Stock Assessment Methods Toolkit


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Documentation for package ‘SAMtool’ version 1.1.2

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SAMtool-package Stock Assessment Methods Toolkit
Assessment Class-'Assessment'
Assessment-class Class-'Assessment'
calculate_TAC Calculate MSY-based TAC from Assessment object
cDD Continuous Delay-differential assessment model
cDD_SS Continuous Delay-differential assessment model
compare_models Compare output from several assessment models
compare_RCM Plot RCM scope output
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?
getinds Characterize posterior predictive data
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_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_ramp Linearly ramped harvest control rules
mahplot Plot statistical power of the indicator with increasing time blocks
make_MP Make a custom management procedure (MP)
Model-based-MP Model-based management procedures
MP Model-based management procedures
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
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
RCM Rapid Conditioning Model (RCM)
RCM-method Rapid Conditioning Model (RCM)
RCModel Class-'RCModel'
RCModel-class Class-'RCModel'
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)
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_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
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
Sub_cpars Rapid Conditioning Model (RCM)
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
TAC_MSY Calculate MSY-based TAC from Assessment object
userguide Get the SAMtool vignettes
VPA Virtual population analysis (VPA)