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dsem

Dynamic structural equation models

https://github.com/james-thorson-noaa/dsem

Science Score: 39.0%

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    Found 2 DOI reference(s) in README
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    Low similarity (15.5%) to scientific vocabulary
Last synced: 9 months ago · JSON representation

Repository

Dynamic structural equation models

Basic Info
Statistics
  • Stars: 11
  • Watchers: 6
  • Forks: 5
  • Open Issues: 2
  • Releases: 10
Created almost 3 years ago · Last pushed 10 months ago
Metadata Files
Readme Changelog

README.md

Dynamic structural equation models

Codecov test coverage Documentation

Package dsem fits dynamic structural equation models, which includes as nested submodels:

  1. structural equation models
  2. vector autoregressive models
  3. dynamic factor analysis
  4. state-space autoregressive integrated moving average (ARIMA) models

The model has several advantages:

  • It estimates direct, indirect, and total effects among system variables, including simultaneous and lagged effects and recursive (cyclic) dependencies
  • It can estimate the cumulative outcome from press or pulse experiments or initial conditions that differ from the stationary distribution of system dynamics
  • It estimates structural linkages as regression slopes while jointly imputing missing values and/or measurement errors
  • It is rapidly fitted as a Gaussian Markov random field (GMRF) in a Generalized Linear Mixed Model (GLMM), with speed and asymptotics associated with each
  • It allows granular control over the number of parameters (and restrictions on parameters) used to structure the covariance among variables and over time,

dsem is specifically intended as a minimal implementation, and uses standard packages to simplify input/output formatting:

  • Input: time-series defined using class ts, with NA for missing values
  • Input: structural trade-offs specified using syntax defined by package sem
  • Output: visualizing estimated trade-offs using igraph
  • Output: access model output using standard S3-generic functions including summary, predict, residuals, simulate, and AIC

Please see package vignettes for more details regarding syntax and features.

Citation

Thorson, J. T., Andrews, A. G., Essington, T., & Large, S. (2024). Dynamic structural equation models synthesize ecosystem dynamics constrained by ecological mechanisms. Methods in Ecology and Evolution 15(4): 744-755. https://doi.org/10.1111/2041-210X.14289

NOAA Enterprise GitHub disclaimer

This repository is a scientific product and is not official communication of the National Oceanic and Atmospheric Administration, or the United States Department of Commerce. All NOAA GitHub project code is provided on an ‘as is’ basis and the user assumes responsibility for its use. Any claims against the Department of Commerce or Department of Commerce bureaus stemming from the use of this GitHub project will be governed by all applicable Federal law. Any reference to specific commercial products, processes, or services by service mark, trademark, manufacturer, or otherwise, does not constitute or imply their endorsement, recommendation or favoring by the Department of Commerce. The Department of Commerce seal and logo, or the seal and logo of a DOC bureau, shall not be used in any manner to imply endorsement of any commercial product or activity by DOC or the United States Government.

Owner

  • Name: Jim Thorson
  • Login: James-Thorson-NOAA
  • Kind: user
  • Location: Seattle

GitHub Events

Total
  • Create event: 8
  • Release event: 4
  • Issues event: 14
  • Watch event: 1
  • Delete event: 6
  • Issue comment event: 33
  • Push event: 153
  • Pull request event: 14
  • Fork event: 4
Last Year
  • Create event: 8
  • Release event: 4
  • Issues event: 14
  • Watch event: 1
  • Delete event: 6
  • Issue comment event: 33
  • Push event: 153
  • Pull request event: 14
  • Fork event: 4

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 18
  • Total pull requests: 20
  • Average time to close issues: 11 days
  • Average time to close pull requests: 4 days
  • Total issue authors: 10
  • Total pull request authors: 4
  • Average comments per issue: 2.11
  • Average comments per pull request: 0.2
  • Merged pull requests: 14
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 12
  • Pull requests: 6
  • Average time to close issues: 17 days
  • Average time to close pull requests: 5 days
  • Issue authors: 7
  • Pull request authors: 2
  • Average comments per issue: 2.17
  • Average comments per pull request: 0.5
  • Merged pull requests: 4
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • RayCzajaJr (6)
  • agruss2 (2)
  • James-Thorson-NOAA (2)
  • Cole-Monnahan-NOAA (2)
  • kaskr (1)
  • JaneSullivan-NOAA (1)
  • stephendavidgregory (1)
  • mcgoodman (1)
  • Etienne27 (1)
Pull Request Authors
  • James-Thorson-NOAA (26)
  • mcgoodman (3)
  • olivroy (2)
  • Cole-Monnahan-NOAA (1)
Top Labels
Issue Labels
enhancement (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 464 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 11
  • Total maintainers: 1
cran.r-project.org: dsem

Dynamic Structural Equation Models

  • Versions: 11
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 464 Last month
Rankings
Dependent packages count: 28.6%
Dependent repos count: 36.8%
Average: 50.5%
Downloads: 86.0%
Maintainers (1)
James.Thorson@noaa.gov
Last synced: 10 months ago

Dependencies

.github/workflows/R-CMD-check.yaml actions
  • actions/checkout v3 composite
  • r-lib/actions/check-r-package v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
DESCRIPTION cran
  • R >= 4.0.0 depends
  • rstan * enhances
  • tmbstan * enhances
  • Matrix >= 1.6.3 imports
  • TMB >= 1.9.7 imports
  • igraph * imports
  • methods * imports
  • sem * imports
  • AER * suggests
  • MARSS * suggests
  • dynlm * suggests
  • ggplot2 * suggests
  • ggpubr * suggests
  • ggraph * suggests
  • grid * suggests
  • gridExtra * suggests
  • knitr * suggests
  • phylopath * suggests
  • reshape * suggests
  • rmarkdown * suggests
  • testthat * suggests
  • vars * suggests
.github/workflows/pkgdown.yaml actions
  • JamesIves/github-pages-deploy-action v4.4.1 composite
  • actions/checkout v3 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/test-coverage.yaml actions
  • actions/checkout v3 composite
  • actions/upload-artifact v3 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite