fix's AICc degeneracy and resolve minor issues

.github/workflows/R-CMD-check.yaml

@@ -1,100 +1,18 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
-# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
-#
-# NOTE: This workflow is overkill for most R packages and
-# check-standard.yaml is likely a better choice.
-# usethis::use_github_action("check-standard") will install it.
+name: R-CMD-check
 on:
   push:
-    branches: main
+    branches: [main, master]
   pull_request:
-    branches: main
-  schedule:
-    - cron: '0 8 * * 0' # Every Sunday at midnight PST = Monday at 08:00 UTC
-
-name: R-CMD-check.yaml
-
-permissions: read-all
-
+    branches: [main, master, dev]
+permissions:
+  contents: read
 jobs:
   R-CMD-check:
-    runs-on: ${{ matrix.config.os }}
-
-    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
-
-    strategy:
-      fail-fast: false
-      matrix:
-        config:
-          - {os: macos-latest,   r: 'release'}
-
-          - {os: windows-latest, r: 'release'}
-          # use 4.0 or 4.1 to check with rtools40's older compiler
-          - {os: windows-latest, r: 'oldrel-3'}
-
-          - {os: ubuntu-latest,  r: 'devel', http-user-agent: 'release'}
-          - {os: ubuntu-latest,  r: 'release'}
-          - {os: ubuntu-latest,  r: 'oldrel-1'}
-          - {os: ubuntu-latest,  r: 'oldrel-2'}
-          - {os: ubuntu-latest,  r: 'oldrel-3'}
-
-    env:
-      R_KEEP_PKG_SOURCE: yes
-
-    steps:
-      - uses: actions/checkout@v4
-
-      - uses: r-lib/actions/setup-pandoc@v2
-
-      - uses: r-lib/actions/setup-r@v2
-        with:
-          r-version: ${{ matrix.config.r }}
-          http-user-agent: ${{ matrix.config.http-user-agent }}
-          use-public-rspm: true
-
-      - uses: r-lib/actions/setup-r-dependencies@v2
-        with:
-          extra-packages: any::rcmdcheck
-          needs: check
-
-      - uses: r-lib/actions/check-r-package@v2
-        if: github.event_name != 'schedule'
-        with:
-          upload-snapshots: true
-          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
-
-      - name: 🧪 Run R-CMD-check and save summary
-        if: github.event_name == 'schedule' && github.repository_owner == 'poissonconsulting'
-
-        env:
-          OS: ${{ matrix.config.os }}
-          R: ${{ matrix.config.r }}
-        run: |
-          check <- rcmdcheck::rcmdcheck(
-            args = "--no-manual",
-            error_on = "never"
-          )
-          result <- toupper(check$status)
-          log_text <- paste(
-            utils::capture.output(print(check)),
-            collapse = "\n"
-          )
-          filename <- paste0(Sys.getenv("OS"), "-R-", Sys.getenv("R"), ".txt")
-          cat(result, "\n---\n", log_text, "\n", file = filename)
-        shell: Rscript {0}
-
-      - name: 💾 Upload status artifact
-        if: github.event_name == 'schedule' && github.repository_owner == 'poissonconsulting'
-        uses: actions/upload-artifact@v4
-        with:
-          name: ${{ matrix.config.os }}-R-${{ matrix.config.r }}
-          path: ${{ matrix.config.os }}-R-${{ matrix.config.r }}.txt
-          retention-days: 6
-
-      - name: 💾 Upload snapshot artifacts
-        if: github.event_name == 'schedule' && github.repository_owner == 'poissonconsulting'
-        uses: actions/upload-artifact@v4
-        with:
-          name: snapshots-${{ matrix.config.os }}-R-${{ matrix.config.r }}
-          path: tests/testthat/_snaps
-          retention-days: 6
+    uses: poissonconsulting/.github/.github/workflows/R-CMD-check.yaml@v1
+    with:
+      tier: cran
+      jags: false
+      cmdstan: false
+      tex: true
+      private: false
+    secrets: inherit

.github/workflows/check-no-suggests.yaml

@@ -0,0 +1,14 @@
+name: check-no-suggests
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master, dev]
+permissions:
+  contents: read
+jobs:
+  check-no-suggests:
+    uses: poissonconsulting/.github/.github/workflows/check-no-suggests.yaml@v1
+    with:
+      private: false
+    secrets: inherit

.github/workflows/pkgdown.yaml

@@ -1,49 +1,18 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
-# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+name: pkgdown
 on:
   push:
     branches: [main, master]
   pull_request:
+    branches: [main, master, dev]
   release:
     types: [published]
   workflow_dispatch:
-
-name: pkgdown.yaml
-
-permissions: read-all
-
+permissions:
+  contents: write
 jobs:
   pkgdown:
-    runs-on: ubuntu-latest
-    # Only restrict concurrency for non-PR jobs
-    concurrency:
-      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
-    env:
-      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-    permissions:
-      contents: write
-    steps:
-      - uses: actions/checkout@v4
-
-      - uses: r-lib/actions/setup-pandoc@v2
-
-      - uses: r-lib/actions/setup-r@v2
-        with:
-          use-public-rspm: true
-
-      - uses: r-lib/actions/setup-r-dependencies@v2
-        with:
-          extra-packages: any::pkgdown, local::.
-          needs: website
-
-      - name: Build site
-        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
-        shell: Rscript {0}
-
-      - name: Deploy to GitHub pages 🚀
-        if: github.event_name != 'pull_request'
-        uses: JamesIves/github-pages-deploy-action@v4.5.0
-        with:
-          clean: false
-          branch: gh-pages
-          folder: docs
+    uses: poissonconsulting/.github/.github/workflows/pkgdown.yaml@v1
+    with:
+      cmdstan: false
+      private: false
+    secrets: inherit

.github/workflows/rhub.yaml

@@ -5,6 +5,10 @@
 # rhub::rhub_setup()
 #
 # It is unlikely that you need to modify this file manually.
+#
+# Distributed to CRAN-tier packages by poissonconsulting/.github tools/sync-ci.sh.
+# It is dispatch-triggered (run via rhub::rhub_check()), not a push/PR check, so it
+# is vendored as-is rather than called as a reusable workflow.
 
 name: R-hub
 run-name: "${{ github.event.inputs.id }}: ${{ github.event.inputs.name || format('Manually run by {0}', github.triggering_actor) }}"

.github/workflows/test-coverage.yaml

@@ -1,62 +1,16 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
-# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+name: test-coverage
 on:
   push:
-    branches: main
+    branches: [main, master]
   pull_request:
-
-name: test-coverage.yaml
-
-permissions: read-all
-
+    branches: [main, master, dev]
+permissions:
+  contents: read
 jobs:
   test-coverage:
-    runs-on: ubuntu-latest
-    env:
-      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-
-    steps:
-      - uses: actions/checkout@v4
-
-      - uses: r-lib/actions/setup-r@v2
-        with:
-          use-public-rspm: true
-
-      - uses: r-lib/actions/setup-r-dependencies@v2
-        with:
-          extra-packages: any::covr, any::xml2
-          needs: coverage
-
-      - name: Test coverage
-        run: |
-          cov <- covr::package_coverage(
-            quiet = FALSE,
-            clean = FALSE,
-            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
-          )
-          print(cov)
-          covr::to_cobertura(cov)
-        shell: Rscript {0}
-
-      - uses: codecov/codecov-action@v7
-        with:
-          # Fail if error if not on PR, or if on PR and token is given
-          fail_ci_if_error: ${{ github.event_name != 'pull_request' || secrets.CODECOV_TOKEN }}
-          files: ./cobertura.xml
-          plugins: noop
-          disable_search: true
-          token: ${{ secrets.CODECOV_TOKEN }}
-
-      - name: Show testthat output
-        if: always()
-        run: |
-          ## --------------------------------------------------------------------
-          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
-        shell: bash
-
-      - name: Upload test results
-        if: failure()
-        uses: actions/upload-artifact@v4
-        with:
-          name: coverage-test-failures
-          path: ${{ runner.temp }}/package
+    uses: poissonconsulting/.github/.github/workflows/test-coverage.yaml@v1
+    with:
+      cmdstan: false
+      tex: true
+      private: false
+    secrets: inherit

R/glance.R

@@ -23,7 +23,11 @@ generics::glance
   npars <- npars(x)
   log_lik <- logLik(x)
   aic <- 2 * npars - 2 * log_lik
-  aicc <- aic + 2 * npars * (npars + 1) / (nobs - npars - 1)
+  if (isTRUE(nobs <= npars)) {
+    aicc <- Inf
+  } else {
+    aicc <- aic + 2 * npars * (npars + 1) / (nobs - npars - 1)
+  }
 
   tibble(
     dist = dist,
@@ -39,6 +43,10 @@ generics::glance
 #'
 #' Gets a tibble with a single row for each distribution.
 #'
+#' The `aicc` is `Inf` if the number of observations is less than
+#' the number of parameters plus two as the small sample size
+#' correction is undefined.
+#'
 #' @inheritParams params
 #' @return A tidy tibble of the distributions.
 #' @family generics

R/hcp-average.R

@@ -58,6 +58,11 @@ hcp_average <- function(
     )
   }
 
+  ## Compute on the unique values so the various ci/est functions (some of
+  ## which collapse duplicates via group_by()) agree on the row structure,
+  ## then re-expand to the input `value` vector preserving order and duplicates.
+  uvalue <- unique(value)
+
   est_same <- FALSE
   ci_fun <- if (!ci) {
     hcp_noci
@@ -75,7 +80,7 @@ hcp_average <- function(
 
   hcp <- ci_fun(
     x,
-    value = value,
+    value = uvalue,
     ci = ci,
     level = level,
     nboot = nboot,
@@ -98,7 +103,7 @@ hcp_average <- function(
   )
 
   if (est_same) {
-    return(hcp)
+    return(hcp[match(value, hcp$value), ])
   }
 
   est_fun <- if (est_method == "multi") {
@@ -108,7 +113,7 @@ hcp_average <- function(
   }
   est <- est_fun(
     x,
-    value,
+    uvalue,
     ci = FALSE,
     level = level,
     nboot = nboot,
@@ -128,5 +133,6 @@ hcp_average <- function(
     ci_method = "MACL",
     hc = hc
   )
-  replace_estimates(hcp, est)
+  hcp <- replace_estimates(hcp, est)
+  hcp[match(value, hcp$value), ]
 }