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.