edit vignette and add test coverage workflow

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

@@ -30,7 +30,7 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 

.github/workflows/test-coverage.yaml

@@ -0,0 +1,61 @@
+# 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
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+
+name: test-coverage.yaml
+
+permissions: read-all
+
+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")
+          )
+          covr::to_cobertura(cov)
+        shell: Rscript {0}
+
+      - uses: codecov/codecov-action@v4
+        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 }}
+          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
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

vignettes/ComBatQC.Rmd

@@ -86,7 +86,22 @@ result_lmer <- visual_prep(type = "lmer", features = features, batch = batch, co
 comfam_shiny(result_lmer)
 ```
 
+# Export Batch Effect Diagnosis Result
 
+There are two export options: 1) generate a Quarto report (requires Quarto to be installed), and 2) generate a combined Excel file.
+
+-   Generate a Quarto report
+
+```{r, eval=FALSE}
+#library(quarto)
+diag_save(path = "path/to/dir", result = result_lmer, use_quarto = TRUE)
+```
+
+-   Generate a combined EXCEL file
+
+```{r, eval=FALSE}
+diag_save(path = "path/to/dir", result = result_lmer, use_quarto = FALSE)
+```
 
 # Harmonization Using default ComBatFamily Methods
 

vignettes/Post-Harmonization.Rmd

@@ -84,8 +84,13 @@ quantile_type <- c(paste0("quantile_", 100*0.25), "median", paste0("quantile_",
 
 ## Launch Shiny App for Visualization
 
+Users can choose to generate age trend plots using the `ggplot` package or the `plotly` package (if `plotly` is installed).
+
 ```{r, eval=FALSE}
-ComBatFamQC::age_shiny(age_list, features, quantile_type)
+# plotly: interactive plot
+ComBatFamQC::age_shiny(age_list, features, quantile_type, use_plotly = TRUE)
+# ggplot: static plot
+ComBatFamQC::age_shiny(age_list, features, quantile_type, use_plotly = FALSE)
 ```
 
 ## Save Age Trend Table and GAMLSS Model