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tinyVAST (version 1.0.1)

Multivariate Spatio-Temporal Models using Structural Equations

Description

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. (2024) for more details.

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Version

Install

install.packages('tinyVAST')

Monthly Downloads

535

Version

1.0.1

License

GPL-3

Maintainer

James Thorson

Last Published

March 21st, 2025

Functions in tinyVAST (1.0.1)

red_snapper

Presence/absence, count, and biomass data for red snapper
parse_path

Parse path
predict.tinyVAST

Predict using vector autoregressive spatio-temporal model
make_eof_ram

Make a RAM (Reticular Action Model)
reload_model

Reload a previously fitted model
sample_variable

Sample from predictive distribution of a variable
make_sem_ram

Make a RAM (Reticular Action Model) from a SEM (structural equation model)
salmon_returns

North Pacific salmon returns
sfnetwork_evaluator

Construct projection matrix for stream network
vcov.tinyVAST

Extract Variance-Covariance Matrix
simulate.tinyVAST

Simulate new data from a fitted model
sfnetwork_mesh

Make mesh for stream network
residuals.tinyVAST

Calculate deviance or response residuals for tinyVAST
sea_ice

Arctic September sea ice concentrations
tinyVASTcontrol

Control parameters for tinyVAST
tinyVAST

Fit vector autoregressive spatio-temporal model
logLik.tinyVAST

Extract the (marginal) log-likelihood of a tinyVAST model
rmvnorm_prec

Multivariate Normal Random Deviates using Sparse Precision
simulate_sfnetwork

Simulate GMRF for stream network
make_dsem_ram

Make a RAM (Reticular Action Model)
rotate_pca

Rotate factors to match Principal-Components Analysis
summary.tinyVAST

summarize tinyVAST
condition_and_density

Condition and density example
add_predictions

Add predictions to data-list
bering_sea_pollock_ages

Survey catch-rates at age for Alaska pollock in the Eastern and Northern Bering Sea
bering_sea_pollock_vast

Estimated proportion-at-age for Alaska pollock using VAST
deviance_explained

Calculate deviance explained
classify_variables

Classify variables path
cAIC

Calculate conditional AIC
bering_sea

Survey domain for the eastern and northern Bering Sea surveys
integrate_output

Integration for target variable
Families

Additional families
red_snapper_shapefile

Shapefile for red snapper analysis
reexports

Objects exported from other packages
print.tinyVAST

print summary of tinyVAST model