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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

782

Version

1.8.1

License

GPL-3

Issues

Pull Requests

Stars

Forks

Maintainer

Quang Huynh

Last Published

April 28th, 2025

Functions in SAMtool (1.8.1)

HCR_fixedF

Simple fixed F harvest control rule
HCR_escapement

Fixed escapement harvest control rule
DD_TMB

Delay - Difference Stock Assessment in TMB
Assessment-class

Class-Assessment
RCM_assess

The rapid conditioning model as an assessment function
check_RCMdata

Rapid Conditioning Model (RCM)
RCMdata-class

Class-RCMdata
RCModel-class

Class-RCModel
SCA_CAL

Age-structured model using fishery length composition
PRBcalc

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

Statistical catch-at-age (SCA) model
RCM2MOM

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

Stock Assessment Methods Toolkit
Probs

Calculates mahalanobis distance and rejection of the Null operating model
TAC_MSY

Calculate MSY-based TAC from Assessment object
compare_models

Compare output from several assessment models
SP_production

Find the production parameter based on depletion that produces MSY
SCA_DDM

SCA models with time-varying natural mortality
SSS

Simple Stock Synthesis
SCA_RWM

SCA with random walk in M
cDD

Continuous Delay-differential assessment model
Shortcut

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

Virtual population analysis (VPA)
SP

Surplus production model with FMSY and MSY as leading parameters
diagnostic

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

Make a custom management procedure (MP)
plot.prof

Plot profile object
plot_SR

Plot stock-recruitment function
plot.Assessment

Plot Assessment object
plot.retro

Methods for retro object
pcod

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

Plot statistical power of the indicator with increasing time blocks
getinds

Characterize posterior predictive data
plot.RCModel

Plot RCM scope output
prelim_AM

Preliminary Assessments in MSE
plot_steepness

Plots probability distribution function of stock-recruit steepness
plot_timeseries

Plot time series of data
plot_residuals

Plot residuals
plot_lognormalvar

Plots a lognormal variable
profile,Assessment-method

Profile likelihood of assessment models
plot_crosscorr

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

Class-sim
posterior

Sample posterior of TMB models in SAMtool
summary.Assessment

Summary of Assessment object
swordfish

North Atlantic Swordfish dataset
retrospective_AM

retrospective_AM (retrospective of Assessment model in MSE)
plot_betavar

Plots a beta variable
retrospective

Retrospective analysis of assessment models
userguide

Get the SAMtool vignettes
project-class

Class-project
plot_composition

Plot composition data
retro-class

Class-retro
projection

Projections for assessment models
simulate

Generate simulated data from TMB models in SAMtool
prof-class

Class-prof
HCR_MSY

Harvest control rule to fish at some fraction of maximum sustainable yield
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.
Model-based-MP

Model-based management procedures
HCR_segment

Segmented harvest control rules
HCR_ramp

Linearly ramped harvest control rules