`psis.Rd`

Implementation of Pareto smoothed importance sampling (PSIS), a method for stabilizing importance ratios. The version of PSIS implemented here corresponds to the algorithm presented in Vehtari, Gelman and Gabry (2017b). For PSIS diagnostics see the pareto-k-diagnostic page.

psis(log_ratios, ...) # S3 method for array psis(log_ratios, ..., r_eff = NULL, cores = getOption("mc.cores", 1)) # S3 method for matrix psis(log_ratios, ..., r_eff = NULL, cores = getOption("mc.cores", 1)) # S3 method for default psis(log_ratios, ..., r_eff = NULL) # S3 method for psis weights(object, ..., log = TRUE, normalize = TRUE) is.psis(x)

log_ratios | An array, matrix, or vector of importance ratios on the log
scale (for PSIS-LOO these are |
---|---|

... | 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 |

cores | The number of cores to use for parallelization. This defaults to
the option `.Rprofile` file to set `mc.cores` (using the `cores`
argument or setting `mc.cores` interactively or in a script is fine). |

object | For the |

log | For the |

normalize | For the |

x | For |

The `psis`

methods return an object of class `"psis"`

,
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`"psis"`

.`diagnostics`

A named list containing two vectors:

`pareto_k`

: Estimates of the shape parameter \(k\) of the generalized Pareto distribution. See the`pareto-k-diagnostic`

page for details.`n_eff`

: PSIS effective sample size estimates.

Objects of class `"psis"`

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.`tail_len`

Vector of tail lengths used for fitting the generalized Pareto distribution.

`r_eff`

If specified, the user's

`r_eff`

argument.`dims`

Integer vector of length 2 containing

`S`

(posterior sample size) and`N`

(number of observations).

The `weights`

method returns an object with the same dimensions
as the `log_weights`

component of the `"psis"`

object. The
`normalize`

and `log`

arguments control whether the returned
weights are normalized and whether or not to return them on the log scale.

`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.`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.`default`

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

Vehtari, A., Gelman, A., and Gabry, J. (2017a). 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, preprint arXiv:1507.04544).

Vehtari, A., Gelman, A., and Gabry, J. (2017b). Pareto smoothed importance sampling. arXiv preprint: http://arxiv.org/abs/1507.02646/

`loo`

for approximate LOO-CV using PSIS.`pareto-k-diagnostic`

for PSIS diagnostics.

log_ratios <- -1 * example_loglik_array() r_eff <- relative_eff(exp(-log_ratios)) psis_result <- psis(log_ratios, r_eff = r_eff) str(psis_result)#> List of 2 #> $ log_weights: num [1:1000, 1:32] -0.694 -0.941 -0.818 -0.649 -0.816 ... #> $ diagnostics:List of 2 #> ..$ pareto_k: num [1:32] 0.0447 -0.0343 0.0696 -0.052 -0.1168 ... #> ..$ n_eff : num [1:32] 901 960 929 895 936 ... #> - attr(*, "norm_const_log")= num [1:32] 6.22 6.47 6.17 6.47 6.52 ... #> - attr(*, "tail_len")= num [1:32] 99 96 97 100 98 99 99 100 103 97 ... #> - attr(*, "r_eff")= num [1:32] 0.932 0.977 0.968 0.913 0.953 ... #> - attr(*, "dims")= int [1:2] 1000 32 #> - attr(*, "class")= chr [1:2] "psis" "list"plot(psis_result)# extract smoothed weights lw <- weights(psis_result) # default args are log=TRUE, normalize=TRUE ulw <- weights(psis_result, normalize=FALSE) # unnormalized log-weights w <- weights(psis_result, log=FALSE) # normalized weights (not log-weights) uw <- weights(psis_result, log=FALSE, normalize = FALSE) # unnormalized weights