Auxiliary diagnostic analyses used to detect model misspecification and highlight potential solutions in stock assessments: application to yellowfin tuna in the eastern Pacific Ocean

M. Auxiliary diagnostic analyses used to detect model misspecification and highlight potential solutions in stock access publication  November . Integrated models (IMs) for stock assessment are simultaneously fit to diverse data sets to estimate parameters related to biological and fishery processes.Modelmisspecificationmayappearascontradictorysignalsinthedataabouttheseprocessesandmaybiastheestimateofquantitiesofinterest.Auxiliarydiagnosticanalysesmaybeusedtodetectmodelmisspecificationandhighlightpotentialsolutions,butnosetofgoodpracticesonwhattouseexistyet.Inthisstudy,weillustratehowtouseauxiliarydiagnosticanalysesnotonlytoidentifymodelmisspecification,butalsotounderstandwhatdatacomponentsprovidedinformationaboutabundance.Thediagnostictoolsincludedlikelihoodcomponentprofilesonthescalingparameter,age-structuredproductionmodels,catch-curveanalyses,andtwonovelanalyses:empiricalselectivityandmonthlydepletionmodels.Whilethelikelihoodprofileindicatedmodelmisspecification,subsequentanalyseswererequiredtoindicatethecausesasunmodelledchangesinselectivityandspatialstructureofthepopulation.Theconsistencybetweenthecatch-curvemodels,themonthlydepletionmodelsandtheIMinformationonabundancecomesfromastrongsignalsharedbyseveralpurse-seinefisheriesdatasets:thelengthcompositiondata informs absolute abundance while the indices of abundance constrain

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