Merge pull request #186 from UCD-SERG/check-doc-3

Check doc 3

.github/workflows/R-check-docs.yml

@@ -0,0 +1,43 @@
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+
+name: "Documentation check"
+
+jobs:
+  docs-check:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ github.token }}
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - name: Install dependencies
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::roxygen2
+          needs: roxygen2
+
+      - name: Document
+        run: roxygen2::roxygenise()
+        shell: Rscript {0}
+
+      - name: Check for changed files
+        run: |
+          git add --all
+          changes=$(git diff-index HEAD --name-only -- man/ NAMESPACE DESCRIPTION)
+          if [ -n "$changes" ]; then
+            echo "Changes found after documenting."
+            git --no-pager diff
+            echo "$changes"
+            echo "Please update documentation."
+            exit 1
+          else
+            echo "No changes found after documenting."
+            exit 0
+          fi

R/est.incidence.by.R

@@ -5,7 +5,7 @@
 #' response model.
 #'
 #' @param pop_data [data.frame()] with cross-sectional serology data per antibody and age, and additional columns to identify possible `strata`.
-#' @param strata Character vector of stratum-defining variables. Values must be variable names in `pop_data`.
+#' @param strata [character()] vector of stratum-defining variables. Values must be variable names in `pop_data`.
 #' @param curve_strata_varnames A subset of `strata`. Values must be variable names in `curve_params`. Default = "".
 #' @param noise_strata_varnames A subset of `strata`. Values must be variable names in `noise_params`. Default = "".
 #' @param num_cores Number of processor cores to use for calculations when computing by strata. If set to more than 1 and package \pkg{parallel} is available, then the computations are executed in parallel. Default = 1L.