R Observatory: Metrics for ecostate version 0.3.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

ecostate

0.3.0Package record

State-Space Mass-Balance Model for Marine Ecosystems

0packages depend

5.4Kdownloads / year

–test coverage

12/13flavors OK

Overview

About

Maintained by James T. ThorsonCRAN page ↗GitHub ↗Website ↗Issues ↗

Fits a state-space mass-balance model for marine ecosystems, which implements dynamics derived from 'Ecopath with Ecosim' ('EwE') https://ecopath.org/ while fitting to time-series of fishery catch, biomass indices, age-composition samples, and weight-at-age data. 'Ecostate' fits biological parameters (e.g., equilibrium mass) and measurement parameters (e.g., catchability coefficients) jointly with residual variation in process errors, and can include Bayesian priors for parameters.

Changes in 0.3.0

Add fit$simulator() to simulate data
Add vignette showing multi-stanza features by fitting age-composition data using data for Gulf of Alaska pollock and sablefish
Update model description vignette to add overview of age- and size-structured dynamics

From NEWS.md in the release

Install

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

install.packages("ecostate", 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("James-Thorson-NOAA/ecostate")

Development version from James-Thorson-NOAA/ecostate. 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-ecostate

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-ecostate

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-ecostate

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

1ERROR12OK

Check messages

ERRORpackage dependenciesr-release-macos-x86_64

Package required but not available: ‘RTMB’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.

CRAN check page ↗

Slowest check: 2.9 min · r-oldrel-windows-x86_64

Status changes

ERROR12 OK, 1 ERRORNow
ERROR11 OK, 1 ERROR2026-04-25
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.3.0

READMEYes · 444 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 0.3.0Citation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 19
Examples that run: 100%1 run in a plain check
Exported functions with examples: 8%
Documented parameters: 96%
Return-value docs: 100%
Help pages citing references: 5%

Vignettes (1)

ecostate model description

How these are measured

Downloads

5.4K

CRAN downloads in the past year

Rank #11,120 · ~15/day · ~446/mo

Releases R versions

Daily download trend is not available in this view yet.

34730 days

94790 days

5.4K1 year

Compare downloads with other packages →

Also on74 r2u9 autocran

How downloads are counted

Repository

james-thorson-noaa/ecostate ↗Account: James-Thorson-NOAA

13Stars

2Forks

1Open issues

3Open PRs

2Releases

71Commits

2Commit identities

71 commits · Last activity 2026-07-26 · Discussions: 1 post

Responsiveness

How these are sampled

PRs merged (all time): 81%
Median days to close, 50 most recently updated closed issues: 1
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-02-06 · 132026-07-07 · 13

How these are measured

PracticesBeta

5 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/james-thorson-noaa/ecostate on 2026-10-18.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux

Docs source (2)

pkgdown

GitHub Pages site last deployed 2025-05-26

Reproducibility and dev environment (1)

data-raw/

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

Dependencies

Declared dependencies

8 external dependencies (excludes base and recommended)

Installing ecostate adds 35 packages (21 with compiled code, 28 MB of source tarballs). Heaviest: ggplot2 6.0 MB, igraph 4.8 MB, Rcpp 1.8 MB.

Depends (2)

R >= 4.1.0RTMB

Imports (6)

TMBMASScheckmate ggplot2 ggnetwork igraph

LinkingTo (0)

none

Suggests (2)

knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (1)

James T. Thorson

Author, Maintainer since 0.2.0 (2024)

Listed in earlier versions (1)

James T.

no longer listed · 0.2.0 to 0.3.0

Releases (2)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
0.3.0Latest
record
2025-09-08 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
0.2.0
record
2024-11-25
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2024-11-25
Total releases: 2 / 2 yrs
License: GPL-3 OSI
Minimum R: ≥ 4.1.0
Bundled data: 30 KB / 3 files
Download size: 94 KB

Cite

Cite this package

Run in R for the authors' entry:

citation("ecostate")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.1111/faf.12874.

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 ecostate version 0.3.0 [Data set]. HJJB, LLC. Data release v2026-10-21. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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