@@ -14,14 +14,6 @@ __loo__ is an R package that allows users to compute efficient approximate
1414leave-one-out cross-validation for fitted Bayesian models, as well as model
1515weights that can be used to average predictive distributions.
1616
17- Leave-one-out cross-validation (LOO-CV, or LOO for short) and the widely
18- applicable information criterion (WAIC) are methods for estimating pointwise
19- out-of-sample prediction accuracy from a fitted Bayesian model using the
20- log-likelihood evaluated at the posterior simulations of the parameter values.
21- LOO and WAIC have various advantages over simpler estimates of predictive error
22- such as AIC and DIC but are less used in practice because they involve
23- additional computational steps.
24-
2517The __ loo__ R package package implements the fast and stable computations
2618for approximate LOO-CV and WAIC from
2719
@@ -31,28 +23,20 @@ _Statistics and Computing_. 27(5), 1413--1432.
3123doi:10.1007/s11222-016-9696-4. [ Online] ( https://link.springer.com/article/10.1007/s11222-016-9696-4 ) ,
3224[ arXiv preprint arXiv:1507.04544] ( https://arxiv.org/abs/1507.04544 ) .
3325
34- * Vehtari, A., Gelman, A., and Gabry, J. (2017). Pareto smoothed importance sampling.
35- [ arXiv preprint arXiv:1507.02646] ( https://arxiv.org/abs/1507.02646 ) .
36-
37- From existing posterior simulation draws, we compute approximate LOO-CV using
38- Pareto smoothed importance sampling (PSIS), a new procedure for regularizing
39- importance weights. As a byproduct of our calculations, we also obtain
40- approximate standard errors for estimated predictive errors and for comparing
41- predictive errors between two models.
42-
43- We recommend PSIS-LOO-CV instead of WAIC, because PSIS provides useful
44- diagnostics and effective sample size and Monte Carlo standard error estimates.
45-
46- As of version ` 2.0.0 ` , the __ loo__ package also provides methods for using
47- stacking and other model weighting techiques to average Bayesian predictive
48- distributions. For details on stacking and model weighting see:
49-
5026* Yao, Y., Vehtari, A., Simpson, D., and Gelman, A. (2018). Using
5127stacking to average Bayesian predictive distributions. In Bayesian
5228Analysis, doi:10.1214/17-BA1091.
5329[ Online] ( https://projecteuclid.org/euclid.ba/1516093227 ) ,
5430[ arXiv preprint arXiv:1704.02030] ( https://arxiv.org/abs/1704.02030 ) .
5531
32+ From existing posterior simulation draws, we compute approximate LOO-CV using
33+ Pareto smoothed importance sampling (PSIS), a new procedure for regularizing
34+ importance weights. As a byproduct of our calculations, we also obtain
35+ approximate standard errors for estimated predictive errors and for comparing
36+ predictive errors between two models. We recommend PSIS-LOO-CV instead of WAIC,
37+ because PSIS provides useful diagnostics and effective sample size and Monte
38+ Carlo standard error estimates.
39+
5640
5741### Resources
5842
@@ -63,23 +47,25 @@ Analysis, doi:10.1214/17-BA1091.
6347
6448### Installation
6549
66- * Install from CRAN:
50+ * Install the latest release from CRAN:
6751
6852``` r
6953install.packages(" loo" )
7054```
7155
72- * Install from GitHub (requires __ devtools __ package) :
56+ * Install the latest development version from GitHub :
7357
7458``` r
75- if ( ! require( devtools )) install.packages(" devtools " )
76- devtools :: install_github(" stan-dev/loo" )
59+ # install.packages("remotes ")
60+ remotes :: install_github(" stan-dev/loo" )
7761```
62+
7863We do _ not_ recommend setting ` build_vignettes=TRUE ` when installing from GitHub
79- because the vignettes take a long time to build and are always available
64+ because some of the vignettes take a long time to build and are always available
8065online at [ mc-stan.org/loo/articles/] ( https://mc-stan.org/loo/articles/ ) .
8166
8267### Python and Matlab/Octave Code
68+
8369Corresponding Python and Matlab/Octave code can be found at the
8470[ avehtari/PSIS] ( https://github.com/avehtari/PSIS ) repository.
8571
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