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: 1.1.2
Depends: R (≥ 3.5.0), MSEtool (≥ 3.0.0)
Imports: TMB, corpcor, dplyr, gplots, graphics, methods, rmarkdown, snowfall, stats, utils
LinkingTo: TMB, RcppEigen
Suggests: caret, covr, ggplot2, knitr, mvtnorm, numDeriv, reshape2, shiny, testthat
Published: 2021-03-09
Author: Quang Huynh [aut, cre], Tom Carruthers [aut], Adrian Hordyk [aut]
Maintainer: Quang Huynh <quang at>
License: GPL-3
NeedsCompilation: yes
Materials: README NEWS
CRAN checks: SAMtool results


Reference manual: SAMtool.pdf
Vignettes: 1a. Delay-difference and delay-differential models
2. Description of the RCM (Rapid Conditioning Model) for conditioning MSEtool operating models
2a. Mathematical description of the RCM
2b. Configuring selectivity for the RCM
1. User guide to SAMtool and model-based MPs
1b. Statistical catch-at-age (SCA) model
1c. Surplus production model
1d. Virtual population analysis (VPA)
Package source: SAMtool_1.1.2.tar.gz
Windows binaries: r-devel:, r-devel-UCRT:, r-release:, r-oldrel:
macOS binaries: r-release (arm64): SAMtool_1.1.2.tgz, r-release (x86_64): SAMtool_1.1.2.tgz, r-oldrel: SAMtool_1.1.2.tgz
Old sources: SAMtool archive

Reverse dependencies:

Reverse depends: openMSE


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