Stock Assessment Methods Toolkit

Documentation for package ‘SAMtool’ version 1.6.4

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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)