Package: tinyVAST 1.6.3

James T. Thorson

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.

Authors:James T. Thorson [aut, cre], Sean C. Anderson [aut]

tinyVAST_1.6.3.tar.gz
tinyVAST_1.6.3.zip(r-4.7-x86_64)tinyVAST_1.6.3.zip(r-4.7-arm64)tinyVAST_1.6.3.zip(r-4.6-x86_64)tinyVAST_1.6.3.zip(r-4.6-arm64)tinyVAST_1.6.3.zip(r-4.5-x86_64)
tinyVAST_1.6.3.tgz(r-4.6-x86_64)tinyVAST_1.6.3.tgz(r-4.6-arm64)tinyVAST_1.6.3.tgz(r-4.5-x86_64)tinyVAST_1.6.3.tgz(r-4.5-arm64)
tinyVAST_1.6.3.tar.gz(r-4.7-arm64)tinyVAST_1.6.3.tar.gz(r-4.7-x86_64)tinyVAST_1.6.3.tar.gz(r-4.6-arm64)tinyVAST_1.6.3.tar.gz(r-4.6-x86_64)
tinyVAST_1.6.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
tinyVAST/json (API)

# Install 'tinyVAST' in R:

install.packages('tinyVAST', repos = c('https://vast-lib.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/vast-lib/tinyvast/issues

Pkgdown/docs site:https://vast-lib.github.io

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

alaska_sponge_coral_fish - Data to analyze sponge-coral-fish associations
atlantic_yellowtail - Northwest Atlantic yellowtail
bering_sea - Survey domain for the eastern and northern Bering Sea surveys
bering_sea_capelin_forecasts - Data to demonstrate probabilistic forecasting
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
condition_and_density - Condition and density example
red_grouper_diet - Data to demonstrate model-based diet proportions
red_snapper - Presence/absence, count, and biomass data for red snapper
red_snapper_shapefile - Shapefile for red snapper analysis
salmon_returns - North Pacific salmon returns
sea_ice - Arctic September sea ice concentrations

On CRAN:

dynamic-structural-equation-models vector-autoregressive-spatio-temporal-model cpp

7.15 score 17 stars 83 scripts 142 downloads 30 exports 135 dependencies

Last updated from:ddcc6812db. Checks:15 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	OK	351
linux-devel-x86_64	OK	488
source / vignettes	OK	509
linux-release-arm64	OK	339
linux-release-x86_64	OK	462
macos-release-arm64	OK	366
macos-release-x86_64	OK	601
macos-oldrel-arm64	OK	362
macos-oldrel-x86_64	OK	702
windows-devel-arm64	OK	539
windows-devel-x86_64	OK	522
windows-release-arm64	OK	535
windows-release-x86_64	OK	450
windows-oldrel-x86_64	OK	430
wasm-release	OK	265

Exports:add_mesh_covariates add_predictions cAIC conditional_gmrf delta_gamma delta_lognormal deviance_explained integrate_output lognormal make_dsem_ram make_eof_ram make_nngp_domain make_sem_ram nbinom1 nbinom2 project reload_model rmvnorm_prec rotate_pca sample_variable sanity sfnetwork_evaluator sfnetwork_mesh simulate_sfnetwork spatial_cor student term_covariance tinyVAST tinyVASTcontrol tweedie

Dependencies:abind assertthat backports base64enc BH boot broom cachem car carData checkmate class classInt cli codetools colorspace corpcor cowplot cpp11 crayon cv DBI Deriv doBy doParallel dotCall64 dplyr dsem e1071 farver fastmap fields fishMod fmesher FNN foreach forecast Formula fracdiff generics geometries ggforce ggplot2 ggraph ggrepel glmmTMB glue GpGp GPvecchia graphlayouts gridExtra gstat gtable gtools igraph insight intervals isoband iterators jsonlite KernSmooth labeling lattice lifecycle lme4 lmtest lwgeom magrittr maps MASS Matrix MatrixModels memoise mgcv minqa modelr mvtnorm nlme nloptr nnet numDeriv pbkrtest pillar pkgconfig polyclip proxy purrr quantreg R6 rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen Rdpack reformulas rlang RTMB s2 S7 sandwich scales sdmTMB sf sfheaders sfnetworks sftime sp spacetime spam sparseinv SparseM splancs stars stringi stringr survival systemfonts tibble tidygraph tidyr tidyselect timeDate TMB tweenr units urca utf8 vctrs viridis viridisLite withr wk xts zoo

tinyVAST model description

Rendered frommodel-description.Rmdusingknitr::rmarkdown

Last update: 2025-07-19
Started: 2025-03-10

Help page	Topics
Add mesh covariates to vertices and triangles	add_mesh_covariates
Add predictions to data-list	add_predictions
Data to analyze sponge-coral-fish associations	alaska_sponge_coral_fish
Northwest Atlantic yellowtail	atlantic_yellowtail
Survey domain for the eastern and northern Bering Sea surveys	bering_sea
Data to demonstrate probabilistic forecasting	bering_sea_capelin_forecasts
Survey catch-rates at age for Alaska pollock in the Eastern and Northern Bering Sea	bering_sea_pollock_ages
Estimated proportion-at-age for Alaska pollock using VAST	bering_sea_pollock_vast
Calculate conditional AIC	cAIC
Classify variables path	classify_variables
Condition and density example	condition_and_density
Conditional simulation from a GMRF	conditional_gmrf
Calculate deviance explained	deviance_explained
Additional families	delta_gamma delta_lognormal Families
Get data	get_data.tinyVAST
Get response	GetResponse.tinyVAST
Integration for target variable	integrate_output
Extract the (marginal) log-likelihood of a tinyVAST model	logLik.tinyVAST
Make a RAM (Reticular Action Model)	make_dsem_ram
Make a RAM (Reticular Action Model)	make_eof_ram
Make spatial object for NNGP	make_nngp_domain
Make a RAM (Reticular Action Model) from a SEM (structural equation model)	make_sem_ram
Parse path	parse_path
Plot nngp_domain	plot.nngp_domain
Predict using vector autoregressive spatio-temporal model	predict.tinyVAST
print summary of tinyVAST model	print.tinyVAST
Project tinyVAST to future times (EXPERIMENTAL)	project
Data to demonstrate model-based diet proportions	red_grouper_diet
Presence/absence, count, and biomass data for red snapper	red_snapper
Shapefile for red snapper analysis	red_snapper_shapefile
Reload a previously fitted model	reload_model
Calculate deviance or response residuals for tinyVAST	residuals.tinyVAST
Multivariate Normal Random Deviates using Sparse Precision	rmvnorm_prec
Rotate factors to match Principal-Components Analysis	rotate_pca
North Pacific salmon returns	salmon_returns
Sample from predictive distribution of a variable	sample_variable
Sanity check of a tinyVAST model	sanity
Arctic September sea ice concentrations	sea_ice
Construct projection matrix for stream network	sfnetwork_evaluator
Make mesh for stream network	sfnetwork_mesh
Simulate GMRF for stream network	simulate_sfnetwork
Simulate new data from a fitted model	simulate.tinyVAST
Approximate spatial correlation	spatial_cor
summarize tinyVAST	summary.tinyVAST
Extract covariance	term_covariance
Fit vector autoregressive spatio-temporal model	tinyVAST
Control parameters for tinyVAST	tinyVASTcontrol
Extract Variance-Covariance Matrix	vcov.tinyVAST

Package: tinyVAST 1.6.3

tinyVAST: Multivariate Spatio-Temporal Models using Structural Equations

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Help Manual

Usage by other packages (reverse dependencies)