Package: dsem 1.3.0

dsem: Fit Dynamic Structural Equation Models

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."

Authors:James Thorson [aut, cre]

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dsem.pdf |dsem.html✨
dsem/json (API)
NEWS

# Install 'dsem' in R:

install.packages('dsem', repos = c('https://james-thorson-noaa.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/james-thorson-noaa/dsem/issues

Pkgdown site:https://james-thorson-noaa.github.io

Uses libs:

c++– GNU Standard C++ Library v3
openmp– GCC OpenMP (GOMP) support library

Datasets:

bering_sea - Bering Sea marine ecosystem
isle_royale - Isle Royale wolf and moose
sea_otter - Sea otter trophic cascade

On CRAN:

cpp openmp

6.46 score 10 stars 16 scripts 312 downloads 10 exports 28 dependencies

Last updated 4 months agofrom:298cbb73c8. Checks:9 OK. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Jan 15 2025
R-4.5-win-x86_64	OK	Jan 15 2025
R-4.5-linux-x86_64	OK	Jan 15 2025
R-4.4-win-x86_64	OK	Jan 15 2025
R-4.4-mac-x86_64	OK	Jan 15 2025
R-4.4-mac-aarch64	OK	Jan 15 2025
R-4.3-win-x86_64	OK	Jan 15 2025
R-4.3-mac-x86_64	OK	Jan 15 2025
R-4.3-mac-aarch64	OK	Jan 15 2025

Exports:as_fitted_DAG as_sem classify_variables dsem dsem_control list_parameters make_dfa make_dsem_ram parse_path TMBAIC

Dependencies:abind arm boot cli coda cpp11 glue igraph lattice lifecycle lme4 magrittr MASS Matrix mi minqa nlme nloptr pkgconfig rbibutils Rcpp RcppEigen Rdpack reformulas rlang sem TMB vctrs

Demonstration of selected features

James Thorson

Rendered fromvignette.Rmdusingknitr::rmarkdownon Jan 15 2025.

Last update: 2024-03-31
Started: 2023-08-02

Dynamic factor analysis

James Thorson

Rendered fromdynamic_factor_analysis.Rmdusingknitr::rmarkdownon Jan 15 2025.

Last update: 2024-04-01
Started: 2024-03-31

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Convert output from package dsem to phylopath	as_fitted_DAG
Convert dsem to sem output	as_sem
Bering Sea marine ecosystem	bering_sea
Classify variables path	classify_variables
Fit dynamic structural equation model	dsem
Detailed control for dsem structure	dsem_control
Isle Royale wolf and moose	isle_royale
List fixed and random effects	list_parameters
Marglinal log-likelihood	logLik.dsem
Make text for dynamic factor analysis	make_dfa
Make a RAM (Reticular Action Model)	make_dsem_ram
Parse path	parse_path
Simulate dsem	plot.dsem
predictions using dsem	predict.dsem
Print fitted dsem object	print.dsem
Calculate residuals	residuals.dsem
Sea otter trophic cascade	sea_otter
Simulate dsem	simulate.dsem
summarize dsem	summary.dsem
Calculate marginal AIC for a fitted model	TMBAIC
Extract Variance-Covariance Matrix	vcov.dsem