loo (version 2.6.0)

sis: Standard importance sampling (SIS)

Description

Implementation of standard importance sampling (SIS).

Usage

sis(log_ratios, ...)
# S3 method for array
sis(log_ratios, ..., r_eff = NULL, cores = getOption("mc.cores", 1))
# S3 method for matrix
sis(log_ratios, ..., r_eff = NULL, cores = getOption("mc.cores", 1))
# S3 method for default
sis(log_ratios, ..., r_eff = NULL)

Value

The sis() methods return an object of class "sis", which is a named list with the following components:

log_weights

Vector or matrix of smoothed but unnormalized log weights. To get normalized weights use the weights() method provided for objects of class sis.

diagnostics

A named list containing one vector:

• pareto_k: Not used in sis, all set to 0.

• n_eff: effective sample size estimates.

Objects of class "sis" also have the following attributes:

norm_const_log

Vector of precomputed values of colLogSumExps(log_weights) that are used internally by the weights method to normalize the log weights.

r_eff

If specified, the user's r_eff argument.

tail_len

Not used for sis.

dims

Integer vector of length 2 containing S (posterior sample size) and N (number of observations).

method

Method used for importance sampling, here sis.

Arguments

log_ratios

An array, matrix, or vector of importance ratios on the log scale (for Importance sampling LOO, these are negative log-likelihood values). See the Methods (by class) section below for a detailed description of how to specify the inputs for each method.

...

Arguments passed on to the various methods.

r_eff

Vector of relative effective sample size estimates containing one element per observation. The values provided should be the relative effective sample sizes of 1/exp(log_ratios) (i.e., 1/ratios). This is related to the relative efficiency of estimating the normalizing term in self-normalizing importance sampling. See the relative_eff() helper function for computing r_eff. If using psis with draws of the log_ratios not obtained from MCMC then the warning message thrown when not specifying r_eff can be disabled by setting r_eff to NA.

cores

The number of cores to use for parallelization. This defaults to the option mc.cores which can be set for an entire R session by options(mc.cores = NUMBER). The old option loo.cores is now deprecated but will be given precedence over mc.cores until loo.cores is removed in a future release. As of version 2.0.0 the default is now 1 core if mc.cores is not set, but we recommend using as many (or close to as many) cores as possible.

• Note for Windows 10 users: it is strongly recommended to avoid using the .Rprofile file to set mc.cores (using the cores argument or setting mc.cores interactively or in a script is fine).

Methods (by class)

• sis(array): An \(I\) by \(C\) by \(N\) array, where \(I\) is the number of MCMC iterations per chain, \(C\) is the number of chains, and \(N\) is the number of data points.

• sis(matrix): An \(S\) by \(N\) matrix, where \(S\) is the size of the posterior sample (with all chains merged) and \(N\) is the number of data points.

• sis(default): A vector of length \(S\) (posterior sample size).

References

Vehtari, A., Gelman, A., and Gabry, J. (2017). Practical Bayesian model evaluation using leave-one-out cross-validation and WAIC. Statistics and Computing. 27(5), 1413--1432. doi:10.1007/s11222-016-9696-4 (journal version, preprint arXiv:1507.04544).

Vehtari, A., Simpson, D., Gelman, A., Yao, Y., and Gabry, J. (2019). Pareto smoothed importance sampling. preprint arXiv:1507.02646

See Also

• psis() for approximate LOO-CV using PSIS.

• loo() for approximate LOO-CV.

• pareto-k-diagnostic for PSIS diagnostics.

Examples

log_ratios <- -1 * example_loglik_array()
r_eff <- relative_eff(exp(-log_ratios))
sis_result <- sis(log_ratios, r_eff = r_eff)
str(sis_result)

# extract smoothed weights
lw <- weights(sis_result) # default args are log=TRUE, normalize=TRUE
ulw <- weights(sis_result, normalize=FALSE) # unnormalized log-weights

w <- weights(sis_result, log=FALSE) # normalized weights (not log-weights)
uw <- weights(sis_result, log=FALSE, normalize = FALSE) # unnormalized weights