R Observatory: Metrics for SAMtool version 1.9.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

SAMtool

1.9.2

Stock Assessment Methods Toolkit

1packages depend

8.7Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Quang HuynhFirst published 2021-01-2231 releasesCRAN page ↗GitHub ↗

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.

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("SAMtool", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("Blue-Matter/SAMtool")

Development version from Blue-Matter/SAMtool. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-samtool

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-SAMtool

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-SAMtool

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 9.0 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

13

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-03-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 109 wordsVignettesNopkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 71%
Documented parameters: 96%
Return-value docs: 83%
References docs: 38%

Downloads

8.7K

CRAN downloads in the past year

Rank #4,463 · ~24/day · ~729/mo

Releases R versions

Daily download trend is not available in this view yet.

35930 days

1.8K90 days

8.7K1 year

Compare downloads with other packages →

Also on557 r2u24 autocran

Repository

GitHub ↗ blue-matter/samtool

3Stars

0Forks

7Open issues

0Open PRs

4Releases

493Commits

2Contributors

License GPL-3.0 · 493 commits · Last activity 2026-08-20

Stars over time

2024-04-02 · 32026-07-07 · 3

Repository practices

Upstream repositoryBeta

4 development-tooling and community-health practices detected across 4 families in the upstream repository

Checks run against github.com/blue-matter/samtool on 2026-08-23.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

data-raw/

Docs source (1)

README.Rmd

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

25 external dependencies (excludes base and recommended)

Depends (2)

R >= 4.1.0MSEtool

Imports (12)

TMB abind dplyr gplotsgraphicsmethodspbapply rmarkdown snowfallstatsutilsvars

LinkingTo (2)

TMB RcppEigen

Suggests (14)

caret corpcor covr extraDistr ggplot2 Gmisc knitr mvtnorm numDeriv reshape2 shiny testthat tmbstan usethis

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

openMSE

Code & Tests

Datasets

People & History

People (3)

Maintainer (1)

Quang Huynh

Author, Maintainer

Authors (3)

Quang Huynh

Author, Maintainer

Tom Carruthers

Author

Adrian Hordyk

Author

Package Timeline

31 releases. Pick two to compare their code metrics. R releases are shown for context.

1.9.2Latest
2026-06-19 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
1.9.1
2026-01-15 · diff ↗
1.9.0
2025-10-21 · diff ↗
1.8.2
2025-09-05 · diff ↗
1.8.1
2025-04-29 · diff ↗
R
R 4.5.0 released · 2025-04-11
1.8.0
2024-11-08 · diff ↗
1.7.0
2024-08-29 · diff ↗
R
R 4.4.0 released · 2024-04-24
1.6.4
2024-02-15 · diff ↗
1.6.3
2023-11-18 · diff ↗
1.6.2
2023-10-26 · diff ↗
1.6.1
2023-08-23 · diff ↗
1.6.0
2023-07-19 · diff ↗
1.5.3
2023-05-23 · diff ↗

Show 22 earlier events

R
R 4.3.0 released · 2023-04-21
1.5.2
2023-04-05 · diff ↗
1.5.1
2023-02-09 · diff ↗
1.5.0
2023-01-29 · diff ↗
1.4.1
2022-11-16 · diff ↗
1.4.0
2022-06-07 · diff ↗
1.3.1
2022-05-06 · diff ↗
R
R 4.2.0 released · 2022-04-22
1.3.0
2022-04-08 · diff ↗
1.2.6
2022-03-31 · diff ↗
1.2.5
2022-01-12 · diff ↗
1.2.4
2021-12-15 · diff ↗
1.2.3
2021-11-28 · diff ↗
1.2.2
2021-09-16 · diff ↗
1.2.1
2021-08-12 · diff ↗
1.2.0
2021-07-06 · diff ↗
R
R 4.1.0 released · 2021-05-18
1.1.2
2021-03-09 · diff ↗
1.1.1
2021-02-17 · diff ↗
1.1.0
2021-02-02 · diff ↗
1.0.0
2021-01-22
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2021-01-22
Total releases: 31 / 5 yrs
License: GPL-3 OSI
Minimum R: ≥ 4.1.0
Bundled data: 6.9 KB / 2 files
Download size: 313 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("SAMtool")

Format

Huynh, Q., Carruthers, T., & Hordyk, A. (2026). SAMtool: Stock Assessment Methods Toolkit (Version 1.9.2) [Computer software]. https://doi.org/10.32614/CRAN.package.SAMtool

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for SAMtool version 1.9.2 [Data set]. HJJB, LLC. Data release v2026-08-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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