concerning the decline and poor recovery of Pacific herring in Prince William Sound, Alaska

(2011) Walter H. Pearson et al.   REVIEWS IN FISH BIOLOGY AND FISHERIES

Failure of population recovery in relation to disease in Pacific herring

(2010) GD Marty et al.   DISEASES OF AQUATIC ORGANISMS

The North Pacific Climate Transitions of the Winters of 1976/77 and 1988/89

(2010) Sang-Wook Yeh et al.   JOURNAL OF CLIMATE

Multiscale influence of climate on estuarine populations of forage fish: the role of coastal upwelling, freshwater flow and temperature

(2010) JCP Reum et al.   MARINE ECOLOGY PROGRESS SERIES

Central Pacific El Niño and decadal climate change in the North Pacific Ocean

(2010) E. Di Lorenzo et al.   Nature Geoscience

Dealing with missing covariate data in fishery stock assessment models

(2009) Mark N. Maunder et al.   FISHERIES RESEARCH

Testing different methods of incorporating climate data into the assessment of US West Coast sablefish

(2009) M. J. Schirripa et al.   ICES JOURNAL OF MARINE SCIENCE

INCORPORATING COVARIATES INTO FISHERIES STOCK ASSESSMENT MODELS WITH APPLICATION TO PACIFIC HERRING

(2008) Richard B. Deriso et al.   ECOLOGICAL APPLICATIONS

Performance of deviance information criterion model selection in statistical catch-at-age analysis

(2008) Michael J. Wilberg et al.   FISHERIES RESEARCH