SS3.bib

@article{methotstock2013,
	title = {Stock synthesis: {A} biological and statistical framework for fish stock assessment and fishery management},
	volume = {142},
	issn = {01657836},
	shorttitle = {Stock synthesis},
	url = {http://linkinghub.elsevier.com/retrieve/pii/S0165783612003293},
	doi = {10.1016/j.fishres.2012.10.012},
	language = {en},
	urldate = {2014-05-15},
	journal = {Fisheries Research},
	author = {Methot, Richard D. and Wetzel, Chantell R.},
	month = may,
	year = {2013},
	pages = {86--99},
	file = {Methot and Wetzel - 2013 - Stock synthesis A biological and statistical fram.pdf:C\:\\Users\\Chantel.Wetzel\\Zotero\\storage\\S39WU2T9\\Methot and Wetzel - 2013 - Stock synthesis A biological and statistical fram.pdf:application/pdf;Methot_Wetzel_2013_SuplMat_orig.pdf:C\:\\Users\\Chantel.Wetzel\\Zotero\\storage\\IFTF9RVE\\Methot_Wetzel_2013_SuplMat_orig.pdf:application/pdf;Methot_Wetzel_2013_SuplMat_updated.pdf:C\:\\Users\\Chantel.Wetzel\\Zotero\\storage\\FEEG46H2\\Methot_Wetzel_2013_SuplMat_updated.pdf:application/pdf}
}

@article{taylor-stockrecruitment-2013,
	title = {A stock-recruitment relationship based on pre-recruit survival, illustrated with application to spiny dogfish shark},
	volume = {142},
	issn = {01657836},
	url = {http://linkinghub.elsevier.com/retrieve/pii/S0165783612001567},
	doi = {10.1016/j.fishres.2012.04.018},
	language = {en},
	urldate = {2014-05-15},
	journal = {Fisheries Research},
	author = {Taylor, Ian G. and Gertseva, Vladlena and Methot, Richard D. and Maunder, Mark N.},
	month = may,
	year = {2013},
	pages = {15--21},
	file = {Taylor_etal_2013_SpinyDogfish.pdf:C\:\\Users\\Chantel.Wetzel\\Zotero\\storage\\V9BBW4UA\\Taylor_etal_2013_SpinyDogfish.pdf:application/pdf}
}

@article{francis-data-2011,
	title = {Data weighting in statistical fisheries stock assessment models},
	volume = {68},
	issn = {0706-652X, 1205-7533},
	url = {http://www.nrcresearchpress.com/doi/abs/10.1139/f2011-025},
	doi = {10.1139/f2011-025},
	language = {en},
	number = {6},
	urldate = {2016-06-29},
	journal = {Canadian Journal of Fisheries and Aquatic Sciences},
	author = {Francis, R.I.C. Chris and Hilborn, Ray},
	month = jun,
	year = {2011},
	pages = {1124--1138},
	file = {Francis_2011_DataWeighting.pdf:C\:\\Users\\Chantel.Wetzel\\Zotero\\storage\\NAQX3IC8\\Francis_2011_DataWeighting.pdf:application/pdf}
}

@article{maunder-estimation-2003,
	title = {Estimation of recruitment in catch-at-age models},
	volume = {60},
	issn = {0706-652X, 1205-7533},
	url = {http://www.nrcresearchpress.com/doi/abs/10.1139/f03-104},
	doi = {10.1139/f03-104},
	language = {en},
	number = {10},
	urldate = {2016-06-29},
	journal = {Canadian Journal of Fisheries and Aquatic Sciences},
	author = {Maunder, Mark N and Deriso, Richard B},
	month = oct,
	year = {2003},
	pages = {1204--1216},
	file = {Maunder_Deriso_2003_Recruit_CatchatAge.pdf:C\:\\Users\\Chantel.Wetzel\\Zotero\\storage\\BU9W7KVM\\Maunder_Deriso_2003_Recruit_CatchatAge.pdf:application/pdf}
}

@article{methot-adjusting-2011,
	title = {Adjusting for bias due to variability of estimated recruitments in fishery assessment models},
	volume = {68},
	issn = {0706-652X, 1205-7533},
	url = {http://www.nrcresearchpress.com/doi/abs/10.1139/f2011-092},
	doi = {10.1139/f2011-092},
	language = {en},
	number = {10},
	urldate = {2016-06-29},
	journal = {Canadian Journal of Fisheries and Aquatic Sciences},
	author = {Methot, Richard D. and Taylor, Ian G.},
	month = oct,
	year = {2011},
	pages = {1744--1760},
	file = {Methot_and_Taylor_BiasAdjustment.pdf:C\:\\Users\\Chantel.Wetzel\\Zotero\\storage\\59445A8Z\\Methot_and_Taylor_BiasAdjustment.pdf:application/pdf}
}

@article{monnahan2019overcoming,
  title={Overcoming long Bayesian run times in integrated fisheries stock assessments},
  author={Monnahan, Cole C and Branch, Trevor A and Thorson, James T and Stewart, Ian J and Szuwalski, Cody S},
  journal={ICES Journal of Marine Science},
  language = {en},
  doi = {10.1093/icesjms/fsz059},
  volume={76},
  number={6},
  pages={1477--1488},
  year={2019},
  publisher={Oxford University Press}
}

@article{johnson-can-2016,
	title = {Can autocorrelated recruitment be estimated using integrated assessment models and how does it affect population forecasts?},
	volume = {183},
	issn = {01657836},
	url = {http://linkinghub.elsevier.com/retrieve/pii/S0165783616301928},
	doi = {10.1016/j.fishres.2016.06.004},
	language = {en},
	urldate = {2016-07-11},
	journal = {Fisheries Research},
	author = {Johnson, Kelli F. and Councill, Elizabeth and Thorson, James T. and Brooks, Elizabeth and Methot, Richard D. and Punt, André E.},
	month = nov,
	year = {2016},
	pages = {222--232},
	file = {Johnson_Autocorrelation.pdf:C\:\\Users\\Chantel.Wetzel\\Zotero\\storage\\TVZUNUK8\\Johnson_Autocorrelation.pdf:application/pdf}
}

@article{punt_insights_2016,
	title = {Some insights into data weighting in integrated stock assessments},
	volume = {192},
	issn = {01657836},
	url = {http://linkinghub.elsevier.com/retrieve/pii/S0165783615301582},
	doi = {10.1016/j.fishres.2015.12.006},
	language = {en},
	urldate = {2016-07-11},
	journal = {Fisheries Research},
	author = {Punt, André E.},
	month = jan,
	year = {2016},
	pages = {52--65},
	file = {Punt - 2016 - Some insights into data weighting in integrated st.pdf:C\:\\Users\\Chantel.Wetzel\\Zotero\\storage\\Q4HVWB5J\\Punt - 2016 - Some insights into data weighting in integrated st.pdf:application/pdf},
}

@article{piner-evaluation-2016,
	title = {Evaluation of using random-at-length observations and an equilibrium approximation of the population age structure in fitting the von {Bertalanffy} growth function},
	volume = {180},
	issn = {01657836},
	url = {http://linkinghub.elsevier.com/retrieve/pii/S0165783615001733},
	doi = {10.1016/j.fishres.2015.05.024},
	language = {en},
	urldate = {2016-07-11},
	journal = {Fisheries Research},
	author = {Piner, Kevin R. and Lee, Hui-Hua and Maunder, Mark N.},
	month = aug,
	year = {2016},
	pages = {128--137},
	file = {Piner_etal_inpress_vonBert.pdf:C\:\\Users\\Chantel.Wetzel\\Zotero\\storage\\6M8FH22Q\\Piner_etal_inpress_vonBert.pdf:application/pdf}
}

@article{mcallister-bayesian-1997,
	title = {Bayesian stock assessment using catch-age data and the sampling - importance resampling algorithm},
	volume = {54},
	journal = {Canadian Journal of Fisheries and Aquatic Sciences},
	author = {McAllister, M. K. and Ianelli, J. N.},
	year = {1997},
	pages = {284--300},
	file = {f96-285.pdf:C\:\\Users\\Chantel.Wetzel\\Zotero\\storage\\8KE96JUG\\f96-285.pdf:application/pdf}
}

@article{lee-effects-2017,
	title = {Effects of age-based movement on the estimation of growth assuming random-at-age or random-at-length data},
	volume = {90},
	issn = {1095-8649},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/jfb.13177/abstract},
	doi = {10.1111/jfb.13177},
	abstract = {Simulation methods were used to generate paired data from a simulated population that included the age-based process of movement and the length-based process of gear selection. The age-based process caused bias in the estimates of growth parameters assuming random at length, even when relatively few age classes were affected. Methods that assumed random at age were biased by the subsequent inclusion of the length-based process of gear selection. Additional knowledge of the age structure of the sampled area is needed to ensure an unbiased estimate of the growth parameters when using the length-conditional approach in the presence of age-based movement. Estimates of the variability in the length-at-age relationship were better estimated with the length-conditional than the traditional method even when the assumptions of random at length were violated. Inclusion of paired observations of length and associated age inside the population dynamics model may be the most appropriate way of estimating growth.},
	language = {en},
	number = {1},
	journal = {Journal of Fish Biology},
	author = {Lee, H. H. and Thomas, L. R. and Piner, K. R. and Maunder, M. N.},
	month = jan,
	year = {2017},
	keywords = {simulation, age-based growth, gear selection, length-based growth, von Bertalanffy},
	pages = {222--235},
	file = {Full Text PDF:C\:\\Users\\Chantel.Wetzel\\Zotero\\storage\\IDMASUME\\Lee et al. - 2017 - Effects of age-based movement on the estimation of.pdf:application/pdf;Snapshot:C\:\\Users\\Chantel.Wetzel\\Zotero\\storage\\HF78S3C6\\abstract.html:text/html}
}

@article{punt-extending-2019,
	title = {Extending integrated stock assessment models to use non-depensatory three-parameter stock-recruitment relationships},
	volume = {217},
	issn = {01657836},
	url = {http://linkinghub.elsevier.com/retrieve/pii/S0165783617301819},
	doi = {10.1016/j.fishres.2017.07.007},
	language = {en},
	urldate = {2017-08-03},
	journal = {Fisheries Research},
	author = {Punt, André E. and Cope, Jason M.},
	year = {2019},
	pages = {46--57},
	file = {Punt&Cope_in press_3_parm_SRR_SS.pdf:C\:\\Users\\Chantel.Wetzel\\Zotero\\storage\\GNUGMRK6\\Punt&Cope_in press_3_parm_SRR_SS.pdf:application/pdf}
}

@article{thorson-model-based-2017,
	title = {Model-based estimates of effective sample size in stock assessment models using the {Dirichlet}-multinomial distribution},
	volume = {192},
	issn = {01657836},
	url = {http://linkinghub.elsevier.com/retrieve/pii/S0165783616301941},
	doi = {10.1016/j.fishres.2016.06.005},
	language = {en},
	urldate = {2017-10-26},
	journal = {Fisheries Research},
	author = {Thorson, James T. and Johnson, Kelli F. and Methot, Richard D. and Taylor, Ian G.},
	month = aug,
	year = {2017},
	pages = {84--93},
	file = {Thorson et al. - 2017 - Model-based estimates of effective sample size in .pdf:C\:\\Users\\Chantel.Wetzel\\Zotero\\storage\\CNIXBG6C\\Thorson et al. - 2017 - Model-based estimates of effective sample size in .pdf:application/pdf}
}

@article{maunder-growth-2018,
	title = {The growth cessation model: a growth model for species showing a near cessation in growth with application to bigeye tuna ({Thunnus} obesus)},
	volume = {165},
	issn = {0025-3162, 1432-1793},
	shorttitle = {The growth cessation model},
	url = {http://link.springer.com/10.1007/s00227-018-3336-9},
	doi = {10.1007/s00227-018-3336-9},
	language = {en},
	number = {4},
	urldate = {2018-04-05},
	journal = {Marine Biology},
	author = {Maunder, Mark N. and Deriso, Richard B. and Schaefer, Kurt M. and Fuller, Daniel W. and Aires-da-Silva, Alexandre M. and Minte-Vera, Carolina V. and Campana, Steven E.},
	month = apr,
	year = {2018},
	file = {Maunder et al. 2018 (growth cessation model).pdf:C\:\\Users\\Chantel.Wetzel\\Zotero\\storage\\TD36HTIN\\Maunder et al. 2018 (growth cessation model).pdf:application/pdf}
}

@techreport{gertseva-status-2013,
	title = {Status of the darkblotched rockfish resource off the continental {U}.{S}. {Pacific} {Coast} in 2013},
	institution = {Pacific Fishery Management Council, 7700 Ambassador Place NE, Suite 200, Portland, OR 97220},
	author = {Gertseva, Vladlena and {Thorson, James T}},
	year = {2013}
}

@article{lee-use-2019,
	title = {On the use of conditional age at length data as a likelihood component in integrated population dynamics models},
	volume = {216},
	issn = {01657836},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0165783619301043},
	doi = {10.1016/j.fishres.2019.04.007},
	abstract = {Integrated population dynamics models use a variety of data types, and all the data used impact modeled processes and estimated dynamics. Paired age-length data treated as conditional age-at-length (CAAL) data are increasingly being used as a data component in stock assessment models. The original intent of the use of CAAL data was to directly estimate the length-at-age process, including the associated variability in length-at-age. However, we show that introduction of CAAL data that are not representative of the age-structure of the population can cause bias and imprecision in estimates of not only growth, but also dynamics and management quantities. Estimation of an appropriate age-based observations-modeled process may improve model performance. We also show that even the use of representative CAAL data in a model with misspecified age-based systems-modeled processes (natural mortality and time-varying growth) can lead to bias and imprecision in growth, dynamics, and management quantities. In these cases, estimation of an age-based observations-modeled process magnified the bias and imprecision. Greater consideration of this type of data is needed.},
	language = {en},
	urldate = {2019-05-23},
	journal = {Fisheries Research},
	author = {Lee, Huihua and Piner, Kevin R. and Taylor, Ian G. and Kitakado, Toshihide},
	month = aug,
	year = {2019},
	pages = {204--211},
	file = {Lee et al. - 2019 - On the use of conditional age at length data as a .pdf:C\:\\Users\\Chantel.Wetzel\\Zotero\\storage\\46AH2Q25\\Lee et al. - 2019 - On the use of conditional age at length data as a .pdf:application/pdf}
}

@article{xu-new-2019,
	title = {A new semi-parametric method for autocorrelated age- and time-varying selectivity in age-structured assessment models},
	volume = {76},
	issn = {0706-652X, 1205-7533},
	url = {http://www.nrcresearchpress.com/doi/10.1139/cjfas-2017-0446},
	doi = {10.1139/cjfas-2017-0446},
	abstract = {Selectivity is a key parameter in stock assessments that describes how fisheries interact with different ages and sizes of fish. It is usually confounded with other processes (e.g., natural mortality and recruitment) in stock assessments and the assumption of selectivity can strongly affect stock assessment outcome. Here, we introduce a new semi-parametric selectivity method, which we implement and test in Stock Synthesis. This selectivity method includes a parametric component and an autocorrelated nonparametric component consisting of deviations from the parametric component. We explore the new selectivity method using two simulation experiments, which show that the two autocorrelation parameters for selectivity deviations of data-rich fisheries are estimable using either mixed-effect or simpler sample-based algorithms. When selectivity deviations of a data-rich fishery are highly autocorrelated, using the new method to estimate the two autocorrelation parameters leads to more precise estimations of spawning biomass and fully selected fishing mortality. However, this new method fails to improve model performance in low data quality cases where measurement error in the data overwhelms the pattern caused by the autocorrelated process. Finally, we use a case study involving North Sea herring (Clupea harengus) to show that our new method substantially reduces autocorrelations in the Pearson residuals in fit to age composition data.},
	language = {en},
	number = {2},
	urldate = {2019-05-29},
	journal = {Canadian Journal of Fisheries and Aquatic Sciences},
	author = {Xu, Haikun and Thorson, James T. and Methot, Richard D. and Taylor, Ian G.},
	month = feb,
	year = {2019},
	pages = {268--285},
	file = {Xu et al. - 2019 - A new semi-parametric method for autocorrelated ag.pdf:C\:\\Users\\Chantel.Wetzel\\Zotero\\storage\\ZJ64IPKT\\Xu et al. - 2019 - A new semi-parametric method for autocorrelated ag.pdf:application/pdf}
}

@article{xu-comparing-2019,
	title = {Comparing the performance of three data weighting methods when allowing for time-varying selectivity},
	issn = {0706-652X, 1205-7533},
	url = {http://www.nrcresearchpress.com/doi/10.1139/cjfas-2019-0107},
	doi = {10.1139/cjfas-2019-0107},
	language = {en},
	urldate = {2019-09-26},
	journal = {Canadian Journal of Fisheries and Aquatic Sciences},
	author = {Xu, Haikun and Thorson, James T and Methot, Richard D},
	month = jun,
	year = {2019},
	pages = {cjfas--2019--0107},
	file = {Xu et al. - 2019 - Comparing the performance of three data weighting .pdf:C\:\\Users\\Chantel.Wetzel\\Zotero\\storage\\GITXVVB9\\Xu et al. - 2019 - Comparing the performance of three data weighting .pdf:application/pdf}
}

@techreport{grandin-status-2020,
	address = {National Marine Fisheries Service and Fisheries and Ocean Canada},
	title = {Status of {Pacific} {Hake} (whiting) stock in the {U}.{S}. and {Canadian} waters in 2020},
	institution = {Joint Technical Committe of the Pacific Hake/Whiting Agreement Between the Governments of the United States and Canada},
	author = {Grandin, Chris J. and Johnson, Kelli F. and Edwards, Andrew M. and Berger, Aaron M.},
	year = {2020},
	pages = {273},
	file = {hake-assessment-2020-final.pdf:C\:\\Users\\Chantel.Wetzel\\Zotero\\storage\\WLJUJBAG\\hake-assessment-2020-final.pdf:application/pdf}
}

@article{thompson-confounding-1994,
	title = {Confounding of {Gear} {Selectivity} and the {Natural} {Mortality} {Rate} in {Cases} where the {Former} is a {Nonmonotone} {Function} of {Age}},
	volume = {51},
	issn = {0706-652X, 1205-7533},
	url = {http://www.nrcresearchpress.com/doi/10.1139/f94-265},
	doi = {10.1139/f94-265},
	abstract = {An "exponential-logistic" selectivity function is presented in which a single parameter (γ) determines whether gear selectivity is asymptotic (γ = 0) or reaches a maximum at finite age (γ {\textgreater} 0). The function is used to develop a model in which both γ and the natural mortality rate M are formally indeterminate and in which the coming year's catch limit can be viewed as a response function of either estimated γ or estimated M. Decision theory is then used to derive the optimal catch. The optimal catch is shown to increase with the degree of uncertainty surrounding M, although this conclusion may depend on the short managerial time frame assumed. Three "suboptimal" strategies are also considered: (1) setting catch at the level corresponding to the expected value of M, (2) setting catch at the minimum of the response function, and (3) setting catch at the level corresponding to γ = 0. The first suboptimal strategy never results in a catch greater than the optimum and always results in a lower expected loss than the second. The performance of the third strategy (relative to the others) depends on parameter values.},
	language = {en},
	number = {12},
	urldate = {2020-05-18},
	journal = {Canadian Journal of Fisheries and Aquatic Sciences},
	author = {Thompson, Grant G.},
	month = dec,
	year = {1994},
	pages = {2654--2664},
	file = {Thompson - 1994 - Confounding of Gear Selectivity and the Natural Mo.pdf:C\:\\Users\\Chantel.Wetzel\\Zotero\\storage\\W2RDP4YU\\Thompson - 1994 - Confounding of Gear Selectivity and the Natural Mo.pdf:application/pdf}
}

@article{maunder2010bigeye,
  title={Preliminary estimation of age-and sex-specific natural mortality of bigeye tuna in the eastern Pacific Ocean by applying a cohort analysis with auxiliary information to tagging data},
  author={Maunder, Mark N and Aires-da-Silva, Alexandre and Deriso, Richard and Schaefer, Kurt and Fuller, Daniel},
  journal={Inter-Amer. Trop. Tuna Comm., Stock Assessment Report},
  volume={10},
  pages={253--278},
  year={2010}
}

@article{lorenzen2000allometry,
  title={Allometry of natural mortality as a basis for assessing optimal release size in fish-stocking programmes},
  author={Lorenzen, Kai},
  journal={Canadian Journal of Fisheries and Aquatic Sciences},
  volume={57},
  number={12},
  pages={2374--2381},
  year={2000},
  publisher={NRC Research Press Ottawa, Canada}
}

@article{lehodey2008spatial,
  title={A spatial ecosystem and populations dynamics model (SEAPODYM)--Modeling of tuna and tuna-like populations},
  author={Lehodey, Patrick and Senina, Inna and Murtugudde, Raghu},
  journal={Progress in Oceanography},
  volume={78},
  number={4},
  pages={304--318},
  year={2008},
  publisher={Elsevier}
}

@article{then2015evaluating,
  title={Evaluating the predictive performance of empirical estimators of natural mortality rate using information on over 200 fish species},
  author={Then, Amy Y and Hoenig, John M and Hall, Norman G and Hewitt, David A and Handling editor: Ernesto Jardim},
  journal={ICES Journal of Marine Science},
  volume={72},
  number={1},
  pages={82--92},
  year={2015},
  publisher={Oxford University Press}
}

@article{gulland1987natural,
  title={Natural mortality and size},
  author={Gulland, JA},
  journal={Marine Ecology Progress Series},
  volume={39},
  number={2},
  pages={197--199},
  year={1987}
}

@article{lorenzen1996relationship,
  title={The relationship between body weight and natural mortality in juvenile and adult fish: a comparison of natural ecosystems and aquaculture},
  author={Lorenzen, K},
  journal={Journal of Fish Biology},
  volume={49},
  number={4},
  pages={627--642},
  year={1996},
  publisher={Wiley Online Library}
}

@incollection{maunder2011M,
  title={Proposed formulation for age-specific patterns in natural mortality},
  author={Maunder, Mark N.},
  pages={38},
  year={2011}, 
  booktitle={Estimating natural mortality in stock assessment applications},
  editor={Brodziak, J and Ianelli, J. and Lorenzen, K. and Methot, R.D., Jr.},
  publisher={U.S. Department of Commerce, NOAA Tech. Memo},
  address={Silver Spring, Maryland, USA}
}

@article{schnute1981growth,
  title={A versatile growth model with statistically stable parameters},
  author={Schnute, Jon},
  journal={Canadian Journal of Fisheries and Aquatic Science},
  volume={38},
  pages={1128--1140},
  year={1981}
}

@article{richards1959growth,
  title={A flexible growth function for empirical use},
  author={Richards, F.J.},
  journal={Journal of Experimental Botany},
  volume={10},
  number={29},
  pages={290--300},
  year={1959}
}