Assessment-class        Class-'Assessment'
DD_TMB                  Delay - Difference Stock Assessment in TMB
HCR_FB                  A Harvest Control Rule using B/BMSY and F/FMSY
                        to adjust TAC or TAE.
HCR_MSY                 Harvest control rule to fish at some fraction
                        of maximum sustainable yield
HCR_escapement          Fixed escapement harvest control rule
HCR_fixedF              Simple fixed F harvest control rule
HCR_ramp                Linearly ramped harvest control rules
HCR_segment             Segmented harvest control rules
HCRlin                  Generic linear harvest control rule based on
                        biomass
Model-based-MP          Model-based management procedures
PRBcalc                 Calculate mahalanobis distance (null and
                        alternative MSEs) and statistical power for all
                        MPs in an MSE
Probs                   Calculates mahalanobis distance and rejection
                        of the Null operating model
RCM2MOM                 Convert RCM to a multi-fleet operating model
                        (MOM)
RCM_assess              The rapid conditioning model as an assessment
                        function
RCMdata-class           Class-'RCMdata'
RCModel-class           Class-'RCModel'
SAMtool-package         Stock Assessment Methods Toolkit
SCA                     Statistical catch-at-age (SCA) model
SCA_CAL                 Age-structured model using fishery length
                        composition
SCA_DDM                 SCA models with time-varying natural mortality
SCA_RWM                 SCA with random walk in M
SP                      Surplus production model with FMSY and MSY as
                        leading parameters
SP_production           Find the production parameter based on
                        depletion that produces MSY
SSS                     Simple Stock Synthesis
Shortcut                Assessment emulator as a shortcut to model
                        fitting in closed-loop simulation
TAC_MSY                 Calculate MSY-based TAC from Assessment object
VPA                     Virtual population analysis (VPA)
cDD                     Continuous Delay-differential assessment model
check_RCMdata           Rapid Conditioning Model (RCM)
compare_models          Compare output from several assessment models
diagnostic              Diagnostic of assessments in MSE: did Assess
                        models converge during MSE?
getinds                 Characterize posterior predictive data
mahplot                 Plot statistical power of the indicator with
                        increasing time blocks
make_interim_MP         Make a custom management procedure (MP)
pcod                    Pacific cod in Area 5ABCD (Hecate Strait and
                        Queen Charlotte Sound), British Columbia,
                        Canada
plot.Assessment         Plot Assessment object
plot.RCModel            Plot RCM scope output
plot.prof               Plot profile object
plot.retro              Methods for retro object
plot_SR                 Plot stock-recruitment function
plot_betavar            Plots a beta variable
plot_composition        Plot composition data
plot_crosscorr          Produce a cross-correlation plot of the derived
                        data arising from getinds(MSE_object)
plot_lognormalvar       Plots a lognormal variable
plot_residuals          Plot residuals
plot_steepness          Plots probability distribution function of
                        stock-recruit steepness
plot_timeseries         Plot time series of data
posterior               Sample posterior of TMB models in SAMtool
prelim_AM               Preliminary Assessments in MSE
prof-class              Class-'prof'
profile,Assessment-method
                        Profile likelihood of assessment models
project-class           Class-'project'
projection              Projections for assessment models
retro-class             Class-'retro'
retrospective           Retrospective analysis of assessment models
retrospective_AM        retrospective_AM (retrospective of Assessment
                        model in MSE)
sim-class               Class-'sim'
simulate                Generate simulated data from TMB models in
                        SAMtool
summary.Assessment      Summary of Assessment object
swordfish               North Atlantic Swordfish dataset
userguide               Get the SAMtool vignettes
