Function reference • tinyVAST

All functions

add_predictions(): Add predictions to data-list

bering_sea: Survey domain for the eastern and northern Bering Sea surveys

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

classify_variables(): Classify variables path

condition_and_density: Condition and density example

deviance_explained(): Calculate deviance explained

delta_lognormal() delta_gamma(): Additional families

integrate_output(): Monte Carlo integration for abundance

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

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

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

parse_path(): Parse path

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

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

red_snapper_shapefile: Shapefile for red snapper analysis

reload_model(): Reload a previously fitted model

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

rmvnorm_prec(): Multivariate Normal Random Deviates using Sparse Precision

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

salmon_returns: North Pacific salmon returns

sample_variable(): Sample from predictive distribution of a variable

sea_ice: Arctic September sea ice concentrations

sfnetwork_evaluator(): Construct projection matrix for stream network

sfnetwork_mesh(): Make mesh for stream network

simulate_sfnetwork(): Simulate GMRF for stream network

summary(<tinyVAST>): summarize tinyVAST

tinyVAST(): Fit vector autoregressive spatio-temporal model

tinyVASTcontrol(): Control parameters for tinyVAST

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