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loo (version 2.4.0)

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

52,845

Version

2.4.0

License

GPL (>= 3)

Maintainer

Jonah Gabry

Last Published

December 5th, 2020

Functions in loo (2.4.0)

E_loo

Compute weighted expectations
ap_psis

Pareto smoothed importance sampling (PSIS) using approximate posteriors
.thin_draws

Thin a draws object
compare

Model comparison (deprecated, old version)
elpd

Generic (expected) log-predictive density
extract_log_lik

Extract pointwise log-likelihood from a Stan model
example_loglik_array

Objects to use in examples and tests
.compute_point_estimate

Compute a point estimate from a draws object
.ndraws

The number of posterior draws in a draws object.
find_model_names

Find the model names associated with "loo" objects
loo-glossary

LOO package glossary
importance_sampling.default

Importance sampling (default)
importance_sampling.array

Importance sampling of array
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
kfold-helpers

Helper functions for K-fold cross-validation
nobs.psis_loo_ss

The number of observations in a psis_loo_ss object.
obs_idx

Get observation indices used in subsampling
loo_model_weights

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

Model comparison
pareto-k-diagnostic

Diagnostics for Pareto smoothed importance sampling (PSIS)
loo

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

Estimate parameters of the Generalized Pareto distribution
print.loo

Print methods
loo_approximate_posterior

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

Efficient LOO-CV and WAIC for Bayesian models
importance_sampling

A parent class for different importance sampling methods.
loo_subsample

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

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

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

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

Extract importance sampling weights
parallel_psis_list

Parallel psis list computations
waic

Widely applicable information criterion (WAIC)
sis

Standard importance sampling (SIS)
old-extractors

Extractor methods
relative_eff

Convenience function for computing relative efficiencies
tis

Truncated importance sampling (TIS)
psis

Pareto smoothed importance sampling (PSIS)
nlist

Named lists
psis_approximate_posterior

Diagnostics for Laplace and ADVI approximations and Laplace-loo and ADVI-loo
update.psis_loo_ss

Update psis_loo_ss objects
psislw

Pareto smoothed importance sampling (deprecated, old version)