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) |