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paramix 0.0.3

Documentation and Vignettes

• Added a dedicated vignette reproducing-paper-analysis describing how to run the simulation study from Goodfellow et al. (2025) doi:10.1371/journal.pcbi.1013420, including reference tables comparing calculated outputs with published findings.
• Updated package citation metadata in DESCRIPTION and inst/CITATION for the published PLOS Computational Biology paper.
• Extended and clarified mathematical formulations in roxygen documentation and vignettes.
• Added a package hex logo in man/figures/logo.png and configured pkgdown favicons with light/dark theme support.
• Removed generated documentation (man/*.Rd) and intermediate vignette outputs from version control, managing them dynamically through just docs.

Error Handling and Validation

• Centralized user-facing error and warning signaling into reusable, named format templates in R/messages.R.
• Added comprehensive unit test coverage for all input validation and signaling paths in tests/testthat/test-messages.R.
• Integrated roxyglobals to automate global variable declarations in R/globals.R.

Demonstration Analysis and Reproducibility

• Modernized the bundled analysis scripts in inst/analysis/ to support updated demographic data (UN WPP 2022/2024) and modern socialmixr (>= 0.5.0) contact matrix interfaces.
• Added automated numerical assertions in inst/analysis/scripts/run_numbers.R comparing calculated 65+ IFR increases, averted deaths, and averted YLLs directly against published benchmarks.
• Added just test-analysis workflow and a dedicated CI action to verify that the reproduction pipeline executes successfully.

Build and Developer Workflows

• Standardized developer workflows via justfile recipes (format, lint, docs, install, test, coverage, site, check).
• Enforced code formatting via air and static linting via lintr.
• Added automated package spell checking via tests/spelling.R and inst/WORDLIST.
• Modernized GitHub Actions CI workflows for multi-platform checks (Linux, macOS, Windows), automated linting, test coverage reporting, and automated pkgdown deployment.

paramix 0.0.2

• Extended documentation to clarify mathematical formulation of the mixing table.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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