loo_model_weights.Rd
Model averaging via stacking of predictive distributions, pseudoBMA weighting or pseudoBMA+ weighting with the Bayesian bootstrap. See Yao et al. (2018) and Vehtari, Gelman, and Gabry (2017a,2017b) for background.
loo_model_weights(x, ...) # S3 method for default loo_model_weights(x, ..., method = c("stacking", "pseudobma"), optim_method = "BFGS", optim_control = list(), BB = TRUE, BB_n = 1000, alpha = 1, r_eff_list = NULL, cores = getOption("mc.cores", 1)) stacking_weights(lpd_point, optim_method = "BFGS", optim_control = list()) pseudobma_weights(lpd_point, BB = TRUE, BB_n = 1000, alpha = 1)
x  A list of pointwise loglikelihood matrices or "psis_loo" objects
(objects returned by 

...  Unused, except for the generic to pass arguments to individual methods. 
method  Either 
optim_method  The optimization method to use if

optim_control  If 
BB  Logical used when 
BB_n  For pseudoBMA+ weighting only, the number of samples to use for the Bayesian bootstrap. The default is 1000. 
alpha  Positive scalar shape parameter in the Dirichlet distribution used for the Bayesian bootstrap. The default is 1, which corresponds to a uniform distribution on the simplex space. 
r_eff_list  Optionally, a list of relative effective sample size
estimates for the likelihood 
cores  The number of cores to use for parallelization. This defaults to
the option 
lpd_point  A matrix of pointwise leaveoneout (or Kfold) log
likelihoods evaluated for different models. It should be a \(N\) by
\(K\) matrix where \(N\) is sample size and \(K\) is the number of
models. Each column corresponds to one model. These values can be
calculated approximately using 
A numeric vector containing one weight for each model.
loo_model_weights
is a wrapper around the stacking_weights
and
pseudobma_weights
functions that implements stacking, pseudoBMA, and
pseudoBMA+ weighting for combining multiple predictive distributions. We can
use approximate or exact leaveoneout crossvalidation (LOOCV) or Kfold CV
to estimate the expected log predictive density (ELPD).
The stacking method (method="stacking"
) combines all models by
maximizing the leaveoneout predictive density of the combination
distribution. That is, it finds the optimal linear combining weights for
maximizing the leaveoneout log score.
The pseudoBMA method (method="pseudobma"
) finds the relative weights
proportional to the ELPD of each model. However, when
method="pseudobma"
, the default is to also use the Bayesian bootstrap
(BB=TRUE
), which corresponds to the pseudoBMA+ method. The Bayesian
bootstrap takes into account the uncertainty of finite data points and
regularizes the weights away from the extremes of 0 and 1.
In general, we recommend stacking for averaging predictive distributions, while pseudoBMA+ can serve as a computationally easier alternative.
Vehtari, A., Gelman, A., and Gabry, J. (2017a). Practical Bayesian model evaluation using leaveoneout crossvalidation and WAIC. Statistics and Computing. 27(5), 14131432. doi:10.1007/s1122201696964. ( 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/
Yao, Y., Vehtari, A., Simpson, D., and Gelman, A. (2018) Using stacking to average Bayesian predictive distributions. Bayesian Analysis, advance publication, doi:10.1214/17BA1091. (online).
The loo package vignettes for demonstrations.
loo
for details on leaveoneout ELPD estimation.
constrOptim
for the choice of optimization methods and controlparameters.
relative_eff
for computing r_eff
.
# NOT RUN { ### Demonstrating usage after fitting models with RStan library(rstan) # generate fake data from N(0,1). N < 100 y < rnorm(N, 0, 1) # Suppose we have three models: N(1, sigma), N(0.5, sigma) and N(0.6,sigma). stan_code < " data { int N; vector[N] y; real mu_fixed; } parameters { real<lower=0> sigma; } model { sigma ~ exponential(1); y ~ normal(mu_fixed, sigma); } generated quantities { vector[N] log_lik; for (n in 1:N) log_lik[n] = normal_lpdf(y[n] mu_fixed, sigma); }" mod < stan_model(model_code = stan_code) fit1 < sampling(mod, data=list(N=N, y=y, mu_fixed=1)) fit2 < sampling(mod, data=list(N=N, y=y, mu_fixed=0.5)) fit3 < sampling(mod, data=list(N=N, y=y, mu_fixed=0.6)) model_list < list(fit1, fit2, fit3) log_lik_list < lapply(model_list, extract_log_lik) # optional but recommended r_eff_list < lapply(model_list, function(x) { ll_array < extract_log_lik(x, merge_chains = FALSE) relative_eff(exp(ll_array)) }) # stacking method: wts1 < loo_model_weights( log_lik_list, method = "stacking", r_eff_list = r_eff_list, optim_control = list(reltol=1e10) ) print(wts1) # can also pass a list of psis_loo objects to avoid recomputing loo loo_list < lapply(1:length(log_lik_list), function(j) { loo(log_lik_list[[j]], r_eff = r_eff_list[[j]]) }) wts2 < loo_model_weights( loo_list, method = "stacking", optim_control = list(reltol=1e10) ) all.equal(wts1, wts2) # pseudoBMA+ method: set.seed(1414) loo_model_weights(loo_list, method = "pseudobma") # pseudoBMA method (set BB = FALSE): loo_model_weights(loo_list, method = "pseudobma", BB = FALSE) # calling stacking_weights or pseudobma_weights directly lpd1 < loo(log_lik_list[[1]], r_eff = r_eff_list[[1]])$pointwise[,1] lpd2 < loo(log_lik_list[[2]], r_eff = r_eff_list[[2]])$pointwise[,1] lpd3 < loo(log_lik_list[[3]], r_eff = r_eff_list[[3]])$pointwise[,1] stacking_weights(cbind(lpd1, lpd2, lpd3)) pseudobma_weights(cbind(lpd1, lpd2, lpd3)) pseudobma_weights(cbind(lpd1, lpd2, lpd3), BB = FALSE) # }