extract_log_lik: Extract Pointwise Log-likelihood From Model

In kenkellner/ubms: Bayesian Models for Data from Unmarked Animals using 'Stan'

Extract Pointwise Log-likelihood From Model

Description

Extracts the pointwise log-likelihood matrix or array from a model. This is useful as an input for functions in the loo package. If called on a ubmsFit object, the log-likelihood matrix or array is calculated using the posterior distributions of the parameters; the log-likelihood values are not actually saved inside the model object. If called on a stanfit object, loo::extract_log_lik is used. In this case, the log-likelihood must be saved as one of the output parameters in Stan.

Usage

extract_log_lik(object, parameter_name = "log_lik", merge_chains = TRUE)

Arguments

object	A ubmsFit or stanfit object
parameter_name	The name of the log-likelihood parameter in the Stan output; ignored when object is a ubmsFit
merge_chains	If TRUE (the default), all Markov chains are merged together (i.e., stacked) and a matrix is returned. If ‘FALSE’ they are kept separate and an array is returned.

Value

A matrix (samples x sites) or array (samples x chains x sites)

kenkellner/ubms documentation built on March 1, 2025, 7:02 a.m.