climatehealth development notes

1.0.2

• Improved accessibility of saved plot outputs across the package:
  • added shared helpers for accessible base R, ggplot2, and patchwork outputs
  • applies consistent SOSCHI styling, accessible colours, figure titles, logos, and wrapped alternative-text captions
  • improves sizing, layout, and pagination for multi-panel indicator reports
• Integrated descriptive statistics more closely with the main analysis workflows:
  • added optional descriptive-statistics controls to the indicator do_analysis() functions where relevant
  • supports summary statistics, correlation outputs, moving-average plots, missing-data summaries, and outlier checks alongside indicator outputs
  • preserves run-scoped descriptive output folders and forwards the selected correlation method through the indicator workflows
• Updated indicator workflows and outputs:
  • air pollution now supports additional continuous covariates in regional GAMs, normalises custom column names, ignores unusable covariates, handles no-excess national power outputs, and returns API-safe results
  • wildfire handling was improved for region/date ordering, region-level outputs, PM2.5 scaling, VIF/QAIC checks, descriptive-statistics column mapping, and missing population checks
  • mental health and temperature-related workflows gained more reproducible attribution options, clearer model-validation outputs, and refreshed documentation
  • malaria and diarrhea workflows gained optional descriptive statistics, API-mode safeguards, and accessible output updates
• Improved API/runtime support:
  • added an air pollution endpoint to the bundled plumber API
  • added support for base64-encoded map zip uploads for malaria and diarrhea API requests
  • prevents API-mode calls from writing plot/CSV outputs or returning non-JSON-safe fitted model objects
• Refreshed package documentation and presentation:
  • added UNSC endorsement and CRAN availability information to the README
  • added SOSCHI branding/logo assets for README and report outputs
  • added a README notes column to flag the ongoing temperature-related health effects review work
  • updated indicator titles and documentation for consistency
• Improved package maintenance and CI reliability:
  • expanded unit and integration coverage for accessibility, descriptive statistics, API mode, and indicator workflows
  • keeps heavy integration tests opt-in for coverage reporting and extends the Codecov step timeout
  • removed unused plotting helpers/dependencies and added png for logo rendering

1.0.1

• CRAN resubmission focused on Fedora Linux check reliability and test stability.
• Fixed INLA model execution under check-core constraints:
  • limits INLA thread usage when _R_CHECK_LIMIT_CORES_ is set
  • keeps compatibility across INLA versions by conditionally passing thread-related arguments only when supported
• Hardened CRAN behavior for fragile INLA end-to-end disease tests:
  • retained CRAN-safe skips for diarrhea and malaria integration paths
  • avoids Fedora-specific parallel worker failures seen in prior checks
• Improved integration-test governance in CI:
  • heavy integration tests are opt-in via RUN_INTEGRATION=true
  • standard PR/push CI remains fast and high-signal by default
• Build hygiene improvement:
  • excludes .covrignore from package build input via .Rbuildignore

1.0.0

• Added new descriptive statistics public APIs:
  • run_descriptive_stats()
  • run_descriptive_stats_api()
• Added run-scoped output folders for descriptive stats:
  • <output_path>/descriptive_stats/<run_id>/All/
  • <output_path>/descriptive_stats/<run_id>/<Region>/
• Kept backward-compatible aliases with runtime deprecation warnings:
  • common_descriptive_stats_core()
  • common_descriptive_stats()
  • common_descriptive_stats_api()
• Improved descriptive stats robustness:
  • correlation now validates and filters numeric columns explicitly
  • centralized preflight column and parameter validation for enabled features
  • typed summary behavior for non-numeric columns
  • safer plot device cleanup with managed PDF helper
• Expanded tests for wrapper behavior, run-folder outputs, API payload validation, endpoint-style contract responses, and deprecated alias compatibility.
• Moved API runtime assets previously held in climatehealth_pipelines into the package:
  • plumber routes and startup scripts under inst/plumber/
  • throttling modules and tests
  • package-scoped API and developer config templates under inst/extdata/config_templates/
  • operational helper scripts under inst/scripts/
• Improved package/API compatibility for runtime usage:
  • enabled API mode in plumber runtime
  • added direct endpoint bindings for descriptive statistics, malaria, and diarrhea
  • enforced API-safe return payloads for malaria and diarrhea in API mode
  • extended internals to accept API-style record payloads and map records
  • updated throttle estimation to size JSON-record payloads instead of file paths
• Cleaned up the air pollution module:
  • standardized argument and variable naming
  • refreshed documentation
  • resolved R CMD check notes for global variable bindings
  • added backward-compatible support for legacy air_pollution_do_analysis() argument names
  • expanded air pollution regression and integration tests