R Observatory: Metrics for rFAMS version 0.0.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

rFAMS

0.0.3Package record

Fisheries Analysis and Modeling Simulator

0packages depend

3.5Kdownloads / year

89.4%test coverage

13/13flavors OK

Overview

About

Maintained by Jason C. DollCRAN page ↗GitHub ↗Issues ↗

Simulates the dynamics of exploited fish populations using the Jones modification of the Beverton-Holt equilibrium yield equation to compute yield-per-recruit and dynamic pool models (Ricker 1975) https://publications.gc.ca/site/eng/480738/publication.html. Allows users to evaluate minimum, slot, and inverted length limits on exploited fisheries using specified life history parameters. Users can simulate population under a variety of conditional fishing mortality and conditional natural mortality. Calculated quantities include number of fish harvested and dying naturally, mean weight and length of fish harvested, number of fish that reach specified lengths of interest, total number of fish and biomass in the population, and stock density indices.

Changes in 0.0.3

This is the start of the next version
Removed yprBH_MinLL_fixed() and yprBH_Min_var(), and replaced with a single function ypr_BH_MinLL(). The new function will allow for single or multiple minimum length limits with the same function.
Modified ypr_BH_MinLL() to require vector input for minLL, cf, and cm. Instead of asking users to supply min, max, and increment for each, the user now supplies a single or multiple values in a vector. The vector can be of any sequence.
Modified ypr_BH_SlotLL() to require vector input for cm. Instead of asking users to supply min, max, and increment for each, the user now supplies a single or multiple values in a vector. The vector can be of any sequence.
Renamed dpmBH_MinLL_fixed() to dpmBH_MinLL() for consistent function names.
iCheckCondMort(): Added. Currently only used in showMorts(). However, I think that this is more general than some other functions and, thus, could replace iCheckcf(), iCheckcm(), iCheckcfVect(), iCheckcmVect(), and possibly a few others.
iErrGT(): Modified to allow for checks on a vector rather than just a single value, which it still works for.
iErrLT(): Modified to allow for checks on a vector rather than just a single value, which it still works for.
seeMorts(): Added.
Internal checks have been expanded to cover more user inputs and provide better warnings.
_func() have are no longer "exported". They remain in the package but a help document is not created for them. These functions are not intended to be directly interacted with by the user.

From NEWS.md in the release

Install

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

install.packages("rFAMS", 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("fishR-Core-Team/rFAMS")

Development version from fishR-Core-Team/rFAMS. 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-rfams

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-rFAMS

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-rFAMS

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: 1.6 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK13 OK2026-05-02

Show 2 earlier changesHide 2 earlier changes

ERROR11 OK, 1 ERROR2026-04-25
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.0.3

READMEYes · 415 wordsVignettes· In the repository, left out of the releaseNEWSYes · 100% structured · mentions 0.0.3Citation fileYes · computed when R runs it

The repository also keeps web-only articles.

Help pages: 38 (31 internal)
Examples that run: 100%7 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 3%

How these are measured

Downloads

3.5K

CRAN downloads in the past year

Rank #14,343 · ~10/day · ~294/mo

Releases R versions

Daily download trend is not available in this view yet.

26430 days

83390 days

3.5K1 year

Compare downloads with other packages →

Also on54 r2u5 autocran

How downloads are counted

Repository

fishr-core-team/rfams ↗Organization: fishR-Core-Team

1Stars

0Forks

5Open issues

0Open PRs

2Releases

238Commits

3Commit identities

License file reads as GPL-2.0 · 238 commits · Last activity 2026-03-17 · 0% stars, 30d · Default branch at 0.0.3.9000, ahead of CRAN 0.0.3 (checked 2026-10-22)

Responsiveness

How these are sampled

PRs merged (all time): 96%
Median days to close, 50 most recently updated closed issues: 2
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2026-03-27 · 12026-07-07 · 1

How these are measured

PracticesBeta

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

Checks run against github.com/fishr-core-team/rfams on 2026-10-22.

Continuous integration (2)

GitHub ActionsR CMD check workflow

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

Governance and community (1)

Code of conduct

Docs source (3)

README.Rmdpkgdown

GitHub Pages site last deployed 2026-03-17

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

12 external dependencies (excludes base and recommended)

Installing rFAMS adds 64 packages (32 with compiled code, 56 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, doBy 4.3 MB.

Depends (1)

R >= 4.1.0

Imports (3)

statspurrr FSA

LinkingTo (0)

none

Suggests (10)

dplyr ggplot2 metR knitr rmarkdown testthat zipfR quarto FSAdata tidyr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (2)

Jason C. Doll

Author, Maintainer since 0.0.2 (2026)

Derek H. Ogle

Author

Listed in earlier versions (2)

Jason C.

no longer listed · 0.0.2 to 0.0.3

Derek H.

no longer listed · 0.0.2 to 0.0.3

Releases (2)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
0.0.3Latest
record
2026-03-17 · current release · diff ↗ ·
removed 6 exports
dpmBH, dpmBH_func, yprBH_func, yprBH_minLL_fixed, yprBH_minLL_var, yprBH_slot_func

added 3 exports
dpmBH_MinLL, seeMorts, yprBH_MinLL
0.0.2
record
2026-02-10
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2026-02-10
Total releases: 2 / 1 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 4.1.0
Download size: 128 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("rFAMS")

The package provides a citation file that builds its entry when R runs it. Run citation() to see it.

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 rFAMS version 0.0.3 [Data set]. HJJB, LLC. Data release v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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