pkgdown + doc

.github/workflows/test-coverage-pkgdown.yaml

@@ -0,0 +1,94 @@
+# 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:
+      branches: [main, master]
+    release:
+      types: [published]
+    workflow_dispatch:
+
+name: pkgdown
+
+jobs:
+    test-covr:
+        runs-on: ubuntu-latest
+        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::pak
+                any::covr
+                any::devtools
+                any::DT
+                any::htmltools
+                needs: coverage
+
+        - name: Cache C++ and R dependencies
+          uses: actions/cache@v4
+          with:
+              path: |
+                  ~/.cache/R
+                  ~/.local/share/R
+              key: dependencies-${{ runner.os }}-${{ hashFiles('**/DESCRIPTION') }}
+              restore-keys: |
+                dependencies-${{ runner.os }}-
+
+        - name: Run tests and generate covr report
+          run: |
+            Rscript -e 'covr::report(file = "coverage_report.html")'
+
+        - name: Upload covr report as artifact
+          uses: actions/upload-artifact@v4
+          with:
+            name: covr-report
+            path: coverage_report.html
+
+    pkgdown:
+        needs: test-covr
+        runs-on: ubuntu-latest
+        # Only restrict concurrency for non-PR jobs
+        concurrency:
+          group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+        env:
+          GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+        permissions:
+          contents: write
+        steps:
+        - uses: actions/checkout@v4
+
+        - name: Download covr report
+          uses: actions/download-artifact@v4
+          with:
+            name: covr-report
+            path: .
+
+        - uses: r-lib/actions/setup-pandoc@v2
+
+        - uses: r-lib/actions/setup-r@v2
+          with:
+            use-public-rspm: true
+
+        - uses: r-lib/actions/setup-r-dependencies@v2
+          with:
+            extra-packages: any::pkgdown, local::.
+            needs: website
+
+        - name: Build site
+          run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+          shell: Rscript {0}
+
+        - name: Deploy to GitHub pages 🚀
+          if: github.event_name != 'pull_request'
+          uses: JamesIves/[email protected]
+          with:
+            clean: false
+            branch: gh-pages
+            folder: docs

DESCRIPTION

@@ -8,6 +8,6 @@ Description: A package for computing spatially enhanced and entropy-derived matr
 License: MIT License
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 LinkingTo: Rcpp, RcppArmadillo
-Imports: Rcpp, sf, dplyr, nngeo, spdep, testthat (>= 3.0.0), covr, ggplot2, withr
+Imports: Rcpp, sf, dplyr, nngeo, spdep, testthat (>= 3.0.0), covr, ggplot2, withr, pkgdown

NAMESPACE

@@ -4,6 +4,7 @@ export(cppJSD)
 export(distJSD)
 export(distJSD2)
 export(plot_dists)
+export(scale_minmax)
 export(speedmat)
 export(speedmat.coord)
 export(speedmat.jsdist)

R/speedmat.r

@@ -110,8 +110,11 @@ speedmat_legacy <- function(sf,
 }
 
 
-
-scale_minmax = function(x) {(x - min(x)) / (max(x) - min(x))}
+#' Max-Min scaling
+#' @param x numeric vector
+#' @returns numeric vector
+#' @export
+scale_minmax <- function(x) {(x - min(x)) / (max(x) - min(x))}
 
 
 #' @title SpEED matrix for matching analysis

_pkgdown.yml

@@ -0,0 +1,27 @@
+url: https://niehs.github.io/amadeus/
+template:
+  bootstrap: 5
+  bootswatch: minty
+
+navbar:
+  structure:
+    left:  [reference, search]
+    right: [github]
+
+home:
+  links:
+  - text: Coverage
+    href: /coverage_report.html
+
+references:
+  - subtitle: Core functions
+  - contents:
+    - starts_with("speedmat_")
+
+  - subtitle: Low-level functions
+  - contents:
+    - includes("JSD")
+
+  - subtitle: Helpers
+  - contents:
+    -