R Observatory: Metrics for SAMtool version 1.9.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

SAMtool

1.9.2Package record

Stock Assessment Methods Toolkit

1packages depend

7.6Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Quang HuynhCRAN page ↗GitHub ↗Website ↗Issues ↗

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.

Changes in 1.9.2

Fix plot(RCM) when OM@nsim = 1
Fix RCM2MOM when there is only one single fit (identical simulations).
RCM reports recruitment of NA (rather than zero) in first projection year if spawn_time_frac > 0 (spawn timing in middle of time step).
Add argument to allow Mohn's rho calculation with na.rm = TRUE, e.g., summary(ret, na.rm = TRUE).
Import simulate generic from stats package
Update internal RCM_assess functions for better SPR search (avoid errors in selectivity and wider range of F)

From NEWS.md in the release

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. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 8.9 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK12 OK2026-04-25
NOTE11 OK, 3 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.9.2

READMEYes · 109 wordsVignettesNoNEWSYes · 100% structured · mentions 1.9.2Citation fileNoWebsiteYes · pkgdown

Help pages: 61includes a package overview page
Examples that run: 71%29 run in a plain check · 12 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 66%
Documented parameters: 96%
Return-value docs: 83%
Help pages citing references: 38%

How these are measured

Downloads

7.6K

CRAN downloads in the past year

Rank #5,143 · ~21/day · ~632/mo

Releases R versions

Daily download trend is not available in this view yet.

65530 days

1.6K90 days

7.6K1 year

Compare downloads with other packages →

Also on483 r2u9 autocran

How downloads are counted

Repository

blue-matter/samtool ↗Organization: Blue-Matter

3Stars

0Forks

10Open issues

0Open PRs

4Releases

493Commits

2Commit identities

License file reads as GPL-3.0 · 493 commits · Last activity 2026-08-20 · 0% stars, 30d · Default branch at 1.9.3, ahead of CRAN 1.9.2 (checked 2026-10-11)

Responsiveness

How these are sampled

PRs merged (all time): not measured
Median days to close, 50 most recently updated closed issues: 3
Median days to close, 50 most recently updated closed PRs: not measured

Stars over time

2024-04-02 · 32026-07-07 · 3

How these are measured

PracticesBeta

9 development-tooling and community-health practices detected across 5 families in the upstream repository

Checks run against github.com/blue-matter/samtool on 2026-10-11.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux and Windows, and on R-devel

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2026-08-20 · The repository has a site deploy workflow

pkgdown site last built 2026-08-20

Coverage (1)

Coverage reporting

Reproducibility and dev environment (1)

data-raw/

Show all practicesHide 1 practice

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

25 external dependencies (excludes base and recommended)

Installing SAMtool adds 65 packages (36 with compiled code, 50 MB of source tarballs). Heaviest: ggplot2 6.0 MB, bslib 5.6 MB, gplots 4.6 MB.

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

Depends 1

Depends, Imports or LinkingTo, most downloaded first

openMSE

How these are counted

Code & Tests

Datasets

People & History

People (3)

Quang Huynh

Author, Maintainer since 1.0.0 (2021)

Tom Carruthers

Author

Adrian Hordyk

Author

Releases (31)

Pick two releases to compare their code metrics.

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

Show 22 earlier eventsHide 22 earlier events

R
R 4.3.0 released · 2023-04-21
1.5.2
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2023-04-05 · diff ↗
1.5.1
record
2023-02-09 · diff ↗
1.5.0
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2023-01-29 · diff ↗ ·
removed 1 export
profile

added 2 exports
sim, simulate
1.4.1
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2022-11-16 · diff ↗
1.4.0
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2022-06-07 · diff ↗
1.3.1
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2022-05-06 · diff ↗
R
R 4.2.0 released · 2022-04-22
1.3.0
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2022-04-08 · diff ↗
1.2.6
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2022-03-31 · diff ↗ ·
added 6 exports
HCR_fixedF, RCM2MOM, RCM_assess, RCMstan, make_projection_MP, posterior
1.2.5
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2022-01-12 · diff ↗
1.2.4
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2021-12-15 · diff ↗
1.2.3
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2021-11-28 · diff ↗
1.2.2
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2021-09-16 · diff ↗ ·
added 1 export
make_interim_MP
1.2.1
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2021-08-12 · diff ↗ ·
added 1 export
HCR_segment
1.2.0
record
2021-07-06 · diff ↗ ·
removed 1 export
Sub_cpars

added 6 exports
HCR_escapement, RCMdata, SCA_CAL, SCA_DDM, Shortcut2, check_RCMdata
R
R 4.1.0 released · 2021-05-18
1.1.2
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2021-03-09 · diff ↗
1.1.1
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2021-02-17 · diff ↗
1.1.0
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2021-02-02 · diff ↗
1.0.0
record
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

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 package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 v2026-10-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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