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.

Version:	1.9.1
Depends:	R (≥ 4.1.0), MSEtool (≥ 3.0.0)
Imports:	TMB (≥ 1.9.0), abind, dplyr, gplots, graphics, methods, pbapply, rmarkdown, snowfall, stats, utils, vars
LinkingTo:	TMB, RcppEigen
Suggests:	caret, corpcor, covr, extraDistr, ggplot2, Gmisc, knitr, mvtnorm, numDeriv, reshape2, shiny, testthat, tmbstan, usethis
Published:	2026-01-15
DOI:	10.32614/CRAN.package.SAMtool
Author:	Quang Huynh [aut, cre], Tom Carruthers [aut], Adrian Hordyk [aut]
Maintainer:	Quang Huynh <quang at bluematterscience.com>
BugReports:	https://github.com/Blue-Matter/SAMtool/issues
License:	GPL-3
URL:	https://openmse.com, https://samtool.openmse.com, https://github.com/Blue-Matter/SAMtool
NeedsCompilation:	yes
Materials:	README, NEWS
CRAN checks:	SAMtool results

Documentation:

Reference manual:

SAMtool.html , SAMtool.pdf

Downloads:

Package source:	SAMtool_1.9.1.tar.gz
Windows binaries:	r-devel: SAMtool_1.9.1.zip, r-release: SAMtool_1.9.1.zip, r-oldrel: SAMtool_1.9.1.zip
macOS binaries:	r-release (arm64): SAMtool_1.9.1.tgz, r-oldrel (arm64): SAMtool_1.9.1.tgz, r-release (x86_64): SAMtool_1.9.1.tgz, r-oldrel (x86_64): SAMtool_1.9.1.tgz
Old sources:	SAMtool archive

Reverse dependencies:

Reverse depends:

openMSE

Linking:

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