Stock Assessment Methods Toolkit
Class-Assessment
Continuous Delay-differential assessment model
Compare output from several assessment models
Delay - Difference Stock Assessment in TMB
Diagnostic of assessments in MSE: did Assess models converge during MS...
Characterize posterior predictive data
Fixed escapement harvest control rule
A Harvest Control Rule using B/BMSY and F/FMSY to adjust TAC or TAE.
Simple fixed F harvest control rule
Harvest control rule to fish at some fraction of maximum sustainable y...
Linearly ramped harvest control rules
Segmented harvest control rules
Generic linear harvest control rule based on biomass
Plot statistical power of the indicator with increasing time blocks
Make a custom management procedure (MP)
Model-based management procedures
Plots a beta variable
Plot composition data
Produce a cross-correlation plot of the derived data arising from geti...
Plots a lognormal variable
Plot residuals
Plot stock-recruitment function
Plots probability distribution function of stock-recruit steepness
Plot time series of data
Plot Assessment object
Plot profile object
Plot RCM scope output
Methods for retro object
Sample posterior of TMB models in SAMtool
Calculate mahalanobis distance (null and alternative MSEs) and statist...
Preliminary Assessments in MSE
Calculates mahalanobis distance and rejection of the Null operating mo...
Class-prof
Profile likelihood of assessment models
Class-project
Projections for assessment models
The rapid conditioning model as an assessment function
Rapid Conditioning Model (RCM)
Convert RCM to a multi-fleet operating model (MOM)
Class-RCMdata
Class-RCModel
Class-retro
retrospective_AM (retrospective of Assessment model in MSE)
Retrospective analysis of assessment models
Stock Assessment Methods Toolkit
Age-structured model using fishery length composition
SCA models with time-varying natural mortality
SCA with random walk in M
Statistical catch-at-age (SCA) model
Assessment emulator as a shortcut to model fitting in closed-loop simu...
Class-sim
Generate simulated data from TMB models in SAMtool
Find the production parameter based on depletion that produces MSY
Surplus production model with FMSY and MSY as leading parameters
Simple Stock Synthesis
Summary of Assessment object
Calculate MSY-based TAC from Assessment object
Get the SAMtool vignettes
Virtual population analysis (VPA)
Simulation tools for closed-loop simulation are provided for the 'MSEtool' operating model to inform data-rich fisheries. 'SAMtool' provides a conditioning model, assessment models of varying complexity with standardized reporting, model-based management procedures, and diagnostic tools for evaluating assessments inside closed-loop simulation.
Useful links