tis: Truncated importance sampling (TIS)

In jgabry/loo: Efficient Leave-One-Out Cross-Validation and WAIC for Bayesian Models

Truncated importance sampling (TIS)

Description

Implementation of truncated (self-normalized) importance sampling (TIS), truncated at S^(1/2) as recommended by Ionides (2008).

Usage

tis(log_ratios, ...)

## S3 method for class 'array'
tis(log_ratios, ..., r_eff = 1, cores = getOption("mc.cores", 1))

## S3 method for class 'matrix'
tis(log_ratios, ..., r_eff = 1, cores = getOption("mc.cores", 1))

## Default S3 method:
tis(log_ratios, ..., r_eff = 1)

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. If r_eff is not provided then the reported (T)IS effective sample sizes and Monte Carlo error estimates can be over-optimistic. If the posterior draws are (near) independent then r_eff=1 can be used. r_eff has to be a scalar (same value is used for all observations) or a vector with length equal to the number of observations. The default value is 1. See the relative_eff() helper function for computing r_eff.
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).

Value

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

log_weights

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

diagnostics

A named list containing one vector:

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

• n_eff: Effective sample size estimates.

Objects of class "tis" 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 tis.

dims

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

method

Method used for importance sampling, here tis.

Methods (by class)

• tis(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.

• tis(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.

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

References

Ionides, Edward L. (2008). Truncated importance sampling. Journal of Computational and Graphical Statistics 17(2): 295–311.

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))
tis_result <- tis(log_ratios, r_eff = r_eff)
str(tis_result)

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

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

jgabry/loo documentation built on Nov. 26, 2024, 5:29 p.m.