dsem

3.0.0

Dynamic Structural Equation Models

1packages depend

8.4Kdownloads / year

50.5%test coverage

13/13checks pass

Overview

About

Maintained by James ThorsonFirst published 2023-12-0815 releasesCRAN page ↗GitHub ↗

Applies dynamic structural equation models to time-series data with generic and simplified specification for simultaneous and lagged effects. Methods are described in Thorson et al. (2024) "Dynamic structural equation models synthesize ecosystem dynamics constrained by ecological mechanisms."

Install

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

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

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

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-dsem

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-dsem

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

Health

CRAN checks

13OK

Slowest check: 14.1 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.20

50.5%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-07-22
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-05-02
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-03-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 544 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 97%
Return-value docs: 78%
References docs: 20%

Downloads

8.4K

CRAN downloads in the past year

Rank #4,007 · ~23/day · ~698/mo

Releases R versions

Daily download trend is not available in this view yet.

61030 days

2.4K90 days

8.4K1 year

Compare downloads with other packages →

Also on496 r2u38 autocran

Repository

GitHub ↗ james-thorson-noaa/dsem

22Stars

6Forks

3Open issues

1Open PRs

14Releases

74Commits

3Contributors

74 commits · Last activity 2026-07-10 · +10% stars, 30d

Stars over time

2025-02-18 · 112026-07-14 · 22

Repository practices

Upstream repositoryBeta

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

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

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

data-raw/

Coverage (1)

Codecov

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

Dependencies

Declared dependencies

20 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.0.0

Imports (11)

TMBMatrixigraphutilsRTMB ggraph ggplot2gridmethodsstatscheckmate

LinkingTo (2)

TMB RcppEigen

Suggests (12)

knitr AER phylopath rmarkdown reshape gridExtra dynlm MARSS ggpubr vars testthat DHARMa

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

tinyVAST

Code & Tests

Code Composition

R 5,536 (52%)Vignettes 2,388 (22%)Rd 1,893 (18%)C++ 648 (6%)Other 230 (2%)

Code characteristics

Object systems

S38

Cyclomatic complexity: 4.0 median / 48 max
Test cases: 16 / 0.20 per code line

Test coverage

Line coverage

50%

Expression

49.1%

Tests / Examples

50.5% / 44% ex

Functions

55 23 exported

Complexity

7.1 avg / 48 max

Call network

55 nodes / 39 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

55 functions

Function	Cyclo	Coverage
TMBAIC exp	3	0%
cAIC exp	4	0%
lognormal exp	3	0%
loo_residuals exp	11	0%
make_dfa exp	6	0%
make_msv exp	7	0%

Datasets

Bundled datasets · 6

Name	Class	Rows × Cols	Also ships in
bering_sea	data.frame	61 × 8	–
hare_lynx	data.frame	21 × 3	–
isle_royale	data.frame	61 × 3	–
lake_washington	data.frame	396 × 6	–
paramesium_didinium	data.frame	71 × 3	–
pdo_departure_bay	data.frame	104 × 3	–

People & History

People (4)

Maintainer (1)

James Thorson

Author, Maintainer

Authors (1)

James Thorson

Author, Maintainer

Contributors (2)

Maurice Goodman

Contributor · added in 1.4.1

Wouter van der Bijl

Contributor · added in 1.5.0

Other (1)

Giovanni M. Marchetti

Contractor · added in 1.6.0

Package Timeline

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

3.0.0Latest
2026-06-16 · current release · diff ↗
2.0.1
2026-05-14 · diff ↗
2.0.0
2026-05-12 · diff ↗
R
R 4.6.0 released · 2026-04-24
1.7.0
2025-09-16 · diff ↗
R
R 4.5.0 released · 2025-04-11
1.6.0
2025-03-22 · diff ↗
1.5.0
2025-02-13 · diff ↗
1.4.1
2025-02-02 · diff ↗
1.4.0
2025-01-13 · diff ↗
1.3.0
2024-07-22 · diff ↗
R
R 4.4.0 released · 2024-04-24
1.2.1
2024-04-03 · diff ↗
1.2.0
2024-03-31 · diff ↗
1.1.0
2024-02-17 · diff ↗
1.0.2
2024-02-02 · diff ↗

Show 3 earlier events

1.0.1
2024-01-18 · diff ↗
1.0.0
2023-12-08
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2023-12-08
Total releases: 15 / 3 yrs
License: GPL-3 OSI
Minimum R: ≥ 4.0.0
Bundled data: 17 KB / 7 files
Download size: 1.5 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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