Merge pull request #55 from tidymodels/develop

CRAN Release Update

Author: marlycormar

.Rbuildignore

@@ -12,4 +12,8 @@
 ^CODE_OF_CONDUCT\.md$
 ^\.github$
 ^codecov\.yml$
-^README\.Rmd$
+^CRAN-SUBMISSION$
+^vignettes$
+^scripts$
+^[.]?air[.]toml$
+^\.vscode$

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

@@ -8,9 +8,10 @@ on:
   push:
     branches: [main, master]
   pull_request:
-    branches: [main, master]
 
-name: R-CMD-check
+name: R-CMD-check.yaml
+
+permissions: read-all
 
 jobs:
   R-CMD-check:
@@ -25,24 +26,22 @@ jobs:
           - {os: macos-latest,   r: 'release'}
 
           - {os: windows-latest, r: 'release'}
-          # Use 3.6 to trigger usage of RTools35
-          - {os: windows-latest, r: '3.6'}
-          # use 4.1 to check with rtools40's older compiler
-          - {os: windows-latest, r: '4.1'}
-
-          - {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'}
-          - {os: ubuntu-latest,   r: 'oldrel-4'}
+          # use 4.0 or 4.1 to check with rtools40's older compiler
+          - {os: windows-latest, r: 'oldrel-4'}
+
+          - {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'}
+          - {os: ubuntu-latest,  r: 'oldrel-4'}
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -60,3 +59,4 @@ jobs:
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.github/workflows/format-suggest.yaml

@@ -0,0 +1,46 @@
+# Workflow derived from https://github.com/posit-dev/setup-air/tree/main/examples
+
+on:
+  # Using `pull_request_target` over `pull_request` for elevated `GITHUB_TOKEN`
+  # privileges, otherwise we can't set `pull-requests: write` when the pull
+  # request comes from a fork, which is our main use case (external contributors).
+  #
+  # `pull_request_target` runs in the context of the target branch (`main`, usually),
+  # rather than in the context of the pull request like `pull_request` does. Due
+  # to this, we must explicitly checkout `ref: ${{ github.event.pull_request.head.sha }}`.
+  # This is typically frowned upon by GitHub, as it exposes you to potentially running
+  # untrusted code in a context where you have elevated privileges, but they explicitly
+  # call out the use case of reformatting and committing back / commenting on the PR
+  # as a situation that should be safe (because we aren't actually running the untrusted
+  # code, we are just treating it as passive data).
+  # https://securitylab.github.com/resources/github-actions-preventing-pwn-requests/
+  pull_request_target:
+
+name: format-suggest.yaml
+
+jobs:
+  format-suggest:
+    name: format-suggest
+    runs-on: ubuntu-latest
+
+    permissions:
+      # Required to push suggestion comments to the PR
+      pull-requests: write
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          ref: ${{ github.event.pull_request.head.sha }}
+
+      - name: Install
+        uses: posit-dev/setup-air@v1
+
+      - name: Format
+        run: air format .
+
+      - name: Suggest
+        uses: reviewdog/action-suggester@v1
+        with:
+          level: error
+          fail_level: error
+          tool_name: air

.vscode/extensions.json

@@ -0,0 +1,5 @@
+{
+    "recommendations": [
+        "Posit.air-vscode"
+    ]
+}

.vscode/settings.json

@@ -0,0 +1,10 @@
+{
+    "[r]": {
+        "editor.formatOnSave": true,
+        "editor.defaultFormatter": "Posit.air-vscode"
+    },
+    "[quarto]": {
+        "editor.formatOnSave": true,
+        "editor.defaultFormatter": "quarto.quarto"
+    }
+}

DESCRIPTION

@@ -1,51 +1,52 @@
 Package: applicable
 Title: A Compilation of Applicability Domain Methods
-Version: 0.0.1.1
+Version: 0.2.1
 Authors@R: c(
     person("Marly", "Gotti", , "marlygotti@gmail.com", role = c("aut", "cre")),
     person("Max", "Kuhn", , "max@posit.co", role = "aut"),
-    person("Posit Software, PBC", role = c("cph", "fnd"))
+    person("Posit Software, PBC", role = c("cph", "fnd"),
+           comment = c(ROR = "03wc8by49"))
   )
 Description: A modeling package compiling applicability domain methods in
-    R.  It combines different methods to measure the amount of
-    extrapolation new samples can have from the training set. See Netzeva
-    et al (2005) <doi:10.1177/026119290503300209> for an overview of
-    applicability domains.
+    R. It combines different methods to measure the amount of
+    extrapolation new samples can have from the training set. See
+    <doi:10.4018/IJQSPR.2016010102> for an overview of applicability
+    domains.
 License: MIT + file LICENSE
 URL: https://github.com/tidymodels/applicable,
     https://applicable.tidymodels.org
 BugReports: https://github.com/tidymodels/applicable/issues
 Depends: 
-    ggplot2,
-    R (>= 3.6)
+    ggplot2 (>= 4.0.2),
+    R (>= 4.1)
 Imports: 
     dplyr,
     glue,
-    hardhat (>= 1.3.0),
+    hardhat (>= 1.3.1),
     Matrix,
     proxyC,
     purrr,
-    rlang (>= 1.1.1),
+    rlang,
     stats,
     tibble,
     tidyr,
     tidyselect,
     utils
 Suggests: 
     covr,
+    isotree (>= 0.6.1-1),
     knitr,
     modeldata,
-    recipes (>= 1.0.8),
+    recipes (>= 1.0.10),
     rmarkdown,
     spelling,
-    testthat (>= 3.2.0),
+    testthat (>= 3.0.0),
     xml2
-VignetteBuilder: 
-    knitr
-Config/Needs/website: tidyverse/tidytemplate
+Config/Needs/website: tidyverse/tidytemplate, quarto
 Config/testthat/edition: 3
+Config/usethis/last-upkeep: 2026-02-19
 Encoding: UTF-8
 Language: en-US
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.3

LICENSE

@@ -1,2 +1,2 @@
-YEAR: 2023
+YEAR: 2026
 COPYRIGHT HOLDER: applicable authors

LICENSE.md

@@ -1,6 +1,6 @@
 # MIT License
 
-Copyright (c) 2023 applicable authors
+Copyright (c) 2026 applicable authors
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

NAMESPACE

@@ -5,6 +5,11 @@ S3method(apd_hat_values,default)
 S3method(apd_hat_values,formula)
 S3method(apd_hat_values,matrix)
 S3method(apd_hat_values,recipe)
+S3method(apd_isolation,data.frame)
+S3method(apd_isolation,default)
+S3method(apd_isolation,formula)
+S3method(apd_isolation,matrix)
+S3method(apd_isolation,recipe)
 S3method(apd_pca,data.frame)
 S3method(apd_pca,default)
 S3method(apd_pca,formula)
@@ -18,13 +23,16 @@ S3method(apd_similarity,recipe)
 S3method(autoplot,apd_pca)
 S3method(autoplot,apd_similarity)
 S3method(print,apd_hat_values)
+S3method(print,apd_isolation)
 S3method(print,apd_pca)
 S3method(print,apd_similarity)
 S3method(score,apd_hat_values)
+S3method(score,apd_isolation)
 S3method(score,apd_pca)
 S3method(score,apd_similarity)
 S3method(score,default)
 export(apd_hat_values)
+export(apd_isolation)
 export(apd_pca)
 export(apd_similarity)
 export(autoplot.apd_pca)
@@ -34,14 +42,10 @@ export(score.default)
 import(rlang)
 importFrom(Matrix,Matrix)
 importFrom(Matrix,colSums)
-importFrom(dplyr,"%>%")
 importFrom(dplyr,count)
 importFrom(dplyr,group_by)
 importFrom(dplyr,matches)
 importFrom(dplyr,mutate)
-importFrom(dplyr,mutate_all)
-importFrom(dplyr,rename_all)
-importFrom(dplyr,sample_n)
 importFrom(dplyr,select)
 importFrom(dplyr,slice)
 importFrom(dplyr,starts_with)
@@ -68,6 +72,6 @@ importFrom(stats,quantile)
 importFrom(stats,setNames)
 importFrom(tibble,as_tibble)
 importFrom(tibble,tibble)
-importFrom(tidyr,gather)
+importFrom(tidyr,pivot_longer)
 importFrom(tidyselect,vars_select)
 importFrom(utils,globalVariables)

NEWS.md

@@ -1,9 +1,34 @@
-applicable 0.0.1.1
-==================
+# applicable (development version)
+
+- Improved `autoplot.apd_pca()` selector handling to fail early with a clear error when `...` selectors match no columns.
+- Modernized package code, tests, and vignettes to use base R pipes (`|>`) and replaced superseded tidyverse helpers (`pivot_longer()`, `across()`, and `rename_with()`).
+- Updated tests to use stricter modern expectations, including replacing success-path `expect_error(..., regexp = NA)` checks with `expect_no_error()`.
+- Expanded isolation-method maintenance and coverage work, including formula-interface checks, `check_isotree()` test paths, and refreshed isolation `.Rd` documentation.
+- Added a helper script (`scripts/test-changed-functions.R`) to report changed functions, check test references, run testthat, and run `covr` coverage for changed code.
+- Improved CRAN/release readiness with additional housekeeping: build ignore updates for `scripts/`, version/roxygen metadata maintenance, link/DOI and vignette compliance fixes, plus spelling/WORDLIST updates.
+- Included prior plotting/printing refinements: PCA plot sizing/faceting and print-method formatting cleanups.
+- Updated Quarto vignette chunk options to in-body YAML style and bumped package version in `DESCRIPTION` to `0.2.1`.
+- Switched Ames dataset documentation links from `http` to `https` in source, vignette text, and generated `.Rd` docs.
+- Refreshed website/project assets and configuration files (including favicon assets and editor/project config updates).
+
+# applicable 0.1.1
+
+
+- Changes in [apd_isolation()] because [isotree::isolation.forest()] changed their default for the number of dimensions to 1. 
+
+- Updated snapshot unit tests that changed from rlang's changes related to the call/traceback. 
+
+# applicable 0.1.0
+
+
+Added isolation forest methods via the isotree package in the function `apd_isolation()`.
+
+# applicable 0.0.1.1
+
 
 Minor patch release: fixed failing units tests due to recent package updates.
 
-applicable 0.0.1
-==================
+# applicable 0.0.1
+
 
 * First CRAN version.