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@@ -14,14 +14,6 @@ __loo__ is an R package that allows users to compute efficient approximate
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leave-one-out cross-validation for fitted Bayesian models, as well as model
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weights that can be used to average predictive distributions.
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Leave-one-out cross-validation (LOO-CV, or LOO for short) and the widely
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applicable information criterion (WAIC) are methods for estimating pointwise
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out-of-sample prediction accuracy from a fitted Bayesian model using the
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log-likelihood evaluated at the posterior simulations of the parameter values.
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LOO and WAIC have various advantages over simpler estimates of predictive error
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such as AIC and DIC but are less used in practice because they involve
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additional computational steps.
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The __loo__ R package package implements the fast and stable computations
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for approximate LOO-CV and WAIC from
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@@ -31,28 +23,20 @@ _Statistics and Computing_. 27(5), 1413--1432.
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doi:10.1007/s11222-016-9696-4. [Online](https://link.springer.com/article/10.1007/s11222-016-9696-4),
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[arXiv preprint arXiv:1507.04544](https://arxiv.org/abs/1507.04544).
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* Vehtari, A., Gelman, A., and Gabry, J. (2017). Pareto smoothed importance sampling.
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[arXiv preprint arXiv:1507.02646](https://arxiv.org/abs/1507.02646).
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From existing posterior simulation draws, we compute approximate LOO-CV using
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Pareto smoothed importance sampling (PSIS), a new procedure for regularizing
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importance weights. As a byproduct of our calculations, we also obtain
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approximate standard errors for estimated predictive errors and for comparing
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predictive errors between two models.
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We recommend PSIS-LOO-CV instead of WAIC, because PSIS provides useful
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diagnostics and effective sample size and Monte Carlo standard error estimates.
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As of version `2.0.0`, the __loo__ package also provides methods for using
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stacking and other model weighting techiques to average Bayesian predictive
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distributions. For details on stacking and model weighting see:
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* Yao, Y., Vehtari, A., Simpson, D., and Gelman, A. (2018). Using
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stacking to average Bayesian predictive distributions. In Bayesian
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Analysis, doi:10.1214/17-BA1091.
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[Online](https://projecteuclid.org/euclid.ba/1516093227),
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[arXiv preprint arXiv:1704.02030](https://arxiv.org/abs/1704.02030).
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From existing posterior simulation draws, we compute approximate LOO-CV using
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Pareto smoothed importance sampling (PSIS), a new procedure for regularizing
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importance weights. As a byproduct of our calculations, we also obtain
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approximate standard errors for estimated predictive errors and for comparing
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predictive errors between two models. We recommend PSIS-LOO-CV instead of WAIC,
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because PSIS provides useful diagnostics and effective sample size and Monte
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Carlo standard error estimates.
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### Resources
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### Installation
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* Install from CRAN:
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* Install the latest release from CRAN:
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```r
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install.packages("loo")
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```
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* Install from GitHub (requires __devtools__ package):
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* Install the latest development version from GitHub:
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```r
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if (!require(devtools)) install.packages("devtools")
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devtools::install_github("stan-dev/loo")
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# install.packages("remotes")
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remotes::install_github("stan-dev/loo")
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```
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We do _not_ recommend setting `build_vignettes=TRUE` when installing from GitHub
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because the vignettes take a long time to build and are always available
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because some of the vignettes take a long time to build and are always available
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online at [mc-stan.org/loo/articles/](https://mc-stan.org/loo/articles/).
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### Python and Matlab/Octave Code
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Corresponding Python and Matlab/Octave code can be found at the
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[avehtari/PSIS](https://github.com/avehtari/PSIS) repository.
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