Learn R Programming

tinyVAST (version 1.2.0)

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.

Copy Link

Version

Install

install.packages('tinyVAST')

Monthly Downloads

535

Version

1.2.0

License

GPL-3

Maintainer

James Thorson

Last Published

July 19th, 2025

Functions in tinyVAST (1.2.0)

make_sem_ram

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

Additional families
get_data.tinyVAST

Get data
sample_variable

Sample from predictive distribution of a variable
make_dsem_ram

Make a RAM (Reticular Action Model)
rotate_pca

Rotate factors to match Principal-Components Analysis
predict.tinyVAST

Predict using vector autoregressive spatio-temporal model
project

Project tinyVAST to future times (EXPERIMENTAL)
tinyVASTcontrol

Control parameters for tinyVAST
red_snapper

Presence/absence, count, and biomass data for red snapper
vcov.tinyVAST

Extract Variance-Covariance Matrix
term_covariance

Extract covariance
tinyVAST

Fit vector autoregressive spatio-temporal model
logLik.tinyVAST

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

Parse path
sfnetwork_mesh

Make mesh for stream network
residuals.tinyVAST

Calculate deviance or response residuals for tinyVAST
simulate.tinyVAST

Simulate new data from a fitted model
reload_model

Reload a previously fitted model
simulate_sfnetwork

Simulate GMRF for stream network
summary.tinyVAST

summarize tinyVAST
print.tinyVAST

print summary of tinyVAST model
red_snapper_shapefile

Shapefile for red snapper analysis
sfnetwork_evaluator

Construct projection matrix for stream network
reexports

Objects exported from other packages
sea_ice

Arctic September sea ice concentrations
classify_variables

Classify variables path
GetResponse.tinyVAST

Get response
bering_sea_pollock_ages

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

Calculate conditional AIC
add_predictions

Add predictions to data-list
conditional_gmrf

Conditional simulation from a GMRF
deviance_explained

Calculate deviance explained
bering_sea

Survey domain for the eastern and northern Bering Sea surveys
bering_sea_pollock_vast

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

Condition and density example
integrate_output

Integration for target variable
make_eof_ram

Make a RAM (Reticular Action Model)
rmvnorm_prec

Multivariate Normal Random Deviates using Sparse Precision
salmon_returns

North Pacific salmon returns