loo.brmsfit: Efficient approximate leave-one-out cross-validation (LOO)

Description Usage Arguments Details Value References Examples

View source: R/loo.R

Description

Perform approximate leave-one-out cross-validation based on the posterior likelihood using the loo package. For more details see loo.

Usage

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## S3 method for class 'brmsfit'
loo(
  x,
  ...,
  compare = TRUE,
  resp = NULL,
  pointwise = FALSE,
  moment_match = FALSE,
  reloo = FALSE,
  k_threshold = 0.7,
  save_psis = FALSE,
  moment_match_args = list(),
  reloo_args = list(),
  model_names = NULL
)

Arguments

x

A brmsfit object.

...

More brmsfit objects or further arguments passed to the underlying post-processing functions. In particular, see prepare_predictions for further supported arguments.

compare

A flag indicating if the information criteria of the models should be compared to each other via loo_compare.

resp

Optional names of response variables. If specified, predictions are performed only for the specified response variables.

pointwise

A flag indicating whether to compute the full log-likelihood matrix at once or separately for each observation. The latter approach is usually considerably slower but requires much less working memory. Accordingly, if one runs into memory issues, pointwise = TRUE is the way to go.

moment_match

Logical; Indicate whether loo_moment_match should be applied on problematic observations. Defaults to FALSE. For most models, moment matching will only work if you have set save_pars = save_pars(all = TRUE) when fitting the model with brm. See loo_moment_match.brmsfit for more details.

reloo

Logical; Indicate whether reloo should be applied on problematic observations. Defaults to FALSE.

k_threshold

The threshold at which pareto k estimates are treated as problematic. Defaults to 0.7. Only used if argument reloo is TRUE. See pareto_k_ids for more details.

save_psis

Should the "psis" object created internally be saved in the returned object? For more details see loo.

moment_match_args

Optional list of additional arguments passed to loo_moment_match.

reloo_args

Optional list of additional arguments passed to reloo.

model_names

If NULL (the default) will use model names derived from deparsing the call. Otherwise will use the passed values as model names.

Details

See loo_compare for details on model comparisons. For brmsfit objects, LOO is an alias of loo. Use method add_criterion to store information criteria in the fitted model object for later usage.

Value

If just one object is provided, an object of class loo. If multiple objects are provided, an object of class loolist.

References

Vehtari, A., Gelman, A., & Gabry J. (2016). Practical Bayesian model evaluation using leave-one-out cross-validation and WAIC. In Statistics and Computing, doi:10.1007/s11222-016-9696-4. arXiv preprint arXiv:1507.04544.

Gelman, A., Hwang, J., & Vehtari, A. (2014). Understanding predictive information criteria for Bayesian models. Statistics and Computing, 24, 997-1016.

Watanabe, S. (2010). Asymptotic equivalence of Bayes cross validation and widely applicable information criterion in singular learning theory. The Journal of Machine Learning Research, 11, 3571-3594.

Examples

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## Not run: 
# model with population-level effects only
fit1 <- brm(rating ~ treat + period + carry,
            data = inhaler)
(loo1 <- loo(fit1))

# model with an additional varying intercept for subjects
fit2 <- brm(rating ~ treat + period + carry + (1|subject),
            data = inhaler)
(loo2 <- loo(fit2))   

# compare both models
loo_compare(loo1, loo2)                      

## End(Not run)

brms documentation built on Aug. 23, 2021, 5:08 p.m.