All functions |
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Class- |
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Delay - Difference Stock Assessment in TMB |
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A Harvest Control Rule using B/BMSY and F/FMSY to adjust TAC or TAE. |
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Harvest control rule to fish at some fraction of maximum sustainable yield |
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Fixed escapement harvest control rule |
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Simple fixed F harvest control rule |
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Linearly ramped harvest control rules |
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Segmented harvest control rules |
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Generic linear harvest control rule based on biomass |
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Model-based management procedures |
Calculate mahalanobis distance (null and alternative MSEs) and statistical power for all MPs in an MSE |
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Calculates mahalanobis distance and rejection of the Null operating model |
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Rapid Conditioning Model (RCM) |
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Convert RCM to a multi-fleet operating model (MOM) |
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The rapid conditioning model as an assessment function |
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Class- |
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Class- |
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Stock Assessment Methods Toolkit |
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Statistical catch-at-age (SCA) model |
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Age-structured model using fishery length composition |
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SCA models with time-varying natural mortality |
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SCA with random walk in M |
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Surplus production model with FMSY and MSY as leading parameters |
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Find the production parameter based on depletion that produces MSY |
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Simple Stock Synthesis |
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Assessment emulator as a shortcut to model fitting in closed-loop simulation |
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Calculate MSY-based TAC from Assessment object |
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Virtual population analysis (VPA) |
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Continuous Delay-differential assessment model |
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Compare output from several assessment models |
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Diagnostic of assessments in MSE: did Assess models converge during MSE? |
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Characterize posterior predictive data |
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Plot statistical power of the indicator with increasing time blocks |
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Make a custom management procedure (MP) |
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Pacific cod in Area 5ABCD (Hecate Strait and Queen Charlotte Sound), British Columbia, Canada |
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Plot Assessment object |
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Plot RCM scope output |
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Plot profile object |
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Methods for retro object |
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Plot stock-recruitment function |
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Plots a beta variable |
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Plot composition data |
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Produce a cross-correlation plot of the derived data arising from getinds(MSE_object) |
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Plots a lognormal variable |
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Plot residuals |
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Plots probability distribution function of stock-recruit steepness |
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Plot time series of data |
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Sample posterior of TMB models in SAMtool |
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Preliminary Assessments in MSE |
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Class- |
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Profile likelihood of assessment models |
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Class- |
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Projections for assessment models |
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Class- |
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Retrospective analysis of assessment models |
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retrospective_AM (retrospective of Assessment model in MSE) |
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Class- |
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Generate simulated data from TMB models in SAMtool |
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Summary of Assessment object |
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North Atlantic Swordfish dataset |
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Get the SAMtool vignettes |