Changelog • omopHeor

omopHeor 0.7.3

Inline Architecture Diagrams & Pipeline Documentation:
- Added developer-facing inline ASCII diagrams and step-by-step comments across key algorithms in CohortUtilisation, CohortCosts, and CohortEconomics.
- Diagrams illustrate in-database interval collapsing, multi-window temporal alignment, polymorphic OMOP COST table linkage, Markov state trajectory transitions, and Monte Carlo PSA cycle rollouts.
- Inline comments are maintained using # (standard comments) so they do not leak into roxygen .Rd or pkgdown user-facing documentation.

Configurable Episode Gap Threshold (gapDays) in Inpatient & Visit Utilization:
- CohortUtilisation::addInpatients() & CohortUtilisation::addIcuStays(): Added gapDays = 1L (with collapseGap = NULL alias) allowing users to configure the allowable discharge-to-admission gap (e.g. gapDays = 0L for strict overlap only, gapDays = 1L for next-day transfers, gapDays = N for multi-day washouts).
- CohortUtilisation::addVisits(): Added gapDays and propagated it through to the inpatient domain enricher.
- CohortUtilisation::computeHospitalizationCohorts() / compute_hospitalization_cohorts(): Added gapDays / collapseGap / collapse_gap to control interval collapsing boundaries during cohort generation.
- CohortEconomics::extract_hcru(): Added gap_days = 1L (with gapDays = NULL alias) to apply the configurable gap during inpatient episode collapsing and readmission detection.
- CohortUtilisation::validateGapDays(): Added centralized argument validation for non-negative integers ( $\ge 0$ ).

Inpatient Overlapping & Contiguous Stay Collapsing:
- CohortUtilisation::addInpatients(): Integrated interval collapsing (cummax + gap <= 1 day) when collapseOverlapping = TRUE (default), merging intra-hospital department transfers and contiguous admissions into discrete hospitalization episodes without double-counting LOS days or generating false readmissions.
- CohortUtilisation::computeHospitalizationCohorts(): Added lifecycle guidance pointing users to addInpatients() for in-database HCRU characterization.

Same-Day & Overlapping Visit Deduplication for HCRU:
- CohortUtilisation::addOutpatientVisits(): Added countBy = c("days", "records") (default: "days") and collapseOverlapping = TRUE to count distinct calendar visit dates and eliminate administrative duplicate record overestimation.
- CohortUtilisation::addEmergencyCare(): Collapses same-day emergency encounters and overlapping care spans by default into distinct emergency presentations.
- CohortUtilisation::addVisits(): Propagates countBy and collapseOverlapping across Inpatient, Outpatient, and Emergency care settings in a single call.
- CohortEconomics::extract_hcru(): Harmonized to calculate distinct visit dates in study$hcru$patient_summary and study$hcru$outpatient while keeping study$costs and total_cost 100% exhaustive at the financial event level.
- Specialty-stratified deduplication: Outpatient visits calculate distinct dates per specialty independently while maintaining distinct global outpatient visit day totals.

Metapackage Renamed to omopHeor:
- Renamed umbrella metapackage from hermes to omopHeor to eliminate namespace collision with existing Bioconductor package (hermes for RNA-Seq QC).
- Dynamic startup hook updated to display omopHeor version and attached packages upon library(omopHeor).
- Verified 100% namespace availability across CRAN and Bioconductor.
CRAN Policy & Package Footprint Compliance:
- CohortCosts Size Reduction: Removed 46.2 MB of static catalog files from inst/extdata/ to keep package archive < 50 KB (well within CRAN’s < 5 MB limit).
- Dependency Sanitization: Purged Remotes: and GitHub-only packages (Cohort2Trajectory, TrajectoryMarkovAnalysis) across all DESCRIPTION files.
- Acronym Expansion: Expanded all domain acronyms on first mention in all DESCRIPTION files (OMOP, CDM, HCRU, HEOR, CEA) and wrapped software package names in single quotes.
- Import Standardization: Fixed dbplyr, dplyr, and rlang imports to eliminate unused namespace NOTEs on R CMD check.
- Canonical URLs: Updated repository and website links to canonical HTTPS without 301 redirects (https://www.iomed.health/, https://github.com/iomedhealth/hermes/issues).