Package: SAMtool 1.8.0

Quang Huynh

SAMtool: Stock Assessment Methods Toolkit

Simulation tools for closed-loop simulation are provided for the 'MSEtool' operating model to inform data-rich fisheries. 'SAMtool' provides a conditioning model, assessment models of varying complexity with standardized reporting, model-based management procedures, and diagnostic tools for evaluating assessments inside closed-loop simulation.

Authors:Quang Huynh [aut, cre], Tom Carruthers [aut], Adrian Hordyk [aut]

SAMtool_1.8.0.tar.gz
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SAMtool.pdf |SAMtool.html✨
SAMtool/json (API)
NEWS

# Install 'SAMtool' in R:
install.packages('SAMtool', repos = c('https://blue-matter.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/blue-matter/samtool/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • pcod - Pacific cod in Area 5ABCD (Hecate Strait and Queen Charlotte Sound), British Columbia, Canada
  • swordfish - North Atlantic Swordfish dataset

On CRAN:

6.41 score 3 stars 1 packages 36 scripts 493 downloads 30 mentions 83 exports 74 dependencies

Last updated 17 days agofrom:68365de616. Checks:OK: 9. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 06 2024
R-4.5-win-x86_64OKNov 06 2024
R-4.5-linux-x86_64OKNov 06 2024
R-4.4-win-x86_64OKNov 06 2024
R-4.4-mac-x86_64OKNov 06 2024
R-4.4-mac-aarch64OKNov 06 2024
R-4.3-win-x86_64OKNov 06 2024
R-4.3-mac-x86_64OKNov 06 2024
R-4.3-mac-aarch64OKNov 06 2024

Exports:AssessmentcDDcDD_SScheck_RCMdatacompare_modelscompare_RCMDD_SSDD_TMBDDSS_4010DDSS_75MSYDDSS_MSYdiagnosticdiagnostic_AMgetindsHCR_escapementHCR_FBHCR_fixedFHCR_MSYHCR_rampHCR_segmentHCR40_10HCR60_20HCR80_40MSYHCRlinmahplotmake_interim_MPmake_MPmake_projection_MPPerfectplotplot_betavarplot_compositionplot_crosscorrplot_lognormalvarplot_residualsplot_SRplot_steepnessplot_timeseriesposteriorPRBcalcprelim_AMProbsprofprofileprojectprojectionRCMRCM_assessRCM2MOMRCMdataRCModelRCMstanretroretrospectiveretrospective_AMSCASCA_4010SCA_75MSYSCA_CALSCA_DDMSCA_MSYSCA_PopeSCA_RWMSCA2ShortcutShortcut2simsimulateSPSP_4010SP_75MSYSP_FoxSP_MSYSP_productionSP_SSSSSSSS_4010SSS_75MSYSSS_MSYsummaryTAC_MSYuserguideVPA

Dependencies:abindbase64encbitopsbslibcachemcaToolsclicolorspacedigestdplyrevaluatefansifarverfastmapfontawesomefsgenericsggplot2ggrepelgluegplotsgridExtragtablegtoolshighrhtmltoolsisobandjquerylibjsonliteKernSmoothknitrlabelinglatticelifecyclelmtestmagrittrMASSMatrixmemoisemgcvmimeMSEtoolmunsellnlmepbapplypillarpkgconfigR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenrlangrmarkdownsandwichsassscalessnowsnowfallstrucchangetibbletidyselecttinytexTMBurcautf8varsvctrsviridisLitewithrxfunyamlzoo

Readme and manuals

Help Manual

Help pageTopics
Stock Assessment Methods ToolkitSAMtool-package SAMtool
Class-'Assessment'Assessment Assessment-class
Continuous Delay-differential assessment modelcDD cDD_SS
Rapid Conditioning Model (RCM)check_RCMdata RCM RCM,list,RCMdata-method RCM,OM,Data-method RCM,OM,list-method RCM,OM,RCMdata-method
Compare output from several assessment modelscompare_models
Delay - Difference Stock Assessment in TMBDD_SS DD_TMB
Diagnostic of assessments in MSE: did Assess models converge during MSE?diagnostic diagnostic_AM
Characterize posterior predictive datagetinds
Fixed escapement harvest control ruleHCR_escapement
A Harvest Control Rule using B/BMSY and F/FMSY to adjust TAC or TAE.HCR_FB
Simple fixed F harvest control ruleHCR_fixedF
Harvest control rule to fish at some fraction of maximum sustainable yieldHCR_MSY
Linearly ramped harvest control rulesHCR40_10 HCR60_20 HCR80_40MSY HCR_ramp
Segmented harvest control rulesHCR_segment
Generic linear harvest control rule based on biomassHCRlin
Plot statistical power of the indicator with increasing time blocksmahplot
Make a custom management procedure (MP)make_interim_MP make_MP make_projection_MP
Model-based management proceduresData-rich-MP DDSS_4010 DDSS_75MSY DDSS_MSY Model-based-MP MP SCA_4010 SCA_75MSY SCA_MSY SP_4010 SP_75MSY SP_MSY SSS_4010 SSS_75MSY SSS_MSY
Pacific cod in Area 5ABCD (Hecate Strait and Queen Charlotte Sound), British Columbia, Canadapcod
Plots a beta variableplot_betavar
Plot composition dataplot_composition
Produce a cross-correlation plot of the derived data arising from getinds(MSE_object)plot_crosscorr
Plots a lognormal variableplot_lognormalvar
Plot residualsplot_residuals
Plot stock-recruitment functionplot_SR
Plots probability distribution function of stock-recruit steepnessplot_steepness
Plot time series of dataplot_timeseries
Plot Assessment objectplot,Assessment,missing-method plot,Assessment,retro-method plot.Assessment
Plot profile objectplot,prof,missing-method plot.prof
Plot RCM scope outputcompare_RCM plot,RCModel,missing-method plot.RCModel
Methods for retro objectplot,retro,missing-method plot.retro summary,retro-method summary.retro
Sample posterior of TMB models in SAMtoolposterior posterior,Assessment-method posterior,RCModel-method posterior.Assessment posterior.RCModel RCMstan
Calculate mahalanobis distance (null and alternative MSEs) and statistical power for all MPs in an MSEPRBcalc
Preliminary Assessments in MSEprelim_AM
Calculates mahalanobis distance and rejection of the Null operating modelProbs
Class-'prof'prof prof-class
Profile likelihood of assessment modelsprofile profile,Assessment-method profile,RCModel-method
Class-'project'project project-class
Projections for assessment modelsprojection
The rapid conditioning model as an assessment functionRCM_assess
Convert RCM to a multi-fleet operating model (MOM)RCM2MOM
Class-'RCMdata'RCMdata RCMdata-class
Class-'RCModel'RCModel RCModel-class
Class-'retro'retro retro-class
Retrospective analysis of assessment modelsretrospective retrospective,Assessment-method retrospective,RCModel-method
retrospective_AM (retrospective of Assessment model in MSE)retrospective_AM
Statistical catch-at-age (SCA) modelSCA SCA2 SCA_Pope
Age-structured model using fishery length compositionSCA_CAL
SCA models with time-varying natural mortalitySCA_DDM
SCA with random walk in MSCA_RWM
Assessment emulator as a shortcut to model fitting in closed-loop simulationPerfect Shortcut Shortcut2
Class-'sim'sim sim-class
Generate simulated data from TMB models in SAMtoolsimulate simulate,Assessment-method simulate,RCModel-method simulate.Assessment simulate.RCModel
Surplus production model with FMSY and MSY as leading parametersSP SP_Fox SP_SS
Find the production parameter based on depletion that produces MSYSP_production
Simple Stock SynthesisSSS
Summary of Assessment objectsummary,Assessment-method summary.Assessment
North Atlantic Swordfish datasetswordfish
Calculate MSY-based TAC from Assessment objectcalculate_TAC TAC_MSY
Get the SAMtool vignettesuserguide
Virtual population analysis (VPA)VPA