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Add degree and time of adoption diagnostic function (#57)
* Initial plan * Implement degree_adoption_diagnostic function with comprehensive tests Co-authored-by: gvegayon <893619+gvegayon@users.noreply.github.com> * Fix print method formatting and complete implementation Co-authored-by: gvegayon <893619+gvegayon@users.noreply.github.com> * Review changes: - Expanded degree_adoption_diagnostic to accept generic graphs + TOA - Improved print method with CI-aware interpretation - Updated tests for new input validation * multi-diffusion support (behavior/combine), undirected network support, safer bootstrap & printer; tests + docs added * Refactor degree_adoption_diagnostic: Move to separate file, update documentation syntax, add NEWS entry Co-authored-by: gvegayon <893619+gvegayon@users.noreply.github.com> * Updating docs * Adding new workflow and working on R CMD check * Fixing actions * Updating readme * Fix formatting of valgrind variable in workflow name * Addressing errors and warnings * Updating printer: combo mode + bootstrap NA fix * Updating README and version number * Remove build-targz.yml and update NEWS.md for v1.24.0 Co-authored-by: gvegayon <893619+gvegayon@users.noreply.github.com> * Renaming codechunks to avoid errors * Trying to fix LR ending * Avoiding building manual in valgrind and building to upload --------- Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: gvegayon <893619+gvegayon@users.noreply.github.com> Co-authored-by: aoliveram <anibal.olivera.m@gmail.com> Co-authored-by: George G. Vega Yon <g.vegayon@gmail.com>
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.devcontainer/Dockerfile renamed to .devcontainer/Containerfile

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

‎.devcontainer/devcontainer.json‎

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

‎.github/copilot-instructions.md‎

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

‎.github/workflows/pkgdown.yml‎

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steps:
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- uses: actions/checkout@v4
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- uses: actions/checkout@v5
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- uses: r-lib/actions/setup-pandoc@v2
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- uses: r-lib/actions/setup-r-dependencies@v2
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install-quarto: true
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install-pandoc: true
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- name: Install the package
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- name: Upload artifact for GH pages deployment
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uses: actions/upload-pages-artifact@v3
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uses: actions/upload-pages-artifact@v5
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‎.github/workflows/r.yml‎

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R-CMD-check:
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name: ${{ matrix.config.os }} (${{ matrix.config.r }})
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name: ${{ matrix.config.os }} (${{ matrix.config.r }}) (valgrind:${{ matrix.config.valgrind }})
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strategy:
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config:
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- {os: macOS-latest, r: 'release'}
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- {os: macOS-latest, r: 'devel', http-user-agent: 'release'}
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- {os: windows-latest, r: 'release'}
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# - {os: windows-latest, r: 'devel', http-user-agent: 'release'}
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- {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'}
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- name: Configure git
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run: git config --global core.autocrlf false
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- uses: actions/checkout@v5
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- name: Install valgrind
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if: ${{ matrix.config.valgrind }}
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sudo apt-get install -y --no-install-recommends valgrind
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env:
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run: |
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options(crayon.enabled = TRUE)
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rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran", "--use-valgrind"), error_on = "error", check_dir = "check")
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shell: Rscript {0}
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- uses: r-lib/actions/check-r-package@v2
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if: ${{ matrix.config.valgrind }}
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with:
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args: 'c("--as-cran", "--use-valgrind", "--no-manual")'
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upload-results: true
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build-pkg:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v5
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uses: actions/upload-artifact@main
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- uses: r-lib/actions/setup-r@v2
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path: check
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r-version: 'release'
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use-public-rspm: true
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- name: Build the package
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if: ${{ matrix.config.os == 'ubuntu-latest' && (matrix.config.r == 'release' || matrix.config.r == 'devel') && (matrix.config.valgrind != true) }}
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- uses: r-lib/actions/setup-r-dependencies@v2
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with:
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extra-packages: any::devtools
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- name: Build package
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if: ${{ matrix.config.os == 'ubuntu-latest' && (matrix.config.r == 'release' || matrix.config.r == 'devel') && (matrix.config.valgrind != true) }}
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- name: Upload package artifact
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uses: actions/upload-artifact@v5
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name: netdiffuseR-built-package-${{ matrix.config.os }}-${{ matrix.config.r }}
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path: netdiffuseR_*.tar.gz
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retention-days: 7
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name: R-package
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path: '*.tar.gz'
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‎.gitignore‎

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*.tex
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# Other files
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.vscode/
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config.status
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src/Makevars

‎DESCRIPTION‎

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

‎Makefile‎

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R CMD build .
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Rscript -e 'rmarkdown::render("README.Rmd")'
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README.md: README.qmd
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quarto render README.qmd
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R CMD check --as-cran netdiffuseR_$(VERSION).tar.gz
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check:
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Rscript --vanilla -e 'devtools::check()'
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‎NAMESPACE‎

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S3method(plot_threshold,array)
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S3method(print,degree_adoption_diagnostic)
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‎NEWS.md‎

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

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