Merge branch 'master' into diff-diagnostics

Author: jgabry

.Rbuildignore

@@ -12,7 +12,7 @@ man-roxygen/*
 tests/testthat/Rplots\.pdf
 ^data-raw$
 vignettes/loo2-lfo_cache/*
-vignettes/loo2-non-factorizable_cache/*
+vignettes/loo2-non-factorized_cache/*
 ^\.appveyor\.yml$
 ^\.codecov\.yml$
 .github/*

.github/workflows/pkgdown.yaml

@@ -11,13 +11,13 @@ on:
 
 name: pkgdown.yaml
 
-concurrency:
-  group: pages
-  cancel-in-progress: true
-
 jobs:
   pkgdown:
     runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+      cancel-in-progress: true
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     permissions:
@@ -66,7 +66,7 @@ jobs:
         shell: Rscript {0}
 
       - name: Deploy to GitHub pages 🚀
-        uses: JamesIves/github-pages-deploy-action@v4.5.0
+        uses: JamesIves/github-pages-deploy-action@v4
         with:
           clean: false
           branch: gh-pages

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

README.md

@@ -1,4 +1,4 @@
-# loo <img src="man/figures/stanlogo.png" align="right" width="120" />
+# loo <img src="man/figures/logo.svg" align="right" width="120" />
 
 <!-- badges: start -->
 [![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/loo?color=blue)](https://cran.r-project.org/web/packages/loo)

_pkgdown.yml

@@ -1,46 +1,40 @@
 url: https://mc-stan.org/loo/
+
 destination: "docs/"
+
 template:
   package: pkgdownconfig
+
 development:
   mode: auto
 
 navbar:
   title: "loo"
 
   structure:
-    left: [home, vignettes, functions, pkgs, news, stan]
-    right: [search, bluesky, twitter, forum, github, lightswitch]
+    left: [home, vignettes, functions, news, pkgs, stan]
+    right: [search, bluesky, forum, github, lightswitch]
 
   components:
-    home:
-      icon: fa-home fa-lg
-      href: index.html
-    vignettes:
-      text: Vignettes
-      href: articles/index.html
-    functions:
-      text: Functions
-      href: reference/index.html
     pkgs:
       text: Other Packages
       menu:
-        - text: rstan
-          href: https://mc-stan.org/rstan
-        - text: cmdstanr
-          href: https://mc-stan.org/cmdstanr
-        - text: rstanarm
-          href: https://mc-stan.org/rstanarm
         - text: bayesplot
           href: https://mc-stan.org/bayesplot
-        - text: shinystan
-          href: https://mc-stan.org/shinystan
+        - text: cmdstanr
+          href: https://mc-stan.org/cmdstanr
+        - text: posterior
+          href: https://mc-stan.org/posterior
         - text: projpred
           href: https://mc-stan.org/projpred
+        - text: rstan
+          href: https://mc-stan.org/rstan
+        - text: rstanarm
+          href: https://mc-stan.org/rstanarm
         - text: rstantools
           href: https://mc-stan.org/rstantools
-        - text: posterior
-          href: https://mc-stan.org/posterior
+        - text: shinystan
+          href: https://mc-stan.org/shinystan
 
 articles:
   - title: Getting started

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).