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SAMtool

The Stock Assessment Methods toolkit (SAMtool) is a collection of assessment methods and management procedures that have been developed for more data-intensive applications. This package includes the Rapid Conditioning Model for conditioning operating models in data-moderate and data-rich fisheries.

SAMtool is part of the openMSE collection of packages.

You can learn more about the openMSE packages at the openMSE documentation site.

Installation

You can install the released version of SAMtool from CRAN with:

install.packages("SAMtool")

And the development version from GitHub with:

# install.packages("remotes")
remotes::install_github("Blue-Matter/SAMtool")

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Version

Install

install.packages('SAMtool')

Monthly Downloads

1,304

Version

1.9.0

License

GPL-3

Issues

Pull Requests

Stars

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Maintainer

Quang Huynh

Last Published

October 21st, 2025

Functions in SAMtool (1.9.0)

HCR_MSY

Harvest control rule to fish at some fraction of maximum sustainable yield
Assessment-class

Class-Assessment
DD_TMB

Delay - Difference Stock Assessment in TMB
Model-based-MP

Model-based management procedures
HCR_fixedF

Simple fixed F harvest control rule
HCR_escapement

Fixed escapement harvest control rule
HCRlin

Generic linear harvest control rule based on biomass
RCM2MOM

Convert RCM to a multi-fleet operating model (MOM)
SAMtool-package

Stock Assessment Methods Toolkit
check_RCMdata

Rapid Conditioning Model (RCM)
RCModel-class

Class-RCModel
RCM_assess

The rapid conditioning model as an assessment function
RCMdata-class

Class-RCMdata
SCA

Statistical catch-at-age (SCA) model
SCA_CAL

Age-structured model using fishery length composition
SP_production

Find the production parameter based on depletion that produces MSY
SP

Surplus production model with FMSY and MSY as leading parameters
compare_models

Compare output from several assessment models
cDD

Continuous Delay-differential assessment model
SSS

Simple Stock Synthesis
PRBcalc

Calculate mahalanobis distance (null and alternative MSEs) and statistical power for all MPs in an MSE
mahplot

Plot statistical power of the indicator with increasing time blocks
Shortcut

Assessment emulator as a shortcut to model fitting in closed-loop simulation
make_interim_MP

Make a custom management procedure (MP)
Probs

Calculates mahalanobis distance and rejection of the Null operating model
VPA

Virtual population analysis (VPA)
getinds

Characterize posterior predictive data
diagnostic

Diagnostic of assessments in MSE: did Assess models converge during MSE?
TAC_MSY

Calculate MSY-based TAC from Assessment object
pcod

Pacific cod in Area 5ABCD (Hecate Strait and Queen Charlotte Sound), British Columbia, Canada
plot.Assessment

Plot Assessment object
plot_residuals

Plot residuals
posterior

Sample posterior of TMB models in SAMtool
plot_timeseries

Plot time series of data
sim-class

Class-sim
simulate

Generate simulated data from TMB models in SAMtool
plot_steepness

Plots probability distribution function of stock-recruit steepness
profile,Assessment-method

Profile likelihood of assessment models
project-class

Class-project
projection

Projections for assessment models
retro-class

Class-retro
SCA_DDM

SCA models with time-varying natural mortality
plot_lognormalvar

Plots a lognormal variable
plot.RCModel

Plot RCM scope output
plot.prof

Plot profile object
plot_crosscorr

Produce a cross-correlation plot of the derived data arising from getinds(MSE_object)
SCA_RWM

SCA with random walk in M
userguide

Get the SAMtool vignettes
retrospective_AM

retrospective_AM (retrospective of Assessment model in MSE)
plot_SR

Plot stock-recruitment function
prof-class

Class-prof
retrospective

Retrospective analysis of assessment models
prelim_AM

Preliminary Assessments in MSE
plot.retro

Methods for retro object
summary.Assessment

Summary of Assessment object
plot_composition

Plot composition data
plot_betavar

Plots a beta variable
swordfish

North Atlantic Swordfish dataset
HCR_ramp

Linearly ramped harvest control rules
HCR_segment

Segmented harvest control rules
HCR_FB

A Harvest Control Rule using B/BMSY and F/FMSY to adjust TAC or TAE.