All functions

Assessment-class

Class-Assessment

DD_TMB() DD_SS()

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_ramp() HCR40_10() HCR60_20() HCR80_40MSY()

Linearly ramped harvest control rules

HCRlin()

Generic linear harvest control rule based on biomass

SCA_MSY() SCA_75MSY() SCA_4010() DDSS_MSY() DDSS_75MSY() DDSS_4010() SP_MSY() SP_75MSY() SP_4010() SSS_MSY() SSS_75MSY() SSS_4010()

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

check_RCMdata() RCM()

Rapid Conditioning Model (RCM)

RCMdata-class

Class-RCMdata

RCModel-class

Class-RCModel

SAMtool-package

Stock Assessment Methods Toolkit

SCA() SCA2() SCA_Pope()

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() SP_SS() SP_Fox()

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() Perfect()

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() cDD_SS()

Continuous Delay-differential assessment model

compare_models()

Compare output from several assessment models

diagnostic() diagnostic_AM()

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_MP()

Make a custom management procedure (MP)

plot(<Assessment>,<missing>) plot(<Assessment>,<retro>)

Plot Assessment object

plot(<RCModel>,<missing>) compare_RCM()

Plot RCM scope output

plot(<prof>,<missing>)

Plot profile object

plot(<retro>,<missing>) summary(<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

prelim_AM()

Preliminary Assessments in MSE

prof-class

Class-prof

profile()

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)

summary(<Assessment>)

Summary of Assessment object

swordfish

North Atlantic Swordfish dataset

userguide()

Get the SAMtool vignettes