Package index • tinyVAST

Fitting and predicting

Core tools for model fitting, prediction, and inspection.

tinyVAST(): Fit vector autoregressive spatio-temporal model

tinyVASTcontrol(): Control parameters for tinyVAST

predict(<tinyVAST>): Predict using vector autoregressive spatio-temporal model

summary(<tinyVAST>): summarize tinyVAST

residuals(<tinyVAST>): Calculate deviance or response residuals for tinyVAST

integrate_output(): Integration for target variable

cAIC(): Calculate conditional AIC

deviance_explained(): Calculate deviance explained

delta_lognormal() delta_gamma(): Additional families

reload_model(): Reload a previously fitted model

rotate_pca(): Rotate factors to match Principal-Components Analysis

sample_variable(): Sample from predictive distribution of a variable

vcov(<tinyVAST>): Extract Variance-Covariance Matrix

Graph constructors

Tools to specify interactions.

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

make_dsem_ram(): Make a RAM (Reticular Action Model)

make_eof_ram(): Make a RAM (Reticular Action Model)

Stream network utilities

Tools to work with stream networks.

sfnetwork_evaluator(): Construct projection matrix for stream network

sfnetwork_mesh(): Make mesh for stream network

simulate_sfnetwork(): Simulate GMRF for stream network

Data sets

Data sets used for illustration and testing.

sea_ice: Arctic September sea ice concentrations

salmon_returns: North Pacific salmon returns

condition_and_density: Condition and density example

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

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

red_snapper: Presence/absence, count, and biomass data for red snapper

red_snapper_shapefile: Shapefile for red snapper analysis