tidymodels · EmilHvitfeldt · Mar 7, 2023 · Mar 7, 2023 · Mar 7, 2023 · Mar 7, 2023
diff --git a/CODE_OF_CONDUCT.md → .github/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md → .github/CODE_OF_CONDUCT.md
@@ -6,8 +6,8 @@ We as members, contributors, and leaders pledge to make participation in our
 community a harassment-free experience for everyone, regardless of age, body
 size, visible or invisible disability, ethnicity, sex characteristics, gender
 identity and expression, level of experience, education, socio-economic status,
-nationality, personal appearance, race, religion, or sexual identity and
-orientation.
+nationality, personal appearance, race, caste, color, religion, or sexual
+identity and orientation.
 
 We pledge to act and interact in ways that contribute to an open, welcoming,
 diverse, inclusive, and healthy community.
@@ -21,25 +21,25 @@ community include:
 * Being respectful of differing opinions, viewpoints, and experiences
 * Giving and gracefully accepting constructive feedback
 * Accepting responsibility and apologizing to those affected by our mistakes,
-and learning from the experience
+  and learning from the experience
 * Focusing on what is best not just for us as individuals, but for the overall
-community
+  community
 
 Examples of unacceptable behavior include:
 
-* The use of sexualized language or imagery, and sexual attention or
-advances of any kind
+* The use of sexualized language or imagery, and sexual attention or advances of
+  any kind
 * Trolling, insulting or derogatory comments, and personal or political attacks
 * Public or private harassment
-* Publishing others' private information, such as a physical or email
-address, without their explicit permission
+* Publishing others' private information, such as a physical or email address,
+  without their explicit permission
 * Other conduct which could reasonably be considered inappropriate in a
-professional setting
+  professional setting
 
 ## Enforcement Responsibilities
 
-Community leaders are responsible for clarifying and enforcing our standards
-of acceptable behavior and will take appropriate and fair corrective action in
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
 response to any behavior that they deem inappropriate, threatening, offensive,
 or harmful.
 
@@ -50,17 +50,17 @@ decisions when appropriate.
 
 ## Scope
 
-This Code of Conduct applies within all community spaces, and also applies
-when an individual is officially representing the community in public spaces.
-Examples of representing our community include using an official e-mail
-address, posting via an official social media account, or acting as an appointed
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail address,
+posting via an official social media account, or acting as an appointed
 representative at an online or offline event.
 
 ## Enforcement
 
 Instances of abusive, harassing, or otherwise unacceptable behavior may be
-reported to the community leaders responsible for enforcement at [INSERT CONTACT
-METHOD]. All complaints will be reviewed and investigated promptly and fairly.
+reported to the community leaders responsible for enforcement at [email protected]. 
+All complaints will be reviewed and investigated promptly and fairly.
 
 All community leaders are obligated to respect the privacy and security of the
 reporter of any incident.
@@ -114,15 +114,13 @@ community.
 ## Attribution
 
 This Code of Conduct is adapted from the [Contributor Covenant][homepage],
-version 2.0,
-available at https://www.contributor-covenant.org/version/2/0/
-code_of_conduct.html.
+version 2.1, available at
+<https://www.contributor-covenant.org/version/2/1/code_of_conduct.html>.
 
-Community Impact Guidelines were inspired by [Mozilla's code of conduct
-enforcement ladder](https://github.com/mozilla/diversity).
-
-[homepage]: https://www.contributor-covenant.org
+Community Impact Guidelines were inspired by
+[Mozilla's code of conduct enforcement ladder][https://github.com/mozilla/inclusion].
 
 For answers to common questions about this code of conduct, see the FAQ at
-https://www.contributor-covenant.org/faq. Translations are available at https://
-www.contributor-covenant.org/translations.
+<https://www.contributor-covenant.org/faq>. Translations are available at <https://www.contributor-covenant.org/translations>.
+
+[homepage]: https://www.contributor-covenant.org
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -22,25 +22,26 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: macOS-latest,   r: 'release'}
+          - {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'}
 
-          # Use older ubuntu to maximise backward compatibility
-          - {os: ubuntu-20.04,   r: 'devel', http-user-agent: 'release'}
-          - {os: ubuntu-20.04,   r: 'release'}
-          - {os: ubuntu-20.04,   r: 'oldrel-1'}
-          - {os: ubuntu-20.04,   r: 'oldrel-2'}
-          - {os: ubuntu-20.04,   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:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - uses: r-lib/actions/setup-pandoc@v2
 

diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -20,7 +20,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -39,7 +39,7 @@ jobs:
 
       - name: Deploy to GitHub pages 🚀
         if: github.event_name != 'pull_request'
-        uses: JamesIves/[email protected].4
+        uses: JamesIves/github-pages-deploy-action@v4.4.1
         with:
           clean: false
           branch: gh-pages

diff --git a/.github/workflows/pr-commands.yaml b/.github/workflows/pr-commands.yaml
@@ -14,7 +14,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - uses: r-lib/actions/pr-fetch@v2
         with:
@@ -51,7 +51,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - uses: r-lib/actions/pr-fetch@v2
         with:

diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
@@ -15,7 +15,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - uses: r-lib/actions/setup-r@v2
         with:
@@ -27,5 +27,24 @@ jobs:
           needs: coverage
 
       - name: Test coverage
-        run: covr::codecov(quiet = FALSE)
+        run: |
+          covr::codecov(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+          )
         shell: Rscript {0}
+
+      - 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@v3
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,9 +1,11 @@
 Package: themis
 Title: Extra Recipes Steps for Dealing with Unbalanced Data
 Version: 1.0.0.9000
-Authors@R: 
-    person("Emil", "Hvitfeldt", , "[email protected]", role = c("aut", "cre"),
-           comment = c(ORCID = "0000-0002-0679-1945"))
+Authors@R: c(
+    person("Emil", "Hvitfeldt", , "[email protected]", role = c("aut", "cre"),
+           comment = c(ORCID = "0000-0002-0679-1945")),
+    person(given = "Posit Software, PBC", role = c("cph", "fnd"))
+  )
 Description: A dataset with an uneven number of cases in each class is
     said to be unbalanced. Many models produce a subpar performance on
     unbalanced datasets. A dataset can be balanced by increasing the

diff --git a/LICENSE b/LICENSE
@@ -1,2 +1,2 @@
-YEAR: 2020
-COPYRIGHT HOLDER: Emil Hvitfeldt
+YEAR: 2023
+COPYRIGHT HOLDER: themis authors
diff --git a/LICENSE.md b/LICENSE.md
@@ -1,6 +1,6 @@
 # MIT License
 
-Copyright (c) 2020 Emil Hvitfeldt
+Copyright (c) 2023 themis 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

diff --git a/README.Rmd b/README.Rmd
@@ -38,8 +38,8 @@ install.packages("themis")
 Install the development version from GitHub with:
 
 ``` r
-# install.packages("remotes")
-remotes::install_github("tidymodels/themis")
+# install.packages("pak")
+pak::pak("tidymodels/themis")
 ```
 
 ## Example
@@ -73,6 +73,7 @@ ds_rec %>%
 Below is some unbalanced data. Used for examples latter.
 
 ```{r}
+#| fig-alt: "Bar chart with 5 columns. class on the x-axis and count on the y-axis. Class a has height 10, b has 20, c has 30, d has 40, and e has 50."
 example_data <- data.frame(class = letters[rep(1:5, 1:5 * 10)],
                            x = rnorm(150))
 
@@ -99,6 +100,7 @@ The following methods all share the tuning parameter `over_ratio`, which is the
 By setting `over_ratio = 1` you bring the number of samples of all minority classes equal to 100% of the majority class.
 
 ```{r}
+#| fig-alt: "Bar chart with 5 columns. class on the x-axis and count on the y-axis. class a, b, c, d, and e all have a height of 50."
 recipe(~., example_data) %>%
   step_upsample(class, over_ratio = 1) %>%
   prep() %>%
@@ -110,6 +112,7 @@ recipe(~., example_data) %>%
 and by setting `over_ratio = 0.5` we upsample any minority class with less samples then 50% of the majority up to have 50% of the majority.
 
 ```{r}
+#| fig-alt: "Bar chart with 5 columns. class on the x-axis and count on the y-axis. Class a has height 25, b has 25, c has 30, d has 40, and e has 50."
 recipe(~., example_data) %>%
   step_upsample(class, over_ratio = 0.5) %>%
   prep() %>%
@@ -131,6 +134,7 @@ Most of the the following methods all share the tuning parameter `under_ratio`,
 By setting `under_ratio = 1` you bring the number of samples of all majority classes equal to 100% of the minority class.
 
 ```{r}
+#| fig-alt: "Bar chart with 5 columns. class on the x-axis and count on the y-axis. Class a, b, c, d, and e all have a height of 10."
 recipe(~., example_data) %>%
   step_downsample(class, under_ratio = 1) %>%
   prep() %>%
@@ -142,6 +146,7 @@ recipe(~., example_data) %>%
 and by setting `under_ratio = 2` we downsample any majority class with more then 200% samples of the minority class down to have to 200% samples of the minority.
 
 ```{r}
+#| fig-alt: "Bar chart with 5 columns. class on the x-axis and count on the y-axis. Class a has height 10, b, c, d, and e have ha height of 20."
 recipe(~., example_data) %>%
   step_downsample(class, under_ratio = 2) %>%
   prep() %>%

diff --git a/README.md b/README.md
@@ -34,8 +34,8 @@ install.packages("themis")
 Install the development version from GitHub with:
 
 ``` r
-# install.packages("remotes")
-remotes::install_github("tidymodels/themis")
+# install.packages("pak")
+pak::pak("tidymodels/themis")
 ```
 
 ## Example
@@ -93,7 +93,7 @@ example_data %>%
   geom_bar()
 ```
 
-<img src="man/figures/README-unnamed-chunk-2-1.png" width="100%" />
+<img src="man/figures/README-unnamed-chunk-2-1.png" alt="Bar chart with 5 columns. class on the x-axis and count on the y-axis. Class a has height 10, b has 20, c has 30, d has 40, and e has 50." width="100%" />
 
 ### Upsample / Over-sampling
 
@@ -121,7 +121,7 @@ recipe(~., example_data) %>%
   geom_bar()
 ```
 
-<img src="man/figures/README-unnamed-chunk-3-1.png" width="100%" />
+<img src="man/figures/README-unnamed-chunk-3-1.png" alt="Bar chart with 5 columns. class on the x-axis and count on the y-axis. class a, b, c, d, and e all have a height of 50." width="100%" />
 
 and by setting `over_ratio = 0.5` we upsample any minority class with
 less samples then 50% of the majority up to have 50% of the majority.
@@ -135,7 +135,7 @@ recipe(~., example_data) %>%
   geom_bar()
 ```
 
-<img src="man/figures/README-unnamed-chunk-4-1.png" width="100%" />
+<img src="man/figures/README-unnamed-chunk-4-1.png" alt="Bar chart with 5 columns. class on the x-axis and count on the y-axis. Class a has height 25, b has 25, c has 30, d has 40, and e has 50." width="100%" />
 
 ### Downsample / Under-sampling
 
@@ -161,7 +161,7 @@ recipe(~., example_data) %>%
   geom_bar()
 ```
 
-<img src="man/figures/README-unnamed-chunk-5-1.png" width="100%" />
+<img src="man/figures/README-unnamed-chunk-5-1.png" alt="Bar chart with 5 columns. class on the x-axis and count on the y-axis. Class a, b, c, d, and e all have a height of 10." width="100%" />
 
 and by setting `under_ratio = 2` we downsample any majority class with
 more then 200% samples of the minority class down to have to 200%
@@ -176,26 +176,26 @@ recipe(~., example_data) %>%
   geom_bar()
 ```
 
-<img src="man/figures/README-unnamed-chunk-6-1.png" width="100%" />
+<img src="man/figures/README-unnamed-chunk-6-1.png" alt="Bar chart with 5 columns. class on the x-axis and count on the y-axis. Class a has height 10, b, c, d, and e have ha height of 20." width="100%" />
 
 ## Contributing
 
 This project is released with a [Contributor Code of
 Conduct](https://contributor-covenant.org/version/2/0/CODE_OF_CONDUCT.html).
 By contributing to this project, you agree to abide by its terms.
 
--   For questions and discussions about tidymodels packages, modeling,
-    and machine learning, [join us on RStudio
-    Community](https://community.rstudio.com/new-topic?category_id=15&tags=tidymodels,question).
+- For questions and discussions about tidymodels packages, modeling, and
+  machine learning, [join us on RStudio
+  Community](https://community.rstudio.com/new-topic?category_id=15&tags=tidymodels,question).
 
--   If you think you have encountered a bug, please [submit an
-    issue](https://github.com/tidymodels/themis/issues).
+- If you think you have encountered a bug, please [submit an
+  issue](https://github.com/tidymodels/themis/issues).
 
--   Either way, learn how to create and share a
-    [reprex](https://reprex.tidyverse.org/articles/articles/learn-reprex.html)
-    (a minimal, reproducible example), to clearly communicate about your
-    code.
+- Either way, learn how to create and share a
+  [reprex](https://reprex.tidyverse.org/articles/articles/learn-reprex.html)
+  (a minimal, reproducible example), to clearly communicate about your
+  code.
 
--   Check out further details on [contributing guidelines for tidymodels
-    packages](https://www.tidymodels.org/contribute/) and [how to get
-    help](https://www.tidymodels.org/help/).
+- Check out further details on [contributing guidelines for tidymodels
+  packages](https://www.tidymodels.org/contribute/) and [how to get
+  help](https://www.tidymodels.org/help/).
diff --git a/man/figures/logo.png b/man/figures/logo.png
diff --git a/man/themis-package.Rd b/man/themis-package.Rd