# Stock Assessment Methods Toolkit

## Documentation for package ‘SAMtool’ version 1.6.0

- DESCRIPTION file.
- Package NEWS.

## Help Pages

A C D G H M P R S T U V

SAMtool-package | Stock Assessment Methods Toolkit

## -- A --

Assessment | Class-'Assessment'
Assessment-class | Class-'Assessment'

## -- C --

calculate_TAC | Calculate MSY-based TAC from Assessment object
cDD | Continuous Delay-differential assessment model
cDD_SS | Continuous Delay-differential assessment model
check_RCMdata | Rapid Conditioning Model (RCM)
compare_models | Compare output from several assessment models
compare_RCM | Plot RCM scope output

## -- D --

Data-rich-MP | Model-based management procedures
DDSS_4010 | Model-based management procedures
DDSS_75MSY | Model-based management procedures
DDSS_MSY | Model-based management procedures
DD_SS | Delay - Difference Stock Assessment in TMB
DD_TMB | Delay - Difference Stock Assessment in TMB
diagnostic | Diagnostic of assessments in MSE: did Assess models converge during MSE?
diagnostic_AM | Diagnostic of assessments in MSE: did Assess models converge during MSE?

## -- G --

getinds | Characterize posterior predictive data

## -- H --

HCR40_10 | Linearly ramped harvest control rules
HCR60_20 | Linearly ramped harvest control rules
HCR80_40MSY | Linearly ramped harvest control rules
HCRlin | Generic linear harvest control rule based on biomass
HCR_escapement | Fixed escapement harvest control rule
HCR_FB | A Harvest Control Rule using B/BMSY and F/FMSY to adjust TAC or TAE.
HCR_fixedF | Simple fixed F harvest control rule
HCR_MSY | Harvest control rule to fish at some fraction of maximum sustainable yield
HCR_ramp | Linearly ramped harvest control rules
HCR_segment | Segmented harvest control rules

## -- M --

mahplot | Plot statistical power of the indicator with increasing time blocks
make_interim_MP | Make a custom management procedure (MP)
make_MP | Make a custom management procedure (MP)
make_projection_MP | Make a custom management procedure (MP)
Model-based-MP | Model-based management procedures
MP | Model-based management procedures

## -- P --

pcod | Pacific cod in Area 5ABCD (Hecate Strait and Queen Charlotte Sound), British Columbia, Canada
Perfect | Assessment emulator as a shortcut to model fitting in closed-loop simulation
plot-method | Plot Assessment object
plot-method | Plot RCM scope output
plot-method | Plot profile object
plot-method | Methods for retro object
plot.Assessment | Plot Assessment object
plot.prof | Plot profile object
plot.RCModel | Plot RCM scope output
plot.retro | Methods for retro object
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_SR | Plot stock-recruitment function
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
posterior-method | Sample posterior of TMB models in SAMtool
posterior.Assessment | Sample posterior of TMB models in SAMtool
posterior.RCModel | Sample posterior of TMB models in SAMtool
PRBcalc | Calculate mahalanobis distance (null and alternative MSEs) and statistical power for all MPs in an MSE
prelim_AM | Preliminary Assessments in MSE
Probs | Calculates mahalanobis distance and rejection of the Null operating model
prof | Class-'prof'
prof-class | Class-'prof'
profile | Profile likelihood of assessment models
profile-method | Profile likelihood of assessment models
project | Class-'project'
project-class | Class-'project'
projection | Projections for assessment models

## -- R --

RCM | Rapid Conditioning Model (RCM)
RCM-method | Rapid Conditioning Model (RCM)
RCM2MOM | Convert RCM to a multi-fleet operating model (MOM)
RCMdata | Class-'RCMdata'
RCMdata-class | Class-'RCMdata'
RCModel | Class-'RCModel'
RCModel-class | Class-'RCModel'
RCMstan | Sample posterior of TMB models in SAMtool
RCM_assess | The rapid conditioning model as an assessment function
retro | Class-'retro'
retro-class | Class-'retro'
retrospective | Retrospective analysis of assessment models
retrospective-method | Retrospective analysis of assessment models
retrospective_AM | retrospective_AM (retrospective of Assessment model in MSE)

## -- S --

SAMtool | Stock Assessment Methods Toolkit
SCA | Statistical catch-at-age (SCA) model
SCA2 | Statistical catch-at-age (SCA) model
SCA_4010 | Model-based management procedures
SCA_75MSY | Model-based management procedures
SCA_CAL | Age-structured model using fishery length composition
SCA_DDM | SCA models with time-varying natural mortality
SCA_MSY | Model-based management procedures
SCA_Pope | Statistical catch-at-age (SCA) model
SCA_RWM | SCA with random walk in M
Shortcut | Assessment emulator as a shortcut to model fitting in closed-loop simulation
Shortcut2 | Assessment emulator as a shortcut to model fitting in closed-loop simulation
sim | Class-'sim'
sim-class | Class-'sim'
simulate | Generate simulated data from TMB models in SAMtool
simulate-method | Generate simulated data from TMB models in SAMtool
simulate.Assessment | Generate simulated data from TMB models in SAMtool
simulate.RCModel | Generate simulated data from TMB models in SAMtool
SP | Surplus production model with FMSY and MSY as leading parameters
SP_4010 | Model-based management procedures
SP_75MSY | Model-based management procedures
SP_Fox | Surplus production model with FMSY and MSY as leading parameters
SP_MSY | Model-based management procedures
SP_production | Find the production parameter based on depletion that produces MSY
SP_SS | Surplus production model with FMSY and MSY as leading parameters
SSS | Simple Stock Synthesis
SSS_4010 | Model-based management procedures
SSS_75MSY | Model-based management procedures
SSS_MSY | Model-based management procedures
summary-method | Methods for retro object
summary-method | Summary of Assessment object
summary.Assessment | Summary of Assessment object
summary.retro | Methods for retro object
swordfish | North Atlantic Swordfish dataset

## -- T --

TAC_MSY | Calculate MSY-based TAC from Assessment object

## -- U --

userguide | Get the SAMtool vignettes

## -- V --

VPA | Virtual population analysis (VPA)