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."

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cppopenmp

8.11 score 18 stars 1 dependents 68 scripts 839 downloads

tinyVAST - Multivariate Spatio-Temporal Models using Structural Equations

Fits a wide variety of multivariate spatio-temporal models with simultaneous and lagged interactions among variables (including vector autoregressive spatio-temporal ('VAST') dynamics) for areal, continuous, or network spatial domains. It includes time-variable, space-variable, and space-time-variable interactions using dynamic structural equation models ('DSEM') as expressive interface, and the 'mgcv' package to specify splines via the formula interface. See Thorson et al. (2025) <doi:10.1111/geb.70035> for more details.

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dynamic-structural-equation-modelsvector-autoregressive-spatio-temporal-modelcpp

7.83 score 17 stars 74 scripts 610 downloads

ecostate - State-Space Mass-Balance Model for Marine Ecosystems

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.

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5.41 score 13 stars 6 scripts 534 downloads

phylosem - Phylogenetic Structural Equation Model

Applies phylogenetic comparative methods (PCM) and phylogenetic trait imputation using structural equation models (SEM), extending methods from Thorson et al. (2023) <doi:10.1111/2041-210X.14076>. This implementation includes a minimal set of features, to allow users to easily read all of the documentation and source code. PCM using SEM includes phylogenetic linear models and structural equation models as nested submodels, but also allows imputation of missing values. Features and comparison with other packages are described in Thorson and van der Bijl (2023) <doi:10.1111/jeb.14234>.

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cpp

4.56 score 1 stars 18 scripts 191 downloads

mvtweedie - Fit multivariate logit Tweedie model using mgcv or glmmTMB

Defines predict function that transforms output from a Tweedie GLM fitted using mgcv or glmmTMB, and returns predictions of an equivalent multivariate logit Tweedie model. This can then be used for standard plotting and diagnostics.

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4.26 score 12 stars 8 scripts 463 downloads