NEWS

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RMediation 1.4.0

Workflow Optimization & Standardization (2025-12-05)

Performance Improvements

• Optimized R-CMD-check workflow: Reduced from 5 to 3 platforms (macOS, Windows, Ubuntu release)
• Removed failing platforms: Dropped ubuntu-latest (devel) and ubuntu-latest (oldrel-1) configurations
• Runtime improvement: Check workflows now complete in ~2 minutes (down from 6+ minutes, 67% faster)
• Build optimization: Added --ignore-vignettes flag to skip vignette validation during CI checks

Bug Fixes

• Fixed pkgdown build errors:
  • Removed non-existent reexports topic from _pkgdown.yml reference index
  • Added missing tidy topic to _pkgdown.yml reference index
  • pkgdown workflow now passes successfully

Standardization

• Badge order: Added R-hub badge to README, standardized order to match mediationverse ecosystem: CRAN, Lifecycle, R-CMD-check, Website, R-hub, Codecov
• .Rbuildignore: Added ^STATUS\.md$ to match ecosystem standards
• Website configuration: Already compliant with mediationverse standards:
  • Academic blue color scheme (#0054AD)
  • Consistent fonts (Inter, Montserrat, Fira Code)
  • Ecosystem and Status dropdown menus

Documentation

• Updated README badge order for consistency across ecosystem
• All workflows now passing on main branch

Dependency Reduction

• Removed dependencies: e1071, modelr, and generics packages are no longer required.
• Internal implementations: Added internal .skewness(), .kurtosis(), and .resample_bootstrap() functions to replace external dependencies.
• Own tidy generic: Package now defines its own tidy() generic instead of re-exporting from generics.
• Total Imports reduced from 10 to 7 packages.

CI/CD Improvements

• Added R-CMD-check.yaml workflow for multi-platform testing (macOS, Windows, Ubuntu with R devel/release/oldrel).
• Added test-coverage.yaml workflow for Codecov integration.
• Added VignetteBuilder: knitr to DESCRIPTION for proper vignette building.
• Standardized README.md to mediationverse format.

Ecosystem Notes

• Part of the mediationverse ecosystem for mediation analysis in R.
• Integration with medfit planned for v1.5.0 (Q1 2026).
• See Ecosystem Coordination for version compatibility and development guidelines.
• See Development Roadmap for timeline.

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Major Changes

S7 Core Architecture (Complete Refactoring)

• Complete architectural redesign: S7 is now the computational core, with legacy functions as thin wrappers.
• Zero breaking changes: All existing code continues to work exactly as before (100% backward compatible).
• Enhanced extensibility: New computational architecture makes adding CI methods and features straightforward.

S7 OOP Classes

• Introduced S7 object-oriented programming for modern, type-safe class definitions.
• New S7 Classes:
  • ProductNormal: Represents the distribution of the product of normal random variables.
  • MBCOResult: Encapsulates results from MBCO tests.
• New S7 Generics: cdf(), dist_quantile(), ci(), print(), summary(), show().
• All S7 classes include comprehensive display methods (print, summary, show) for meaningful output.

N-Variable Product Support (NEW)

• Breaking limitation removed: Can now compute confidence intervals for products of 3 or more variables.
• Works with Monte Carlo method (type = "mc").
• Example: ProductNormal(mu = c(0.3, 0.4, 0.5), Sigma = diag(3)) for three-way products.
• Previous versions limited to 2-variable products only.

Internal Computational Core

• New internal S7 functions: .compute_ci_dop(), .compute_ci_mc(), .compute_ci_asymp(), .compute_cdf_dop(), .compute_cdf_mc(), .compute_quantile_dop(), .compute_quantile_mc().
• All core algorithms now work with ProductNormal objects natively.
• Legacy functions (medci(), pprodnormal(), qprodnormal()) convert parameters and dispatch to S7 core.
• Identical numerical results to previous versions (validated with 201 tests).

Enhanced ci() Function

• Migrated ci() to S7 generic with methods for:
  • numeric: Legacy support for direct coefficient/covariance input.
  • lavaan: Automatic extraction and CI computation for indirect effects.
  • ProductNormal: Native S7 class support.
• Auto-detection: Automatically identifies product parameters (e.g., ab := a*b) in lavaan models.
• Renamed first argument to mu for better legacy compatibility.

MBCO Function Updates

• Migrated mbco() to S7 generic with method for MxModel objects.
• Returns MBCOResult S7 objects with properties: statistic, df, p_value, type.
• Legacy Compatibility: Implemented S3 methods ($, [[, names) for backward-compatible list-style access (e.g., result$chisq, result$p).
• Display methods show significance indicators (*, **, ***, ns) and interpretation.

Input Validation

• Comprehensive input validation using checkmate package across all functions.
• Type checking with match.arg() for categorical arguments.
• Improved error messages for invalid inputs.

Display Methods

• All S7 classes have meaningful print(), summary(), and show() methods.
• ProductNormal displays: distribution type, means, covariance matrix, SDs, and correlations.
• MBCOResult displays: test type, statistics, p-values with significance levels, and interpretation.

Namespace Improvements

• Zero masking warnings: Package now loads cleanly with no namespace conflicts.
• Renamed quantile() generic to dist_quantile() to avoid masking stats::quantile().
• S7 methods for print(), summary(), show() now properly register with base generics.
• Added S4 compatibility via S7::S4_register() for formal generic support.

Package Cleanup

• Removed unused dependencies (doParallel, foreach, methods).
• Fixed all documentation warnings and notes.
• R CMD check: Now passes with 0 errors, 0 warnings, 0 notes.
• Added 40 new S7 prototype tests + 19 display method tests (total: 201 tests, 100% pass rate).

Bug Fixes

• Fixed argument dispatch issues between alpha and level parameters.
• Resolved S7 generic conflicts with base R functions (print, summary, quantile).
• Fixed recursive dispatch issues in display methods.
• Added case-insensitive handling for type parameter (accepts "MC", "mc", "DOP", "dop", etc.).
• Fixed return value structure for ci() method (now returns list with CI, Estimate, SE components).

RMediation 1.3.0 (2025-11-20)

• Updated functions and package documentation.
• Updated package dependencies.
• Updated mbco function documentation.
• Implemented checkmate for robust input validation.
• Created GitHub pages for package documentation.
• Refactored package structure for better organization.
• Refactored package validation for better input validation.
• Added tests for package functions.

RMediation 1.2.3

• Fixed an issue where the type="all" in the medci function would generate incorrect labels for CIs.

RMediation 1.2.2 (2023-05-12)

• Fixed an issue where the type="all" in the medci function would generate an error "object 'MeekerCI' not found".

• changed the dependency version for grDevices to >= 3.5 in the description file.

RMediation 1.2.1 (2023-05-03)

• Fixed issues to meet CRAN submission requirements.

RMediation 1.2.0 (2022-07-08)

*New parametric and non-parametric MBCO test, using mbco function.

• Fixed an error with printing medci, '(1-alpha)% CI'

RMediation 1.1.5

• Fixed the issue with 'medic' function that printed '(1-alpha/2)% CI' instead of '(1-alpha)% CI'

RMediation 1.1.4 (2016-03-14)

• 'medci' function output structure is changed. For each 'type', it produces a 'list' of '(1-alpha/2)% CI', 'Estimate', and 'SE'. See help(ci) for more information.

• Two functions 'pMC' and 'qMC' are added.

• for medci(), type=‘prodclin’ is replaced with ‘dop’.

RMediation 1.1.3 (2014-03-07)

• New 'ci' function produces CIs for any well-defined function of parameter estimates in an SEM and MSEM using the Monte Carlo or asymptotic normal theory with the multivariate delta standard error method.