This is a major release with many changes. Whenever possible we have opted to deprecate rather than remove old functionality, but it is possible that old code that accesses elements inside loo objects by position rather than name may error.
New package documentation website http://mc-stan.org/loo/ with vignettes, function reference, news.
Updated existing vignette and added two new vignettes demonstrating how to use the package.
New function psis()
replaces psislw()
(now deprecated). This version implements the improvements to the PSIS algorithm described in the latest version of https://arxiv.org/abs/1507.02646. Additional diagnostic information is now also provided, including PSIS effective sample sizes.
New weights()
method for extracting smoothed weights from a psis
object. Arguments log
and normalize
control whether the weights are returned on the log scale and whether they are normalized.
Updated the interface for the loo()
methods to integrate nicely with the new PSIS algorithm. Methods for log-likelihood arrays, matrices, and functions are provided. Several arguments have changed, particularly for the loo.function
method. The documentation at help("loo")
has been updated to describe the new behavior.
The structure of the objects returned by the loo()
function has also changed slightly, as described in the Value section at help("loo", package = "loo")
.
New function loo_model_weights()
computes weights for model averaging as described in https://arxiv.org/abs/1704.02030. Implemented methods include stacking of predictive distributions, pseudo-BMA weighting or pseudo-BMA+ weighting with the Bayesian bootstrap.
Setting options(loo.cores=...)
is now deprecated in favor of options(mc.cores=...)
. For now, if both the loo.cores
and mc.cores
options have been set, preference will be given to loo.cores
until it is removed in a future release. (thanks to @cfhammill)
New functions example_loglik_array()
and example_loglik_matrix()
that provide objects to use in examples and tests.
When comparing more than two models with compare()
, the first column of the output is now the elpd
difference from the model in the first row.
New helper functions for splitting observations for K-fold CV: kfold_split_random()
, kfold_split_balanced()
, kfold_split_stratified()
. Additional helper functions for implementing K-fold CV will be included in future releases.
E_loo
function for computing weighted expectations (means, variances, quantiles).pareto_k_table
and pareto_k_ids
convenience functions for quickly identifying problematic observations(-Inf, 0.5]
, (0.5, 0.7]
, (0.7, 1]
, (1, Inf)
(didn’t used to include 0.7)psislw
instead of print.loo
print.loo
shows a table of pareto k estimates (if any k > 0.7)compare
to allow loo objects to be provided in a list rather than in '...'
compare
. compare
. We have removed the weights because they were based only on the point estimate of the elpd values ignoring the uncertainty. We are currently working on something similar to these weights that also accounts for uncertainty, which will be included in future versions of loo.This update makes it easier for other package authors using loo to write tests that involve running the loo
function. It also includes minor bug fixes and additional unit tests. Highlights:
cores=1
.psislw
function is called in an interactive session.This update provides several important improvements, most notably an alternative method for specifying the pointwise log-likelihood that reduces memory usage and allows for loo to be used with larger datasets. This update also makes it easier to to incorporate loo’s functionality into other packages.
matrix
and function
methods for both loo
and waic
. The matrix method provide the same functionality as in previous versions of loo (taking a log-likelihood matrix as the input). The function method allows the user to provide a function for computing the log-likelihood from the data and posterior draws (which are also provided by the user). The function method is less memory intensive and should make it possible to use loo for models fit to larger amounts of data than before.plot
and print
methods. plot
also provides label_points
argument, which, if TRUE
, will label any Pareto k
points greater than 1/2 by the index number of the corresponding observation. The plot method also now warns about Inf
/NA
/NaN
values of k
that are not shown in the plot.compare
now returns model weights and accepts more than two inputs.options(loo.cores = NUMBER)
.