Function reference • SAMtool

All functions
`Assessment-class` `Assessment`	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_fixedF()`	Simple fixed F harvest control rule
`HCR_ramp()` `HCR40_10()` `HCR60_20()` `HCR80_40MSY()`	Linearly ramped harvest control rules
`HCR_segment()`	Segmented 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)
`RCM2MOM()`	Convert RCM to a multi-fleet operating model (MOM)
`RCM_assess()`	The rapid conditioning model as an assessment function
`RCMdata-class` `RCMdata`	Class-`RCMdata`
`RCModel-class` `RCModel`	Class-`RCModel`
`SAMtool-package` `SAMtool`	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()` `Shortcut2()` `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_interim_MP()` `make_projection_MP()` `make_MP()`	Make a custom management procedure (MP)
`pcod`	Pacific cod in Area 5ABCD (Hecate Strait and Queen Charlotte Sound), British Columbia, Canada
`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
`posterior()` `RCMstan()`	Sample posterior of TMB models in SAMtool
`prelim_AM()`	Preliminary Assessments in MSE
`prof-class` `prof`	Class-`prof`
`profile(<Assessment>)` `profile(<RCModel>)`	Profile likelihood of assessment models
`project-class` `project`	Class-`project`
`projection()`	Projections for assessment models
`retro-class` `retro`	Class-`retro`
`retrospective()`	Retrospective analysis of assessment models
`retrospective_AM()`	retrospective_AM (retrospective of Assessment model in MSE)
`sim-class` `sim`	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

Reference

All functions