ecostate

0.3.0

State-Space Mass-Balance Model for Marine Ecosystems

0packages depend

5.4Kdownloads / year

–test coverage

12/13checks pass

Overview

About

Maintained by James T. ThorsonFirst published 2024-11-252 releasesCRAN page ↗GitHub ↗

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.

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.

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).

Health

CRAN checks

1ERROR12OK

Failing flavors

ERROR r-release-macos-x86_64

Slowest check: 3.7 min · r-devel-linux-x86_64-fedora-clang

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

ERROR2026-04-25
11 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 444 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 96%
Return-value docs: 100%
References docs: 5%

Downloads

5.4K

CRAN downloads in the past year

Rank #8,116 · ~15/day · ~450/mo

Releases R versions

Daily download trend is not available in this view yet.

31730 days

1.3K90 days

5.4K1 year

Compare downloads with other packages →

Also on110 r2u34 autocran

Repository

GitHub ↗ james-thorson-noaa/ecostate

13Stars

2Forks

1Open issues

2Open PRs

2Releases

70Commits

2Contributors

70 commits · Last activity 2026-05-22

Stars over time

2025-02-06 · 132026-07-07 · 13

Repository practices

Upstream repositoryBeta

2 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/james-thorson-noaa/ecostate on 2026-07-19.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

data-raw/

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

8 external dependencies (excludes base and recommended)

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.

Code & Tests

People & History

People (1)

Maintainer (1)

James T. Thorson

Author, Maintainer

Authors (1)

James T. Thorson

Author, Maintainer

Listed in earlier versions (1)

James T.

no longer listed · 0.2.0 to 0.3.0

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
0.3.0Latest
2025-09-08 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
0.2.0
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
Installed size: not tracked yet
With dependencies: not tracked yet

Report a problem with this page →