Merge branch 'main' into upkeep

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

@@ -1,5 +1,9 @@
 # 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.
 on:
   push:
     branches: [main, master]
@@ -21,7 +25,9 @@ jobs:
       matrix:
         config:
           - {os: macos-latest,   r: 'release'}
+
           - {os: windows-latest, r: 'release'}
+
           - {os: ubuntu-latest,  r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,  r: 'release'}
           - {os: ubuntu-latest,  r: 'oldrel-1'}

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

@@ -0,0 +1,60 @@
+# 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 only directly installs "hard" dependencies, i.e. Depends,
+# Imports, and LinkingTo dependencies. Notably, Suggests dependencies are never
+# installed, with the exception of testthat, knitr, and rmarkdown. The cache is
+# never used to avoid accidentally restoring a cache containing a suggested
+# dependency.
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: check-no-suggests.yaml
+
+permissions: read-all
+
+jobs:
+  check-no-suggests:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: ubuntu-latest,   r: 'release'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      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:
+          dependencies: '"hard"'
+          cache: false
+          extra-packages: |
+            any::rcmdcheck
+            any::testthat
+            any::knitr
+            any::rmarkdown
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.github/workflows/pkgdown.yaml

@@ -9,19 +9,22 @@ on:
     types: [published]
   workflow_dispatch:
 
-name: pkgdown
+name: pkgdown.yaml
+
+permissions: read-all
 
 jobs:
   pkgdown:
-    if: "!contains(github.event.head_commit.message, 'skip ci')"
     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@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -40,18 +43,8 @@ jobs:
 
       - name: Deploy to GitHub pages 🚀
         if: github.event_name != 'pull_request'
-        uses: JamesIves/github-pages-deploy-action@v4.4.1
+        uses: JamesIves/github-pages-deploy-action@v4.5.0
         with:
           clean: false
           branch: gh-pages
           folder: docs
-
-      - name: action-slack
-        if: failure()
-        env:
-          SLACK_WEBHOOK_URL: ${{ secrets.SLACK_WEBHOOK_URL }}
-        uses: 8398a7/[email protected]
-        with:
-          status: ${{ job.status }}
-          author_name: "github action: ${{github.workflow}}"
-          fields: repo, ref, commit, author, message

.github/workflows/coverage.yaml → .github/workflows/test-coverage.yaml

@@ -6,46 +6,56 @@ on:
   pull_request:
     branches: [main, master]
 
-name: coverage
+name: test-coverage.yaml
+
+permissions: read-all
 
 jobs:
-  coverage:
-    if: "!contains(github.event.head_commit.message, 'skip ci')"
+  test-coverage:
     runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v3
+      - 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
+          extra-packages: any::covr, any::xml2
           needs: coverage
 
       - name: Test coverage
         run: |
-          covr::codecov(
+          cov <- covr::package_coverage(
             quiet = FALSE,
             clean = FALSE,
-            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
           )
+          covr::to_cobertura(cov)
         shell: Rscript {0}
 
+      - uses: codecov/codecov-action@v4
+        with:
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
+          file: ./cobertura.xml
+          plugin: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
       - name: Show testthat output
         if: always()
         run: |
           ## --------------------------------------------------------------------
-          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
         shell: bash
 
       - name: Upload test results
         if: failure()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: coverage-test-failures
           path: ${{ runner.temp }}/package

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: extras
 Title: Helper Functions for Bayesian Analyses
-Version: 0.7.2.9000
+Version: 0.7.3.9000
 Authors@R: c(
     person("Nicole", "Hill", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-7623-2153")),
@@ -49,3 +49,5 @@ Encoding: UTF-8
 Language: en-US
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.2
+VignetteBuilder: knitr
+Config/Needs/website: poissonconsulting/poissontemplate

NAMESPACE

@@ -83,6 +83,7 @@ export(odds)
 export(odds_ratio)
 export(odds_ratio2)
 export(par_pattern)
+export(params)
 export(pbern)
 export(pextreme)
 export(phi)

NEWS.md

@@ -2,6 +2,10 @@
 
 <!-- NEWS.md is maintained by https://fledge.cynkra.com, contributors should not edit this file -->
 
+# extras 0.7.3
+
+- Ensure all tests, examples, and vignettes run conditionally for packages listed in suggests.
+
 # extras 0.7.2
 
 - Fix behaviour of `dev_beta_binom()` when size \< x.

R/dev.R

@@ -288,11 +288,12 @@ dev_pois_zi <- function(x, lambda, prob = 0, res = FALSE) {
 #' @family dev_dist
 #' @export
 #'
-#' @examples
+#' @examplesIf requireNamespace("sn")
 #' dev_skewnorm(c(-2:2))
 #' dev_skewnorm(-2:2, 0, 1, 5)
 #' dev_skewnorm(-2:2, 0, 1, 5, res = TRUE)
 dev_skewnorm <- function(x, mean = 0, sd = 1, shape = 0, res = FALSE) {
+  rlang::check_installed("sn")
   delta <- shape / sqrt(1 + shape^2)
   mu_z <- sqrt(2 / pi) * delta
   sig_z <- sqrt(1 - mu_z^2)

R/extras-package.R

@@ -3,5 +3,7 @@
 
 ## usethis namespace: start
 #' @importFrom lifecycle deprecated
+#' @import chk
+#' @importFrom stats dbinom dlnorm dnorm dpois dnbinom
 ## usethis namespace: end
 NULL

R/fabs.R

@@ -7,6 +7,7 @@
 #'
 #' @param x An existing R object.
 #' @family translations
+#' @return A numeric vector of the corresponding absolute values.
 #' @export
 #' @examples
 #' fabs(c(0, -1, 2))

R/log-lik.R

@@ -214,11 +214,12 @@ log_lik_pois_zi <- function(x, lambda = 1, prob = 0) {
 #' @family log_lik_dist
 #' @export
 #'
-#' @examples
+#' @examplesIf requireNamespace("sn")
 #' log_lik_skewnorm(c(-2:2))
 #' log_lik_skewnorm(c(-2:2), shape = -2)
 #' log_lik_skewnorm(c(-2:2), shape = 2)
 log_lik_skewnorm <- function(x, mean = 0, sd = 1, shape = 0) {
+  rlang::check_installed("sn")
   log_lik <- dskewnorm(x = x, mean = mean, sd = sd, shape = shape, log = TRUE)
   use_norm <- !is.na(shape) & shape == 0
   lnorm <- log_lik_norm(x = x, mean = mean, sd = sd)

R/numericise.R

@@ -77,6 +77,7 @@ numericise.POSIXct <- function(x, ...) {
 #' @examples
 #'
 #' # hms
+#' @examplesIf requireNamespace("hms")
 #' numericise(hms::as_hms("00:01:03"))
 numericise.hms <- function(x, ...) {
   rlang::check_installed("hms")

R/params.R

@@ -50,6 +50,7 @@
 #' @param x An object.
 #' @aliases parameters arguments args
 #' @usage NULL
+#' @export
 # nocov start
 params <- function(...) NULL
 # nocov end

R/ran.R

@@ -180,11 +180,12 @@ ran_pois_zi <- function(n = 1, lambda = 1, prob = 0) {
 #' @family ran_dist
 #' @export
 #'
-#' @examples
+#' @examplesIf requireNamespace("sn")
 #' ran_skewnorm(10, shape = -1)
 #' ran_skewnorm(10, shape = 0)
 #' ran_skewnorm(10, shape = 1)
 ran_skewnorm <- function(n = 1, mean = 0, sd = 1, shape = 0) {
+  rlang::check_installed("sn")
   chk_whole_number(n)
   chk_gte(n)
   rskewnorm(n = n, mean = mean, sd = sd, shape = shape)

R/res.R

@@ -335,9 +335,10 @@ res_student_standardized <- function(x, mean, sd, theta) {
 #' @family res_dist
 #' @export
 #'
-#' @examples
+#' @examplesIf requireNamespace("sn")
 #' res_skewnorm(c(-2:2))
 res_skewnorm <- function(x, mean = 0, sd = 1, shape = 0, type = "dev", simulate = FALSE) {
+  rlang::check_installed("sn")
   chk_string(type)
   if (!vld_false(simulate)) {
     x <- ran_skewnorm(length(x), mean = mean, sd = sd, shape = shape)

R/sens.R

@@ -62,7 +62,7 @@ sens_student <- function(mean, sd, theta, sd_mult = 2) {
 #' @family sens_dist
 #' @export
 #'
-#' @examples
+#' @examplesIf requireNamespace("sn")
 #' sens_skewnorm(10, 3, -1, 2)
 #' sens_skewnorm(10, 3, 3, 0.8)
 sens_skewnorm <- function(mean, sd, shape, sd_mult = 2) {

R/skewnorm.R

@@ -10,7 +10,7 @@
 #' @rdname skewnorm
 #' @export
 #'
-#' @examples
+#' @examplesIf requireNamespace("sn")
 #' dskewnorm(x = -2:2, mean = 0, sd = 1, shape = 0.1)
 #' dskewnorm(x = -2:2, mean = 0, sd = 1, shape = -1)
 #' qskewnorm(p = c(0.1, 0.4), mean = 0, sd = 1, shape = 0.1)

cran-comments.md

@@ -1,21 +1,10 @@
 ## R CMD check results
 
-0 errors | 0 warnings | 1 note
-
-New maintainer:
-  Nicole Hill <[email protected]>
-Old maintainer(s):
-  Joe Thorley <[email protected]>
+0 errors | 0 warnings | 0 notes
 
 ## CRAN Issues
 
-Fixed the following error by conditionally skipping tests that rely on packages listed in suggests, if those packages are not installed.
-After review, also decided to remove the dependency to the 'aods3' package.
-
-══ Failed tests ════════════════════════════════════════════════════════════════
-── Error ('test-log-lik.R:184:3'): beta_binom log_lik ──────────────────────────
-<packageNotFoundError/error/condition>
-Error in `loadNamespace(x)`: there is no package called 'aods3'
+After feedback, corrected the noSuggests issue to have all tests, examples, and vignettes run conditionally for packages listed under Suggests.
 
 ## revdepcheck results
 

inst/WORDLIST

@@ -12,6 +12,7 @@ Summarise
 Surprisal
 TMB
 WinBUGS
+behaviour
 bern
 bigg
 cdot
@@ -24,7 +25,6 @@ lik
 modelling
 numericise
 skewnorm
-styler
 summarise
 surprisal
 testthat