Package: dsem 3.0.0

dsem: 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], Maurice Goodman [ctb], Wouter van der Bijl [ctb], Giovanni M. Marchetti [ctr]

dsem_3.0.0.tar.gz
dsem_3.0.0.zip(r-4.7)dsem_3.0.0.zip(r-4.6)dsem_3.0.0.zip(r-4.5)
dsem_3.0.0.tgz(r-4.6-x86_64)dsem_3.0.0.tgz(r-4.6-arm64)dsem_3.0.0.tgz(r-4.5-x86_64)dsem_3.0.0.tgz(r-4.5-arm64)
dsem_3.0.0.tar.gz(r-4.7-arm64)dsem_3.0.0.tar.gz(r-4.7-x86_64)dsem_3.0.0.tar.gz(r-4.6-arm64)dsem_3.0.0.tar.gz(r-4.6-x86_64)
dsem_3.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
dsem/json (API)

# 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/docs 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
hare_lynx - Lynx-Hare dynamics
isle_royale - Isle Royale wolf and moose
lake_washington - Lake washington plankton
paramesium_didinium - Paramesium-Didinium dynamics
pdo_departure_bay - Pacific Decadal Oscillation and Departure Bay temperatures
sea_otter - Sea otter trophic cascade

On CRAN:

cpp openmp

8.46 score 21 stars 1 packages 84 scripts 946 downloads 23 exports 55 dependencies

Last updated from:f41fc6d2b4. Checks:13 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	OK	387
linux-devel-x86_64	OK	459
source / vignettes	OK	480
linux-release-arm64	OK	374
linux-release-x86_64	OK	467
macos-release-arm64	OK	284
macos-release-x86_64	OK	1049
macos-oldrel-arm64	OK	224
macos-oldrel-x86_64	OK	506
windows-devel	OK	394
windows-release	OK	398
windows-oldrel	OK	393
wasm-release	OK	272

Exports:as_fitted_DAG cAIC classify_variables convert_equations dsem dsem_control fixed gaussian_fixed_sd list_parameters lognormal loo_residuals make_dfa make_dsem_ram make_matrices make_msv parse_path partition_variance rk4sys stepwise_selection test_dsep TMBAIC total_effect tweedie

Dependencies:backports base64enc cachem checkmate cli cpp11 dplyr farver fastmap generics ggforce ggplot2 ggraph ggrepel glue graphlayouts gridExtra gtable igraph isoband jsonlite labeling lattice lifecycle magrittr MASS Matrix memoise pillar pkgconfig polyclip purrr R6 RColorBrewer Rcpp RcppArmadillo RcppEigen rlang RTMB S7 scales stringi stringr systemfonts tibble tidygraph tidyr tidyselect TMB tweenr utf8 vctrs viridis viridisLite withr

Demonstration of selected features

Rendered fromfeatures.Rmdusingknitr::rmarkdown

Last update: 2026-06-16
Started: 2025-04-08

dsem model description

Rendered frommodel-description.Rmdusingknitr::rmarkdown

Last update: 2026-06-16
Started: 2025-04-08

MGARCH

Multivariate Generalized Autoregressive Conditional Heteroskedasticity (MGARCH) models | Exploratory MGARCH | Confirmatory MGARCH | Comparison

Rendered fromMGARCH.Rmdusingknitr::rmarkdown

Last update: 2026-06-16
Started: 2026-06-16

Nonlinear dynamics

Nonlinearity

Rendered fromnonlinear.Rmdusingknitr::rmarkdown

Last update: 2026-06-16
Started: 2026-05-12

Random slopes

Random slopes models

Rendered fromrandom_slopes.Rmdusingknitr::rmarkdown

Last update: 2026-05-12
Started: 2026-05-12

Spatial diffusion

Approximating diffusive movement among adjacent spatial strata

Rendered fromspatial_diffusion.Rmdusingknitr::rmarkdown

Last update: 2026-05-12
Started: 2025-02-13

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Convert output from package dsem to phylopath	as_fitted_DAG
Bering Sea marine ecosystem	bering_sea
Calculate conditional AIC	cAIC
Classify variables path	classify_variables
Convert equations notation	convert_equations
Fit dynamic structural equation model	dsem
Detailed control for dsem structure	dsem_control
Fit dynamic structural equation model	dsemRTMB
Family for data that are known without error	fixed
Gaussian with known standard deviation for measurement errors	gaussian_fixed_sd
Lynx-Hare dynamics	hare_lynx
Isle Royale wolf and moose	isle_royale
Lake washington plankton	lake_washington
List fixed and random effects	list_parameters
Marginal log-likelihood	logLik.dsem
Lognormal distribution	lognormal
Calculate leave-one-out residuals	loo_residuals
Make text for dynamic factor analysis	make_dfa
Make a RAM (Reticular Action Model)	make_dsem_ram
Make path matrices	make_matrices
Make text for multivariate stochastic volatility model	make_msv
Paramesium-Didinium dynamics	paramesium_didinium
Parse path	parse_path
Partition variance in one variable due to another (EXPERIMENTAL)	partition_variance
Pacific Decadal Oscillation and Departure Bay temperatures	pdo_departure_bay
Simulate dsem	plot.dsem
predictions using dsem	predict.dsem
Print fitted dsem object	print.dsem
Make a RAM (Reticular Action Model)	read_model
Calculate residuals	residuals.dsem
Classical Runge-Kutta for system of equations	rk4sys
Sea otter trophic cascade	sea_otter
Simulate dsem	simulate.dsem
Simulate dsem	stepwise_selection
summarize dsem	summary.dsem
Test d-separation	test_dsep
Calculate marginal AIC for a fitted model	TMBAIC
Calculate total effects	total_effect
Tweedie distribution	tweedie
Extract Variance-Covariance Matrix	vcov.dsem