Package index • tinyVAST

Fitting and diagnostics

Core tools for model fitting and diagnostics.

tinyVAST(): Fit vector autoregressive spatio-temporal model

tinyVASTcontrol(): Control parameters for tinyVAST

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

logLik(<tinyVAST>): Extract the (marginal) log-likelihood of a tinyVAST model

cAIC(): Calculate conditional AIC

deviance_explained(): Calculate deviance explained

delta_lognormal() delta_gamma(): Additional families

simulate(<tinyVAST>): Simulate new data from a fitted model

print(<tinyVAST>): print summary of tinyVAST model

SEM and DSEM constructors

Tools to specify interactions among variables and over time.

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)

Predicting

Core tools for model predictions.

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

integrate_output(): Integration for target variable

sample_variable(): Sample from predictive distribution of a variable

project(): Project tinyVAST to future times (EXPERIMENTAL)

Interpret output

Tools for interpreting output.

summary(<tinyVAST>): summarize tinyVAST

reload_model(): Reload a previously fitted model

term_covariance(): Extract covariance

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

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

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

alaska_sponge_coral_fish: Data to analyze sponge-coral-fish associations

bering_sea_capelin_forecasts: Data to demonstrate probabilistic forecasting

red_grouper_diet: Data to demonstrate model-based diet proportions