R Observatory: Metrics for MSEtool version 3.7.5

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

MSEtool

3.7.5Package record

Management Strategy Evaluation Toolkit

3packages dependsuggested by 1

7.2Kdownloads / year

–test coverage

6/13flavors OK

Overview

About

Maintained by Adrian HordykCRAN page ↗GitHub ↗Website ↗Issues ↗

Development, simulation testing, and implementation of management procedures for fisheries (see Carruthers & Hordyk (2018) doi:10.1111/2041-210X.13081).

Changes in 3.7.5

Fixes

calc_weightedmean_c, used in SSMOM2OM, can return NaN in cpars$Wt_age_C = 0. Overwrite NaN with 0. Occurs with un-exploited age classes, e.g., age zero.

Updates

Add option to turn off Blow calculation in Simulate when control$Bfrac = FALSE
Add spawn_time_frac argument in ASAP2OM
Update gradient in F solver (from TAC) in Project for better precision and maxF constraint
Update SS2MOM for SRR type 7 (survival-based model for elasmobranchs). OM uses custom OM@SRrel = 3
Add dimension names to arrays in MSE output from Project

From NEWS.md in the release

Install

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

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

Development version from Blue-Matter/MSEtool. 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-msetool

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-MSEtool

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-MSEtool

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

7WARNING6OK

Check messages

WARNINGRd cross-referencesr-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-oldrel-windows-x86_64, r-release-linux-x86_64, r-release-windows-x86_64

r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-release-linux-x86_64

Missing link(s) in Rd file 'SS2Data.Rd':
  ‘[r4ss]{SS_output}’

Missing link(s) in Rd file 'SS2DataMOM.Rd':
  ‘[r4ss]{SS_output}’

Missing link(s) in Rd file 'SS2MOM.Rd':
  ‘[r4ss]{SS_output}’

See section 'Cross-references' in the 'Writing R Extensions' manual.

r-devel-windows-x86_64, r-oldrel-windows-x86_64, r-release-windows-x86_64

Missing link(s) in Rd file 'SS2Data.Rd':
  '[r4ss]{SS_output}'

Missing link(s) in Rd file 'SS2DataMOM.Rd':
  '[r4ss]{SS_output}'

Missing link(s) in Rd file 'SS2MOM.Rd':
  '[r4ss]{SS_output}'

See section 'Cross-references' in the 'Writing R Extensions' manual.

WARNINGdependencies in R coder-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-oldrel-windows-x86_64, r-release-linux-x86_64, r-release-windows-x86_64

r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Missing or unexported object:
  ‘r4ss::SS_output’

r-oldrel-windows-x86_64, r-release-windows-x86_64

Missing or unexported object: 'r4ss::SS_output'

r-devel-windows-x86_64

Missing or unexported object:
  'r4ss::SS_output'

r-release-linux-x86_64

Missing or unexported object: ‘r4ss::SS_output’

CRAN check page ↗

Slowest check: 8.7 min · r-oldrel-windows-x86_64

Status changes

WARNING6 OK, 7 WARNINGNow
WARNING11 OK, 2 WARNING2026-10-17
OK13 OK2026-09-08
ERROR12 OK, 1 ERROR2026-09-07
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01

Show 4 earlier changesHide 4 earlier changes

OK12 OK2026-04-25
NOTE11 OK, 3 NOTE2026-04-22
ERROR10 OK, 3 NOTE, 1 ERROR2026-04-18
NOTE11 OK, 3 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 3.7.5

READMEYes · 101 wordsVignettesNoNEWSYes · 100% structured · mentions 3.7.5Citation fileNoWebsiteYes · pkgdown

Help pages: 239 (47 internal)
Examples that run: 47%25 run in a plain check · 28 never run
Exported functions with examples: 28%
Documented parameters: 99%
Return-value docs: 53%
Help pages citing references: 3%

How these are measured

Downloads

7.2K

CRAN downloads in the past year

Rank #4,711 · ~20/day · ~599/mo

Releases R versions

Daily download trend is not available in this view yet.

77330 days

1.7K90 days

7.2K1 year

Compare downloads with other packages →

Also on537 r2u8 autocran

How downloads are counted

Repository

blue-matter/msetool ↗Organization: Blue-Matter

10Stars

4Forks

53Open issues

0Open PRs

10Releases

2,553Commits

4Commit identities

License file reads as GPL-3.0 · 2,553 commits · Last activity 2026-10-20 · Default branch at 4.0.0, ahead of CRAN 3.7.5 (checked 2026-10-18)

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 140
Median days to close, 50 most recently updated closed PRs: 0

Forks over time

2026-07-14 · 32026-09-15 · 4

How these are measured

PracticesBeta

9 development-tooling and community-health practices detected across 6 families in the upstream repository

Checks run against github.com/blue-matter/msetool on 2026-10-18.

Continuous integration (2)

GitHub ActionsR CMD check workflow

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

Docs source (3)

pkgdown

GitHub Pages site last deployed 2025-10-24 · The repository has a site deploy workflow

pkgdown site last built 2025-10-24

Coverage (1)

Coverage reporting (Codecov)

Reproducibility and dev environment (1)

data-raw/

Show all practicesHide 2 practices

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

31 external dependencies (excludes base and recommended)

Installing MSEtool adds 30 packages (14 with compiled code, 19 MB of source tarballs). Heaviest: ggplot2 6.0 MB, Rcpp 1.8 MB, isoband 1.5 MB.

Depends (2)

R >= 4.1.0snowfall

Imports (10)

abind cli dplyrmethodsgrDevicesggplot2parallelRcppstatsutils

LinkingTo (2)

Rcpp RcppArmadillo

Suggests (25)

bootbroom covr crayon DT fmsb kableExtra knitr ggrepel gridExtraMASSmvtnorm openxlsx pak pbapply r4ss readxl reshape2 rfishbase rmarkdown shiny testthat tidyr TMB usethis

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

3direct

0indirect

Depends 3

Suggested by 1

Depends, Imports or LinkingTo, most downloaded first

DLMtool SAMtool openMSE

Suggests, most downloaded first

Slick

How these are counted

Code & Tests

Datasets

People & History

People (4)

Adrian Hordyk

Author, Maintainer since 3.0.0 (2021)

Tom Carruthers

Author

Quang Huynh

Author

Chris Grandin

Contributor

iSCAM functions

Previously maintained by Tom Carruthers (1.0.0 to 2.0.1).

Releases (31)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
3.7.5Latest
record
2025-09-30 · current release · diff ↗
3.7.4
record
2025-06-04 · diff ↗ ·
added 1 export
addMMPs
R
R 4.5.0 released · 2025-04-11
3.7.3
record
2024-11-22 · diff ↗ ·
added 7 exports
Emp, Splot, doHCR, doIfreq, doRec, quantile_plot, smoothy
3.7.2
record
2024-09-23 · diff ↗ ·
added 4 exports
BAM2MOM, PGK, select_MP, tune_MP
R
R 4.4.0 released · 2024-04-24
3.7.1
record
2024-02-06 · diff ↗ ·
added 3 exports
CalcAsymptoticDist, makemov2, simmov2
3.7.0
record
2023-07-20 · diff ↗
R
R 4.3.0 released · 2023-04-21
3.6.2
record
2023-03-28 · diff ↗
3.6.1
record
2023-01-05 · diff ↗
3.6.0
record
2022-10-19 · diff ↗ ·
added 3 exports
Lag_Data, MOM_agg_fleets, addMPs
3.5.0
record
2022-06-07 · diff ↗ ·
added 11 exports
ASAP2Data, ASAP2OM, Assess2MOM, CheckOM, R0conv, SRalphaconv, SRbetaconv, WHAM2OM, getnIVs, hconv, plotRel
R
R 4.2.0 released · 2022-04-22
3.4.0
record
2022-01-05 · diff ↗ ·
added 3 exports
Assess2OM, makeMOM, makeRel

Show 26 earlier eventsHide 26 earlier events

3.3.0
record
2021-11-16 · diff ↗ ·
added 1 export
Awatea2OM
3.2.0
record
2021-08-13 · diff ↗ ·
added 1 export
multiDataS
3.1.1
record
2021-07-08 · diff ↗ ·
added 1 export
plot_SS2MOM
3.1.0
record
2021-07-03 · diff ↗ ·
removed 1 export
MSYCalcs
R
R 4.1.0 released · 2021-05-18
3.0.2
record
2021-03-10 · diff ↗
3.0.1
record
2021-02-02 · diff ↗
3.0.0
record
2021-01-09 · diff ↗ ·
removed 84 exports
Assessment, Awatea2OM, CASAL2OM, CASALpars, DDSS_4010, DDSS_75MSY, DDSS_MSY, DD_SS, DD_TMB, HCR40_10, HCR60_20, HCR_FB, HCR_MSY, HCR_ramp, HCRlin, MPCalcsNAs, NIL, PRBcalc, Probs, ResFromRel, SCA, SCA2, SCA_4010, SCA_75MSY, SCA_MSY, SCA_Pope, SIL, SOL, SP, SP_4010 and 54 more

added 148 exports
AAVE, AAVY, CALsimp, COSEWIC_Blow, COSEWIC_Dplot, COSEWIC_Hplot, COSEWIC_Pplot, COSEWIC_report, COSEWIC_tab, COSEWIC_tab_formatted, CSRA, Can, Cant, ChkYrs, ChooseEffort, ChooseM, ChooseSelect, Converge, Cos_thresh_tab, Cplot, DFO_bar, DFO_hist, DFO_plot, DFO_plot2, DFO_proj, DFO_quant, DFO_report, DFO_spider, DFO_tab, DFO_tab_formatted and 118 more
2.0.1
record
2020-09-29 · diff ↗ ·
added 2 exports
SS2MOM, VPA2OM
2.0.0
record
2020-08-06 · diff ↗
1.7.0
record
2020-06-24 · diff ↗
1.6.0
record
2020-05-05 · diff ↗ ·
removed 1 export
profile_likelihood

added 4 exports
SSS, SSS_4010, SSS_75MSY, SSS_MSY
R
R 4.0.0 released · 2020-04-24
1.5.0
record
2020-03-24 · diff ↗ ·
removed 1 export
plot_SRA_scope
1.4.3
record
2020-01-10 · diff ↗ ·
added 1 export
compare_SRA
1.4.1
record
2019-12-03 · diff ↗
1.4.0
record
2019-12-01 · diff ↗ ·
added 2 exports
project, projection
1.3.0
record
2019-10-01 · diff ↗ ·
added 3 exports
SP_Fox, SRA, Sub_cpars
unarchivedReturned to CRAN
2019-07-30
1.2.1
record
2019-07-30 · diff ↗
archivedRemoved from CRAN
2019-07-20
installation errors were not corrected in time
1.2.0
record
2019-06-17 · diff ↗ ·
removed 6 exports
LinInterp, SRopt, getGpars, getSR, negcorlogspace, optSR

added 38 exports
Assessment, CASAL2OM, CASALpars, MPCalcsNAs, NIL, ResFromRel, SCA_Pope, SIL, SOL, SRA_scope, TAC_MSY, TEG, VPA, cDD, cDD_SS, compare_models, expandHerm, getnIVs, getq_multi, getq_multi_MICE, hrate, ldim, multiData, multiDataS, multiMSE, multidebug, optQ_multi, plotRel, plot_SRA_scope, plotmulti and 8 more
R
R 3.6.0 released · 2019-04-26
1.1.0
record
2018-10-17 · diff ↗ ·
removed 1 export
powdif

added 10 exports
DDSS_4010, DDSS_75MSY, DDSS_MSY, HCR_ramp, SCA_4010, SCA_75MSY, SCA_MSY, SP_4010, SP_75MSY, SP_MSY
1.0.0
record
2018-08-17
R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2018-08-17
Total releases: 31 / 8 yrs
License: GPL-3 OSI
Minimum R: ≥ 4.1.0
Bundled data: 2.9 MB / 58 files
Download size: 3.5 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("MSEtool")

Format

Hordyk, A., Carruthers, T., Grandin, C., & Huynh, Q. (2025). MSEtool: Management Strategy Evaluation Toolkit (Version 3.7.5) [Computer software]. https://doi.org/10.32614/CRAN.package.MSEtool

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 MSEtool version 3.7.5 [Data set]. HJJB, LLC. Data release v2026-10-20. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-20, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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