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loo (version 2.4.1)

Efficient Leave-One-Out Cross-Validation and WAIC for Bayesian Models

Description

Efficient approximate leave-one-out cross-validation (LOO) for Bayesian models fit using Markov chain Monte Carlo, as described in Vehtari, Gelman, and Gabry (2017) . The approximation uses Pareto smoothed importance sampling (PSIS), a new procedure for regularizing importance weights. As a byproduct of the calculations, we also obtain approximate standard errors for estimated predictive errors and for the comparison of predictive errors between models. The package also provides methods for using stacking and other model weighting techniques to average Bayesian predictive distributions.

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Version

Install

install.packages('loo')

Monthly Downloads

52,282

Version

2.4.1

License

GPL (>= 3)

Maintainer

Jonah Gabry

Last Published

December 9th, 2020

Functions in loo (2.4.1)

.compute_point_estimate

Compute a point estimate from a draws object
ap_psis

Pareto smoothed importance sampling (PSIS) using approximate posteriors
extract_log_lik

Extract pointwise log-likelihood from a Stan model
example_loglik_array

Objects to use in examples and tests
compare

Model comparison (deprecated, old version)
elpd

Generic (expected) log-predictive density
E_loo

Compute weighted expectations
.thin_draws

Thin a draws object
.ndraws

The number of posterior draws in a draws object.
find_model_names

Find the model names associated with "loo" objects
importance_sampling.array

Importance sampling of array
kfold-helpers

Helper functions for K-fold cross-validation
importance_sampling.matrix

Importance sampling of matrices
kfold-generic

Generic function for K-fold cross-validation for developers
loo-datasets

Datasets for loo examples and vignettes
importance_sampling.default

Importance sampling (default)
loo-package

Efficient LOO-CV and WAIC for Bayesian models
loo-glossary

LOO package glossary
nobs.psis_loo_ss

The number of observations in a psis_loo_ss object.
loo_moment_match

Moment matching for efficient approximate leave-one-out cross-validation (LOO)
obs_idx

Get observation indices used in subsampling
loo_moment_match_split

Split moment matching for efficient approximate leave-one-out cross-validation (LOO)
importance_sampling

A parent class for different importance sampling methods.
gpdfit

Estimate parameters of the Generalized Pareto distribution
nlist

Named lists
loo_subsample

Efficient approximate leave-one-out cross-validation (LOO) using subsampling
loo_compare

Model comparison
loo_model_weights

Model averaging/weighting via stacking or pseudo-BMA weighting
loo_approximate_posterior

Efficient approximate leave-one-out cross-validation (LOO) for posterior approximations
loo

Efficient approximate leave-one-out cross-validation (LOO)
relative_eff

Convenience function for computing relative efficiencies
parallel_psis_list

Parallel psis list computations
psis

Pareto smoothed importance sampling (PSIS)
sis

Standard importance sampling (SIS)
psislw

Pareto smoothed importance sampling (deprecated, old version)
print_dims

Print dimensions of log-likelihood or log-weights matrix
psis_approximate_posterior

Diagnostics for Laplace and ADVI approximations and Laplace-loo and ADVI-loo
old-extractors

Extractor methods
print.loo

Print methods
pareto-k-diagnostic

Diagnostics for Pareto smoothed importance sampling (PSIS)
tis

Truncated importance sampling (TIS)
update.psis_loo_ss

Update psis_loo_ss objects
weights.importance_sampling

Extract importance sampling weights
waic

Widely applicable information criterion (WAIC)