Merge pull request #311 from stan-dev/update-loo-uncertainty-ref

update LOO uncertainty paper to use BA doi

Author: jgabry

DESCRIPTION

@@ -58,5 +58,5 @@ Config/testthat/start-first: loo_subsampling_cases, loo_subsampling
 Encoding: UTF-8
 LazyData: TRUE
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3
 SystemRequirements: pandoc (>= 1.12.3), pandoc-citeproc

R/loo.R

@@ -446,7 +446,7 @@ pointwise_loo_calcs <- function(ll, psis_object) {
 #' @param diagnostics Named list containing vector `pareto_k` and vector `n_eff`.
 #' @param dims Log likelihood matrix dimensions (attribute of `"psis"` object).
 #' @template is_method
-#' @param is_object An object of class `"psis"/"tis"/"sis"`, as returned by the [psis()/tis()/sis()] function.
+#' @param is_object An object of class `"psis"/"tis"/"sis"`, as returned by the `psis()`/`tis()`/`sis()` function.
 #' @return A `'importance_sampling_loo'` object as described in the Value section of the [loo()]
 #'   function documentation.
 #'

R/loo_subsample.R

@@ -471,7 +471,7 @@ estimator_choices <- function() {
 
 #' Utility function to apply user-specified log-likelihood to a single data point
 #' @details
-#' See [elpd_loo_approximation] and [compute_lpds] for usage examples
+#' See `elpd_loo_approximation` and `compute_lpds` for usage examples
 #' @noRd
 #'
 #' @return lpd value for a single data point i
@@ -487,7 +487,7 @@ lpd_i <- function(i, llfun, data, draws) {
 #' using platform-dependent parallel backends when cores > 1
 #'
 #' @details
-#' See [elpd_loo_approximation] for usage examples
+#' See `elpd_loo_approximation` for usage examples
 #'
 #' @noRd
 #' @return a vector of computed log probability densities

inst/CITATION

@@ -34,7 +34,7 @@ bibentry(bibtype = "Article",
     		    person("Aki", "Vehtari")),
          journal = "Bayesian Analysis",
          year = "2025",
-         note = "accepted for publication",
+         note = "doi:10.1214/24-BA1453",
          header = "To cite when using loo_compare():"
 )
 

man-roxygen/loo-and-compare-references.R

@@ -12,8 +12,8 @@
 #'
 #' Sivula, T, Magnusson, M., Matamoros A. A., and Vehtari, A. (2025).
 #' Uncertainty in Bayesian leave-one-out cross-validation based model
-#' comparison. *Bayesian Analysis*, accepted for publication.
-#' [preprint arXiv:2008.10296v5.](https://arxiv.org/abs/2008.10296v5).
+#' comparison. *Bayesian Analysis*,
+#' [doi:10.1214/25-BA1569](https://doi.org/10.1214/25-BA1569).
 #' 
 #' McLatchie, Y., and Vehtari, A. (2024).  Efficient estimation and
 #' correction of selection-induced bias with order statistics.

man-roxygen/loo-uncertainty-reference.R

@@ -1,5 +1,5 @@
 #' @references
 #' Sivula, T, Magnusson, M., Matamoros A. A., and Vehtari, A. (2025).
 #' Uncertainty in Bayesian leave-one-out cross-validation based model
-#' comparison. *Bayesian Analysis*, accepted for publication.
-#' [preprint arXiv:2008.10296v5.](https://arxiv.org/abs/2008.10296v5).
+#' comparison. *Bayesian Analysis*,
+#' [doi:10.1214/25-BA1569](https://doi.org/10.1214/25-BA1569).