sdmTMB_stacking: Perform stacking with log scores on 'sdmTMB_cv()' output

In pbs-assess/sdmTMB: Spatial and Spatiotemporal SPDE-Based GLMMs with 'TMB'

Perform stacking with log scores on sdmTMB_cv() output

Description

This approach is described in Yao et al. (2018) \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1214/17-BA1091")}. The general method minimizes (or maximizes) some quantity across models. For simple models with normal error, this may be the root mean squared error (RMSE), but other approaches include the log score. We adopt the latter here, where log scores are used to generate the stacking of predictive distributions

Usage

sdmTMB_stacking(model_list, include_folds = NULL)

Arguments

model_list	A list of models fit with sdmTMB_cv() to generate estimates of predictive densities. You will want to set the seed to the same value before fitting each model or manually construct the fold IDs so that they are the same across models.
include_folds	An optional numeric vector specifying which folds to include in the calculations. For example, if 5 folds are used for k-fold cross validation, and the first 4 are needed to generate these weights, include_folds = 1:4.

Value

A vector of model weights.

References

Yao, Y., Vehtari, A., Simpson, D., and Gelman, A. 2018. Using Stacking to Average Bayesian Predictive Distributions (with Discussion). Bayesian Analysis 13(3): 917–1007. International Society for Bayesian Analysis. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1214/17-BA1091")}

Examples

# Set parallel processing if desired. See 'Details' in ?sdmTMB_cv

# Depth as quadratic:
set.seed(1)
m_cv_1 <- sdmTMB_cv(
  density ~ 0 + depth_scaled + depth_scaled2,
  data = pcod_2011, mesh = pcod_mesh_2011,
  family = tweedie(link = "log"), k_folds = 2
)
# Depth as linear:
set.seed(1)
m_cv_2 <- sdmTMB_cv(
  density ~ 0 + depth_scaled,
  data = pcod_2011, mesh = pcod_mesh_2011,
  family = tweedie(link = "log"), k_folds = 2
)

# Only an intercept:
set.seed(1)
m_cv_3 <- sdmTMB_cv(
  density ~ 1,
  data = pcod_2011, mesh = pcod_mesh_2011,
  family = tweedie(link = "log"), k_folds = 2
)

models <- list(m_cv_1, m_cv_2, m_cv_3)
weights <- sdmTMB_stacking(models)
weights

pbs-assess/sdmTMB documentation built on Dec. 20, 2024, 1:51 p.m.