Man pages for SAMtool
Stock Assessment Methods Toolkit
| Assessment-class | Class-'Assessment' |
| cDD | Continuous Delay-differential assessment model |
| compare_models | Compare output from several assessment models |
| DD_TMB | Delay - Difference Stock Assessment in TMB |
| diagnostic | Diagnostic of assessments in MSE: did Assess models converge... |
| getinds | Characterize posterior predictive data |
| HCR_escapement | Fixed escapement harvest control rule |
| HCR_FB | A Harvest Control Rule using B/BMSY and F/FMSY to adjust TAC... |
| HCR_fixedF | Simple fixed F harvest control rule |
| HCRlin | Generic linear harvest control rule based on biomass |
| HCR_MSY | Harvest control rule to fish at some fraction of maximum... |
| HCR_ramp | Linearly ramped harvest control rules |
| HCR_segment | Segmented harvest control rules |
| mahplot | Plot statistical power of the indicator with increasing time... |
| make_MP | Make a custom management procedure (MP) |
| Model-based-MP | Model-based management procedures |
| pcod | Pacific cod in Area 5ABCD (Hecate Strait and Queen Charlotte... |
| plot.Assessment | Plot Assessment object |
| plot_betavar | Plots a beta variable |
| plot_composition | Plot composition data |
| plot_crosscorr | Produce a cross-correlation plot of the derived data arising... |
| plot_lognormalvar | Plots a lognormal variable |
| plot.prof | Plot profile object |
| plot.RCModel | Plot RCM scope output |
| plot_residuals | Plot residuals |
| plot.retro | Methods for retro object |
| plot_SR | Plot stock-recruitment function |
| plot_steepness | Plots probability distribution function of stock-recruit... |
| plot_timeseries | Plot time series of data |
| posterior | Sample posterior of TMB models in SAMtool |
| PRBcalc | Calculate mahalanobis distance (null and alternative MSEs)... |
| prelim_AM | Preliminary Assessments in MSE |
| Probs | Calculates mahalanobis distance and rejection of the Null... |
| prof-class | Class-'prof' |
| profile | Profile likelihood of assessment models |
| project-class | Class-'project' |
| projection | Projections for assessment models |
| 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 | Class-'RCMdata' |
| RCModel-class | Class-'RCModel' |
| retro-class | Class-'retro' |
| retrospective | Retrospective analysis of assessment models |
| retrospective_AM | retrospective_AM (retrospective of Assessment model in MSE) |
| SAMtool-package | Stock Assessment Methods Toolkit |
| SCA | 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 |
| Shortcut | Assessment emulator as a shortcut to model fitting in... |
| sim-class | Class-'sim' |
| simulate | Generate simulated data from TMB models in SAMtool |
| SP | Surplus production model with FMSY and MSY as leading... |
| SP_production | Find the production parameter based on depletion that... |
| SSS | Simple Stock Synthesis |
| summary.Assessment | Summary of Assessment 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) |
