Add degree and time of adoption diagnostic function

.devcontainer/Dockerfile → .devcontainer/Containerfile

@@ -1,16 +1,16 @@
-FROM rocker/tidyverse:4.4.0
+FROM ghcr.io/rocker-org/devcontainer/tidyverse:4.5
 
 # RUN \
 #   echo 'options(repos=c(CRAN="https://packagemanager.posit.co/cran/__linux__/bookworm/latest"))' >> ~/.Rprofile && \
 #   Rscript --vanilla -e 'getOption("repos")'
 
-# Adding R packages
-RUN install2.r Rcpp sna network networkDynamic Matrix MASS MatchIt SparseM igraph \
-  viridisLite covr testthat knitr rmarkdown ape RSiena survival RcppArmadillo
-
-RUN install2.r languageserver httpgd
+RUN install2.r --error languageserver && installGithub.r nx10/httpgd
 
 RUN apt-get update && apt-get install --no-install-recommends -y valgrind gdb \
   libglpk-dev
 
+# Adding R packages
+RUN install2.r --error Rcpp sna network networkDynamic Matrix MASS MatchIt SparseM igraph \
+  viridisLite covr testthat knitr rmarkdown ape RSiena survival RcppArmadillo
+
 CMD ["bash"]

.devcontainer/devcontainer.json

@@ -1,24 +1,25 @@
 // For format details, see https://aka.ms/devcontainer.json. For config options, see the
 // README at: https://github.com/devcontainers/templates/tree/main/src/cpp
 {
-	"name": "epiworldR",
+	"name": "netdiffuseR",
 	"build": {
-		"dockerfile": "Dockerfile"
+		"dockerfile": "Containerfile"
 	},
 	"customizations": {
 		"vscode": {
 			"extensions": [
 				"reditorsupport.r",
 				"rdebugger.r-debugger",
 				"quarto.quarto",
-				"tianyishi.rmarkdown"
+				"tianyishi.rmarkdown",
+				"github.vscode-github-actions"
 			]
 		}
 	},
 	"mounts": [
         // Mount the .vscode configuration into the container
         "source=${localWorkspaceFolder}/.devcontainer/.vscode,target=/workspaces/${localWorkspaceFolderBasename}/.vscode,type=bind,consistency=cached"
-    ]
+    ],
 	// Features to add to the dev container. More info: https://containers.dev/features.
 	// "features": {},
 
@@ -32,5 +33,5 @@
 	// "customizations": {},
 
 	// Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root.
-	// "remoteUser": "root"
+	"remoteUser": "root"
 }

.github/copilot-instructions.md

@@ -0,0 +1,30 @@
+# Copilot Instructions for netdiffuseR
+
+## Documentation Style
+
+When writing roxygen2 documentation, prefer markdown syntax over LaTeX:
+
+- Use `` `code` `` instead of `\code{code}`
+- Use `` `[function()]` `` instead of `\code{\link{function}}`
+- Use markdown bullet lists instead of `\itemize{}`
+- Use markdown formatting for emphasis and structure
+
+## Code Style
+
+- Follow existing code patterns and conventions in the package
+- Use meaningful variable names and keep functions focused
+- Add comments only when they match the existing style or explain complex logic
+- Prefer using existing libraries over adding new dependencies
+
+## Testing
+
+- Add comprehensive tests for new functions
+- Include edge cases and error conditions
+- Test with the existing sample datasets when possible
+- Validate input parameters and handle errors gracefully
+
+## Examples
+
+- Use `\dontrun{}` only when examples take a long time to run
+- Prefer examples that can execute quickly for CRAN checks
+- Use existing package datasets in examples when available

.github/workflows/pkgdown.yml

@@ -24,7 +24,7 @@ jobs:
         id-token: write
         pages: write
       steps:
-        - uses: actions/checkout@v4
+        - uses: actions/checkout@v5
 
         - uses: r-lib/actions/setup-pandoc@v2
           with:
@@ -35,6 +35,8 @@ jobs:
         - uses: r-lib/actions/setup-r-dependencies@v2
           with:
             extra-packages: any::pkgdown
+            install-quarto: true
+            install-pandoc: true
 
         - name: Install the package
           run: R CMD INSTALL .
@@ -44,7 +46,7 @@ jobs:
           shell: Rscript {0}
 
         - name: Upload artifact for GH pages deployment
-          uses: actions/upload-pages-artifact@v3
+          uses: actions/upload-pages-artifact@v5
           with:
             path: "docs/"
 

.github/workflows/r.yml

@@ -15,14 +15,16 @@ jobs:
   R-CMD-check:
     runs-on: ${{ matrix.config.os }}
 
-    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }}) (valgrind:${{ matrix.config.valgrind }})
 
     strategy:
       fail-fast: false
       matrix:
         config:
           - {os: macOS-latest,   r: 'release'}
+          - {os: macOS-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: windows-latest, r: 'release'}
+          # - {os: windows-latest, r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,  r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,  r: 'release'}
           - {os: ubuntu-latest,  r: 'devel', valgrind: true, http-user-agent: 'release'}
@@ -32,9 +34,12 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v4
+      # Fix suggested by
+      # https://msmith.de/2020/03/12/r-cmd-check-github-actions.html
+      - name: Configure git
+        run: git config --global core.autocrlf false
 
-      - uses: r-lib/actions/setup-pandoc@v2
+      - uses: actions/checkout@v5
 
       - uses: r-lib/actions/setup-r@v2
         with:
@@ -46,6 +51,8 @@ jobs:
         with:
           extra-packages: any::rcmdcheck
           needs: check
+          install-quarto: true
+          install-pandoc: true
 
       - uses: r-lib/actions/check-r-package@v2
         if: ${{ matrix.config.valgrind != true }}
@@ -56,36 +63,43 @@ jobs:
           check-dir: '"check"'
           error-on: '"error"'
 
-      - name: Setup valgrind
-        if: ${{ matrix.config.valgrind == true }}
+      - name: Install valgrind
+        if: ${{ matrix.config.valgrind }}
         run: |
           sudo apt-get update
-          sudo apt-get install -y valgrind --no-install-recommends
-        shell: bash
+          sudo apt-get install -y --no-install-recommends valgrind
 
-      - name: Check with Valgrind
-        if: ${{ matrix.config.valgrind == true }}
-        env:
-          _R_CHECK_CRAN_INCOMING_REMOTE_: false
-        run: |
-          options(crayon.enabled = TRUE)
-          rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran", "--use-valgrind"), error_on = "error", check_dir = "check")
-        shell: Rscript {0}
+      - uses: r-lib/actions/check-r-package@v2
+        if: ${{ matrix.config.valgrind }}
+        with:
+          args: 'c("--as-cran", "--use-valgrind", "--no-manual")'
+          upload-results: true
+
+  build-pkg:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v5
 
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@main
+      - uses: r-lib/actions/setup-r@v2
         with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
+          r-version: 'release'
+          use-public-rspm: true
 
-      - name: Build the package
-        if: ${{ matrix.config.os == 'ubuntu-latest' && (matrix.config.r == 'release' || matrix.config.r == 'devel') && (matrix.config.valgrind != true) }}
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::devtools
+
+      - name: Build package
         run: R CMD build .
 
-      - uses: actions/upload-artifact@v4
-        if: ${{ matrix.config.os == 'ubuntu-latest' && (matrix.config.r == 'release' || matrix.config.r == 'devel') && (matrix.config.valgrind != true) }}
+      - name: Upload package artifact
+        uses: actions/upload-artifact@v5
         with:
-          name: netdiffuseR-built-package-${{ matrix.config.os }}-${{ matrix.config.r }}
-          path: netdiffuseR_*.tar.gz
-          retention-days: 7
+          name: R-package
+          path: '*.tar.gz'
+
+
+
+
+
+

.gitignore

@@ -22,3 +22,8 @@ inst/doc
 *.tex
 playground/
 doc/
+
+# Other files
+.vscode/
+config.status
+src/Makevars

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: netdiffuseR
 Title: Analysis of Diffusion and Contagion Processes on Networks
-Version: 1.23.0
+Version: 1.24.0
 Authors@R: c(
   person("George", "Vega Yon", email="g.vegayon@gmail.com", role=c("aut", "cre"),
     comment=c(ORCID = "0000-0002-3171-0844", what="Rewrite functions with Rcpp, plus new features")
@@ -51,7 +51,7 @@ Suggests:
     survival
 VignetteBuilder: knitr
 LinkingTo: Rcpp, RcppArmadillo
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3
 Encoding: UTF-8
 URL: https://github.com/USCCANA/netdiffuseR,
  https://USCCANA.github.io/netdiffuseR/
@@ -66,6 +66,7 @@ Collate:
     'bootnet.r'
     'citer_environment.R'
     'data.r'
+    'degree_adoption_diagnostic.R'
     'diffnet-c.R'
     'diffnet-class.r'
     'diffnet-indexing.r'

Makefile

@@ -9,16 +9,16 @@ help:
 	@echo "  make docs        - Generate documentation"
 
 install: 
-	R CMD INSTALL .
+	Rscript --vanilla -e 'devtools::install()'
 
 build:
 	R CMD build . 
 
-README.md: README.Rmd
-	Rscript -e 'rmarkdown::render("README.Rmd")'
+README.md: README.qmd
+	quarto render README.qmd
 
-check: netdiffuseR_$(VERSION).tar.gz
-	R CMD check --as-cran netdiffuseR_$(VERSION).tar.gz
+check:
+	Rscript --vanilla -e 'devtools::check()'
 
 checkv: netdiffuseR_$(VERSION).tar.gz
 	R CMD check --as-cran --use-valgrind netdiffuseR_$(VERSION).tar.gz

NAMESPACE

@@ -66,6 +66,7 @@ S3method(plot_diffnet2,diffnet)
 S3method(plot_threshold,array)
 S3method(plot_threshold,default)
 S3method(plot_threshold,diffnet)
+S3method(print,degree_adoption_diagnostic)
 S3method(print,diffnet)
 S3method(print,diffnet_bootnet)
 S3method(print,diffnet_diffmap)
@@ -99,6 +100,7 @@ export(classify_adopters)
 export(classify_graph)
 export(compare_matrix)
 export(cumulative_adopt_count)
+export(degree_adoption_diagnostic)
 export(dgr)
 export(diag_expand)
 export(diffmap)

NEWS.md

@@ -1,3 +1,11 @@
+# Changes in netdiffuseR version 1.24.0 (DEV)
+
+* New function `degree_adoption_diagnostic()` analyzes the correlation between network 
+  centrality measures (in-degree and out-degree) and time of adoption to identify 
+  whether opinion leaders were supporters or opposers in diffusion processes.
+  The function supports multi-diffusion objects, undirected networks, and includes
+  bootstrap confidence intervals.
+
 # Changes in netdiffuseR version 1.23.0 (2025-06-10)
 
 * New methods for simulating multi-diffusion models.