All functions 


Class 

Delay  Difference Stock Assessment in TMB 

A Harvest Control Rule using B/BMSY and F/FMSY to adjust TAC or TAE. 

Harvest control rule to fish at some fraction of maximum sustainable yield 

Fixed escapement harvest control rule 

Simple fixed F harvest control rule 

Linearly ramped harvest control rules 

Segmented harvest control rules 

Generic linear harvest control rule based on biomass 


Modelbased management procedures 
Calculate mahalanobis distance (null and alternative MSEs) and statistical power for all MPs in an MSE 

Calculates mahalanobis distance and rejection of the Null operating model 

Rapid Conditioning Model (RCM) 

Convert RCM to a multifleet operating model (MOM) 

The rapid conditioning model as an assessment function 

Class 

Class 

Stock Assessment Methods Toolkit 

Statistical catchatage (SCA) model 

Agestructured model using fishery length composition 

SCA models with timevarying natural mortality 

SCA with random walk in M 

Surplus production model with FMSY and MSY as leading parameters 

Find the production parameter based on depletion that produces MSY 

Simple Stock Synthesis 

Assessment emulator as a shortcut to model fitting in closedloop simulation 

Calculate MSYbased TAC from Assessment object 

Virtual population analysis (VPA) 

Continuous Delaydifferential assessment model 

Compare output from several assessment models 

Diagnostic of assessments in MSE: did Assess models converge during MSE? 

Characterize posterior predictive data 

Plot statistical power of the indicator with increasing time blocks 

Make a custom management procedure (MP) 

Pacific cod in Area 5ABCD (Hecate Strait and Queen Charlotte Sound), British Columbia, Canada 

Plot Assessment object 

Plot RCM scope output 

Plot profile object 

Methods for retro object 

Plot stockrecruitment function 

Plots a beta variable 

Plot composition data 

Produce a crosscorrelation plot of the derived data arising from getinds(MSE_object) 

Plots a lognormal variable 

Plot residuals 

Plots probability distribution function of stockrecruit steepness 

Plot time series of data 

Sample posterior of TMB models in SAMtool 

Preliminary Assessments in MSE 

Class 

Profile likelihood of assessment models 

Class 

Projections for assessment models 

Class 

Retrospective analysis of assessment models 

retrospective_AM (retrospective of Assessment model in MSE) 

Class 

Generate simulated data from TMB models in SAMtool 

Summary of Assessment object 

North Atlantic Swordfish dataset 

Get the SAMtool vignettes 