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SSMSE: An R package for Management Strategy Evaluation with Stock Synthesis Operating Models

CITE Title : SSMSE: An R package for Management Strategy Evaluation with Stock Synthesis Operating Models Personal Author(s) : Doering, Kathryn L.;Vaughan, Nathan R.;Walter, John F.;Methot, Richard D.;Sagarese, Skyler R.;Smith, Matthew;Farmer, Nicholas A.;Calay, Shannon;Cummings, Nancie J.;Johnson, Kelli F.;Marshall, Kristin;Peterson, Cassidy D.;Taylor, Ian G.;Wetzel, Chantel R.; Published Date : 2023 Source : Journal of Open Source Software, 8(90), 4937 DOI : https://doi.org/10.21105/joss.04937 Journal Title : Journal of Open Source Software Doering, Kathryn L. et al. (2023). SSMSE: An R package for Management Strategy Evaluation with Stock Synthesis Operating Models. 8(90). https://doi.org/10.21105/joss.04937 Doering, Kathryn L. et al. "SSMSE: An R package for Management Strategy Evaluation with Stock Synthesis Operating Models" 8, no. 90 (2023), https://doi.org/10.21105/joss.04937 Doering, Kathryn L. et al. "SSMSE: An R package for Management Strategy Evaluation with Stock Synthesis Operating Models" vol. 8, no. 90, 2023, https://doi.org/10.21105/joss.04937 Export RIS Citation Information.

:

Doering, Kathryn L.

;

Vaughan, Nathan R.

2023 | Journal of Open Source Software, 8(90), 4937

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Management Strategy Evaluation (MSE) is a decision-support tool for fisheries management.
A comparison of 4 primary age-structured stock assessment models used in the United States

CITE Title : A comparison of 4 primary age-structured stock assessment models used in the United States Personal Author(s) : Li, Bai;Shertzer, Kyle W.;Lynch, Patrick D.;Ianelli, James N.;Legault, Christopher M.;Williams, Erik H.;Methot Jr., Richard D.;Brooks, Elizabeth N.;Deroba, Jonathan J.;Berger, Aaron M.;Sagarese, Skyler R.;Brodziak, Jon K. T.;Taylor, Ian G.;Karp, Melissa A.;Wetzel, Chantel R.;Supernaw, Matthew; Published Date : 2021 Source : Fishery Bulletin, 119(2-3), 149-167 DOI : https://doi.org/10.7755/FB.119.2-3.5 Journal Title : Fishery Bulletin Li, Bai et al. (2021). A comparison of 4 primary age-structured stock assessment models used in the United States. 119(02). https://doi.org/10.7755/FB.119.2-3.5 Li, Bai et al. "A comparison of 4 primary age-structured stock assessment models used in the United States" 119, no. 02 (2021), https://doi.org/10.7755/FB.119.2-3.5 Li, Bai et al. "A comparison of 4 primary age-structured stock assessment models used in the United States" vol. 119, no. 02, 2021, https://doi.org/10.7755/FB.119.2-3.5 Export RIS Citation Information.

:

Li, Bai ;

Shertzer, Kyle W.

2021 | Fishery Bulletin, 119(2-3), 149-167

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The National Marine Fisheries Service conducts fishery stock assessments to provide the best scientific information available for the U.S. regional fi...
Beyond visualizing catch-at-age models: Lessons learned from the r4ss package about software to support stock assessments

CITE Title : Beyond visualizing catch-at-age models: Lessons learned from the r4ss package about software to support stock assessments Personal Author(s) : Taylor, Ian G.;Doering, Kathryn L.;Johnson, Kelli F.;Wetzel, Chantel R.;Stewart, Ian J.; Published Date : 2021 Source : Fisheries Research, 239, 105924 DOI : https://doi.org/10.1016/j.fishres.2021.105924 Journal Title : Fisheries Research Taylor, Ian G. et al. (2021). Beyond visualizing catch-at-age models: Lessons learned from the r4ss package about software to support stock assessments. 239https://doi.org/10.1016/j.fishres.2021.105924 Taylor, Ian G. et al. "Beyond visualizing catch-at-age models: Lessons learned from the r4ss package about software to support stock assessments" 239 (2021), https://doi.org/10.1016/j.fishres.2021.105924 Taylor, Ian G. et al. "Beyond visualizing catch-at-age models: Lessons learned from the r4ss package about software to support stock assessments" vol. 239, 2021, https://doi.org/10.1016/j.fishres.2021.105924 Export RIS Citation Information.

:

Taylor, Ian G.

;

Doering, Kathryn L.

2021 | Fisheries Research, 239, 105924

No Description
Model-based estimates of effective sample size in stock assessment models using the Dirichlet-multinomial distribution

CITE Title : Model-based estimates of effective sample size in stock assessment models using the Dirichlet-multinomial distribution Personal Author(s) : Thorson, James T.;Johnson, Kelli F.;Methot, Richard D.;Taylor, Ian G.; Published Date : 2017 Source : Fisheries Research, 192, 84-93 DOI : https://doi.org/10.1016/j.fishres.2016.06.005 Journal Title : Fisheries Research Thorson, James T. et al. (2017). Model-based estimates of effective sample size in stock assessment models using the Dirichlet-multinomial distribution. 192https://doi.org/10.1016/j.fishres.2016.06.005 Thorson, James T. et al. "Model-based estimates of effective sample size in stock assessment models using the Dirichlet-multinomial distribution" 192 (2017), https://doi.org/10.1016/j.fishres.2016.06.005 Thorson, James T. et al. "Model-based estimates of effective sample size in stock assessment models using the Dirichlet-multinomial distribution" vol. 192, 2017, https://doi.org/10.1016/j.fishres.2016.06.005 Export RIS Citation Information.

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Thorson, James T.

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Johnson, Kelli F.

2017 | Fisheries Research, 192, 84-93

No Description
A new semi-parametric method for autocorrelated age- and time-varying selectivity in age-structured assessment models

CITE Title : A new semi-parametric method for autocorrelated age- and time-varying selectivity in age-structured assessment models Personal Author(s) : Xu, Haikun;Thorson, James T.;Methot, Richard D.;Taylor, Ian G.; Published Date : 2019 Source : Canadian Journal of Fisheries and Aquatic Sciences, 76(2), 268-285 DOI : https://doi.org/10.1139/cjfas-2017-0446 Journal Title : Canadian Journal of Fisheries and Aquatic Sciences Xu, Haikun et al. (2019). A new semi-parametric method for autocorrelated age- and time-varying selectivity in age-structured assessment models. 76(2). https://doi.org/10.1139/cjfas-2017-0446 Xu, Haikun et al. "A new semi-parametric method for autocorrelated age- and time-varying selectivity in age-structured assessment models" 76, no. 2 (2019), https://doi.org/10.1139/cjfas-2017-0446 Xu, Haikun et al. "A new semi-parametric method for autocorrelated age- and time-varying selectivity in age-structured assessment models" vol. 76, no. 2, 2019, https://doi.org/10.1139/cjfas-2017-0446 Export RIS Citation Information.

:

Xu, Haikun ;

Thorson, James T.

2019 | Canadian Journal of Fisheries and Aquatic Sciences, 76(2), 268-285

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Selectivity is a key parameter in stock assessments that describes how fisheries interact with different ages and sizes of fish. It is usually confoun...
Management Strategy Evaluation of Pacific Hake: Exploring the Robustness of the Current Harvest Policy to Spatial Stock Structure, Shifts in Fishery Selectivity, and Climate-Driven Distribution Shifts

CITE Title : Management Strategy Evaluation of Pacific Hake: Exploring the Robustness of the Current Harvest Policy to Spatial Stock Structure, Shifts in Fishery Selectivity, and Climate-Driven Distribution Shifts Personal Author(s) : Jacobsen, Nis S.;Marshall, Kristin N.;Berger, Aaron M.;Grandin, Chris J.;Taylor, Ian G.; Corporate Authors(s) : United States. National Marine Fisheries Service.;Northwest Fisheries Science Center (U.S.); Published Date : 2021 Series : NOAA Technical Memorandum NMFS-NWFSC ; 168 DOI : https://doi.org/10.25923/x9f9-9b20 Jacobsen, Nis S. et al. (2021). Management Strategy Evaluation of Pacific Hake: Exploring the Robustness of the Current Harvest Policy to Spatial Stock Structure, Shifts in Fishery Selectivity, and Climate-Driven Distribution Shifts. https://doi.org/10.25923/x9f9-9b20 Jacobsen, Nis S. et al. "Management Strategy Evaluation of Pacific Hake: Exploring the Robustness of the Current Harvest Policy to Spatial Stock Structure, Shifts in Fishery Selectivity, and Climate-Driven Distribution Shifts" (2021), https://doi.org/10.25923/x9f9-9b20 Jacobsen, Nis S. et al. "Management Strategy Evaluation of Pacific Hake: Exploring the Robustness of the Current Harvest Policy to Spatial Stock Structure, Shifts in Fishery Selectivity, and Climate-Driven Distribution Shifts" , 2021, https://doi.org/10.25923/x9f9-9b20 Export RIS Citation Information.

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Jacobsen, Nis S. ;

Marshall, Kristin N.

2021 | NOAA Technical Memorandum NMFS-NWFSC ; 168

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The Pacific hake (Merluccius productus) management strategy evaluation (MSE) entered a new iteration in mid-2017. This report documents the MSE proces...
A tale of two species: Disaggregating mixed historical catches of two most common skates in the Northeast Pacific Ocean

CITE Title : A tale of two species: Disaggregating mixed historical catches of two most common skates in the Northeast Pacific Ocean Personal Author(s) : Gertseva, Vladlena;Matson, Sean E.;Taylor, Ian G.; Published Date : 2024 Source : Fisheries Research, 274, 107003 DOI : https://doi.org/10.1016/j.fishres.2024.107003 Journal Title : Fisheries Research Gertseva, Vladlena et al. (2024). A tale of two species: Disaggregating mixed historical catches of two most common skates in the Northeast Pacific Ocean. 274https://doi.org/10.1016/j.fishres.2024.107003 Gertseva, Vladlena and Matson, Sean E. and Taylor, Ian G. "A tale of two species: Disaggregating mixed historical catches of two most common skates in the Northeast Pacific Ocean" 274 (2024), https://doi.org/10.1016/j.fishres.2024.107003 Gertseva, Vladlena et al. "A tale of two species: Disaggregating mixed historical catches of two most common skates in the Northeast Pacific Ocean" vol. 274, 2024, https://doi.org/10.1016/j.fishres.2024.107003 Export RIS Citation Information.

:

Gertseva, Vladlena ;

Matson, Sean E.

2024 | Fisheries Research, 274, 107003

:

Historical catch data represent a key source of information for fisheries stock assessment models. Historically, commercial fishery catch statistics w...
On the use of conditional age at length data as a likelihood component in integrated population dynamics models

CITE Title : On the use of conditional age at length data as a likelihood component in integrated population dynamics models Personal Author(s) : Lee, Huihua;Piner, Kevin R.;Taylor, Ian G.;Kitakado, Toshihide; Published Date : 2019 Source : Fisheries Research, 216, 204-211 DOI : https://doi.org/10.1016/j.fishres.2019.04.007 Journal Title : Fisheries Research Lee, Huihua et al. (2019). On the use of conditional age at length data as a likelihood component in integrated population dynamics models. 216https://doi.org/10.1016/j.fishres.2019.04.007 Lee, Huihua et al. "On the use of conditional age at length data as a likelihood component in integrated population dynamics models" 216 (2019), https://doi.org/10.1016/j.fishres.2019.04.007 Lee, Huihua et al. "On the use of conditional age at length data as a likelihood component in integrated population dynamics models" vol. 216, 2019, https://doi.org/10.1016/j.fishres.2019.04.007 Export RIS Citation Information.

:

Lee, Huihua ;

Piner, Kevin R.

2019 | Fisheries Research, 216, 204-211

:

Integrated population dynamics models use a variety of data types, and all the data used impact modeled processes and estimated dynamics. Paired age-l...
Population genomics of coastal Pacific Hake

CITE Title : Population genomics of coastal Pacific Hake Personal Author(s) : Longo, Gary C.;Head, Melissa A.;Parker‐Stetter, Sandy L.;Taylor, Ian G.;Tuttle, Vanessa J.;Billings, Alicia A.;Gauthier, Stéphane;McClure, Michelle M.;Nichols, Krista M.; Published Date : 2024 Source : North American Journal of Fisheries Management, 44(1), 222-234 DOI : https://doi.org/10.1002/nafm.10969 Journal Title : North American Journal of Fisheries Management Longo, Gary C. et al. (2024). Population genomics of coastal Pacific Hake. 44(1). https://doi.org/10.1002/nafm.10969 Longo, Gary C. et al. "Population genomics of coastal Pacific Hake" 44, no. 1 (2024), https://doi.org/10.1002/nafm.10969 Longo, Gary C. et al. "Population genomics of coastal Pacific Hake" vol. 44, no. 1, 2024, https://doi.org/10.1002/nafm.10969 Export RIS Citation Information.

:

Longo, Gary C.

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Head, Melissa A.

2024 | North American Journal of Fisheries Management, 44(1), 222-234

:

Understanding the genetic structure of harvested fishery species is crucial for accurate stock assessments and effective management strategies. There ...
An Empirical Weight-At-Age Approach Reduces Estimation Bias Compared To Modeling Parametric Growth In Integrated, Statistical Stock Assessment Models When Growth Is Time Varying

CITE Title : An Empirical Weight-At-Age Approach Reduces Estimation Bias Compared To Modeling Parametric Growth In Integrated, Statistical Stock Assessment Models When Growth Is Time Varying Personal Author(s) : Kuriyama, Peter T.;Ono, Kotaro;Hurtado-Ferro, Felipe;Hicks, Allan C.;Taylor, Ian G.;Licandeo, Roberto R.;Johnson, Kelli F.;Anderson, Sean C.;Monnahan, Cole C.;Rudd, Merrill B.;Stawitz, Christine C.;Valero, Juan L.; Published Date : 2016 Source : Fisheries Research 180: 119-127 DOI : https://doi.org/10.1016/j.fishres.2015.09.007 Journal Title : Fisheries Research Kuriyama, Peter T. et al. (2016). An Empirical Weight-At-Age Approach Reduces Estimation Bias Compared To Modeling Parametric Growth In Integrated, Statistical Stock Assessment Models When Growth Is Time Varying. 180https://doi.org/10.1016/j.fishres.2015.09.007 Kuriyama, Peter T. et al. "An Empirical Weight-At-Age Approach Reduces Estimation Bias Compared To Modeling Parametric Growth In Integrated, Statistical Stock Assessment Models When Growth Is Time Varying" 180 (2016), https://doi.org/10.1016/j.fishres.2015.09.007 Kuriyama, Peter T. et al. "An Empirical Weight-At-Age Approach Reduces Estimation Bias Compared To Modeling Parametric Growth In Integrated, Statistical Stock Assessment Models When Growth Is Time Varying" vol. 180, 2016, https://doi.org/10.1016/j.fishres.2015.09.007 Export RIS Citation Information.

:

Kuriyama, Peter T.

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Ono, Kotaro

2016 | Fisheries Research 180: 119-127

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Somatic growth in fishes often varies through time. Despite this, most stock assessments either fix or estimate a time-invariant growth relationship b...
The Effect Of Length Bin Width On Growth Estimation In Integrated Age-Structured Stock Assessments

CITE Title : The Effect Of Length Bin Width On Growth Estimation In Integrated Age-Structured Stock Assessments Personal Author(s) : Monnahan, Cole C.;Ono, Kotaro;Anderson, Sean C.;Rudd, Merrill B.;Hicks, Allan C.;Hurtado-Ferro, Felipe;Johnson, Kelli F.;Kuriyama, Peter T.;Licandeo, Roberto R.;Stawitz, Christine C.;Taylor, Ian G.;Valero, Juan L.; Published Date : 2016 Source : Fisheries Research 180: 103-112 DOI : https://doi.org/10.1016/j.fishres.2015.11.002 Journal Title : Fisheries Research Monnahan, Cole C. et al. (2016). The Effect Of Length Bin Width On Growth Estimation In Integrated Age-Structured Stock Assessments. 180https://doi.org/10.1016/j.fishres.2015.11.002 Monnahan, Cole C. et al. "The Effect Of Length Bin Width On Growth Estimation In Integrated Age-Structured Stock Assessments" 180 (2016), https://doi.org/10.1016/j.fishres.2015.11.002 Monnahan, Cole C. et al. "The Effect Of Length Bin Width On Growth Estimation In Integrated Age-Structured Stock Assessments" vol. 180, 2016, https://doi.org/10.1016/j.fishres.2015.11.002 Export RIS Citation Information.

:

Monnahan, Cole C.

;

Ono, Kotaro

2016 | Fisheries Research 180: 103-112

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Analysts conducting stock assessments using integrated, age-structured models must discretize length data into a limited number of bins (data bins). F...
Leveraging ecological indicators to improve short term forecasts of fish recruitment

CITE Title : Leveraging ecological indicators to improve short term forecasts of fish recruitment Personal Author(s) : Ward, Eric J.;Hunsicker, Mary E.;Marshall, Kristin N.;Oken, Kiva L.;Semmens, Brice X.;Field, John C.;Haltuch, Melissa A.;Johnson, Kelli F.;Taylor, Ian G.;Thompson, Andrew R.;Tolimieri, Nick; Published Date : 2024 Source : Fish and Fisheries (2024) DOI : https://doi.org/10.1111/faf.12850 Journal Title : Fish and Fisheries Ward, Eric J. et al. (2024). Leveraging ecological indicators to improve short term forecasts of fish recruitment. https://doi.org/10.1111/faf.12850 Ward, Eric J. et al. "Leveraging ecological indicators to improve short term forecasts of fish recruitment" (2024), https://doi.org/10.1111/faf.12850 Ward, Eric J. et al. "Leveraging ecological indicators to improve short term forecasts of fish recruitment" , 2024, https://doi.org/10.1111/faf.12850 Export RIS Citation Information.

:

Ward, Eric J.

;

Hunsicker, Mary E.

2024 | Fish and Fisheries (2024)

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Forecasting the recruitment of fish populations with skill has been a challenge in fisheries for over a century. Previous large‐scale meta‐analyse...
Evaluation of alternative modelling approaches to account for spatial effects due to age-based movement

CITE Title : Evaluation of alternative modelling approaches to account for spatial effects due to age-based movement Personal Author(s) : Lee, Hui-Hua;Piner, Kevin R.;Maunder, Mark N.;Taylor, Ian G.;Methot, Richard D.; Published Date : 2017 Source : Canadian Journal of Fisheries and Aquatic Sciences, 74(11), 1832-1844 DOI : https://doi.org/10.1139/cjfas-2016-0294 Journal Title : Canadian Journal of Fisheries and Aquatic Sciences Lee, Hui-Hua et al. (2017). Evaluation of alternative modelling approaches to account for spatial effects due to age-based movement. 74(11). https://doi.org/10.1139/cjfas-2016-0294 Lee, Hui-Hua et al. "Evaluation of alternative modelling approaches to account for spatial effects due to age-based movement" 74, no. 11 (2017), https://doi.org/10.1139/cjfas-2016-0294 Lee, Hui-Hua et al. "Evaluation of alternative modelling approaches to account for spatial effects due to age-based movement" vol. 74, no. 11, 2017, https://doi.org/10.1139/cjfas-2016-0294 Export RIS Citation Information.

:

Lee, Hui-Hua ;

Piner, Kevin R.

2017 | Canadian Journal of Fisheries and Aquatic Sciences, 74(11), 1832-1844

:

Spatial patterns due to age-specific movement have been a source of unmodelled process error. Modeling movement in spatially explicit stock assessment...