R Observatory: Metrics for salmonMSE version 2.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

salmonMSE

2.1.0

Management Strategy Evaluation for Salmon Species

0packages depend

2.9Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Quang HuynhFirst published 2025-09-234 releasesCRAN page ↗GitHub ↗

Simulation tools to evaluate the long-term effects of salmon management strategies, including a combination of habitat, harvest, and habitat actions. The stochastic age-structured operating model accommodates complex life histories, including freshwater survival across early life stages, juvenile survival and fishery exploitation in the marine life stage, partial maturity by age class, and fitness impacts of hatchery programs on natural spawning populations. 'salmonMSE' also provides an age-structured conditioning model to develop operating models fitted to data.

Install

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

install.packages("salmonMSE", 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/salmonMSE")

Development version from Blue-Matter/salmonMSE. 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-salmonmse

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-salmonMSE

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-salmonMSE

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

Health

CRAN checks

13OK

Slowest check: 4.3 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

13

Dependencies · direct

Check history

OK2026-08-04
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-07-22
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-25
11 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-29
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 2 earlier snapshots

WARNING2026-03-22
13 OK · 0 NOTE · 1 WARNING · 0 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 91 wordsVignettesNopkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 94%
Documented parameters: 99%
Return-value docs: 92%
References docs: 13%

Downloads

2.9K

CRAN downloads in the past year

Rank #10,374 · ~8/day · ~245/mo

Releases R versions

Daily download trend is not available in this view yet.

22530 days

93090 days

2.9K1 year

Compare downloads with other packages →

Also on87 r2u18 autocran

Repository

GitHub ↗ blue-matter/salmonmse

0Stars

0Forks

14Open issues

0Open PRs

0Releases

License GPL-3.0 · Last activity 2026-08-15

Issues over time

2026-07-07 · 222026-08-18 · 14

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/salmonmse on 2026-08-16.

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

14 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (13)

abind MSEtool RTMB dplyr ggplot2grDevicesgslmethodsreshape2 rlang rmarkdownstatsutils

LinkingTo (0)

none

Suggests (5)

ggrepel rstan scales testthat tmbstan

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (1)

Maintainer (1)

Quang Huynh

Author, Maintainer

Authors (1)

Quang Huynh

Author, Maintainer

Package Timeline

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

2.1.0Latest
2026-04-25 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
2.0.0
2026-04-16 · diff ↗
1.0.0
2026-03-21 · diff ↗
0.1.0
2026-03-10
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-09-23
Total releases: 4 / 1 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 3.5.0
Bundled data: 4.6 KB / 3 files
Download size: 130 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("salmonMSE")

Format

Huynh, Q. (2026). salmonMSE: Management Strategy Evaluation for Salmon Species (Version 2.1.0) [Computer software]. https://doi.org/10.32614/CRAN.package.salmonMSE

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 salmonMSE version 2.1.0 [Data set]. HJJB, LLC. Data release v2026-08-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

Report a problem with this page →