Merge pull request #246 from larmarange/issue245

order of variable levels with marginal prediction

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

@@ -29,7 +29,7 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -41,9 +41,10 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::rcmdcheck, glmmTMB=?source, lme4=?source
+          extra-packages: any::rcmdcheck, glmmTMB=?source, lme4=?source, emmeans=?ignore-before-r=4.3.0, effects=?ignore-before-r=4.3.0
           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/R-CMD-historic-R-check.yaml

@@ -38,7 +38,7 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::rcmdcheck, emmeans=?ignore-before-r=4.1.0, gam=?ignore-before-r=4.0.0, rstan=?ignore-before-r=4.0.0, multgee=?ignore-before-r=4.0.0, VGAM=?ignore-before-r=4.0.0, glmmTMB=?ignore
+          extra-packages: any::rcmdcheck, emmeans=?ignore-before-r=4.3.0, gam=?ignore-before-r=4.0.0, rstan=?ignore-before-r=4.0.0, multgee=?ignore-before-r=4.0.0, VGAM=?ignore-before-r=4.0.0, glmmTMB=?ignore, effects=?ignore-before-r=4.3.0, survey=?ignore-before-r=4.1.0
           needs: check
 
       - uses: r-lib/actions/check-r-package@v2

.github/workflows/lint.yaml

@@ -14,17 +14,19 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v2
+      - 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::lintr, local::., glmmTMB=?ignore
+          extra-packages: any::lintr, local::.
           needs: lint
 
       - name: Lint
         run: lintr::lint_package()
         shell: Rscript {0}
+        env:
+          LINTR_ERROR_ON_LINT: true

.github/workflows/pkgdown.yaml

@@ -19,8 +19,10 @@ jobs:
       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
 
@@ -30,7 +32,7 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::pkgdown, local::., glmmTMB=?ignore
+          extra-packages: any::pkgdown, local::.
           needs: website
 
       - name: Build site
@@ -39,7 +41,7 @@ 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

.github/workflows/test-coverage.yaml

@@ -15,36 +15,36 @@ jobs:
       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, glmmTMB=?ignore
+          extra-packages: any::covr
           needs: coverage
 
       - name: Test coverage
         run: |
           covr::codecov(
             quiet = FALSE,
             clean = FALSE,
-            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
           )
         shell: Rscript {0}
 
       - 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

@@ -87,4 +87,4 @@ Encoding: UTF-8
 Language: en-US
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1

NEWS.md

@@ -2,15 +2,17 @@
 
 **New supported models**
 
-- Support for `mmrm::mmrm()` models (#228)
-- Support for `survival::cch()` models (#242)
+- support for `mmrm::mmrm()` models (#228)
+- support for `survival::cch()` models (#242)
 
 **New features**
 
 - new `tidy_post_fun` argument in `tidy_plus_plus()` (#235)
 
 **Fix**
 
+- fix the order of the levels of categorical variables in the results of
+  `tidy_marginal_predictions()` (#245)
 - fix in `supported_models`
 - bug fix when using `tidy_parameters()` for mixed models (#238)
 - bug fix for `survey::svyglm()` models with replicate weights (#240)

R/helpers.R

@@ -55,8 +55,7 @@
 }
 
 # copied from broom
-.exponentiate <- function (data, col = "estimate")
-{
+.exponentiate <- function(data, col = "estimate") {
   data <- data %>%
     dplyr::mutate(
       dplyr::across(dplyr::all_of(col), exp)

R/marginal_tidiers.R

@@ -659,6 +659,7 @@ tidy_marginal_predictions <- function(x, variables_list = "auto",
   }
 
   res <- do.call(marginaleffects::avg_predictions, dots) %>%
+    dplyr::arrange(dplyr::pick(dplyr::any_of(c(names(variables)))), "group") %>%
     dplyr::mutate(variable = paste(names(variables), collapse = ":")) %>%
     tidyr::unite(col = "term", sep = " * ", dplyr::all_of(names(variables))) %>%
     dplyr::relocate("variable", "term")