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Dependencies
- medfit is now available on CRAN (v0.2.0/0.2.1).
Removed
Remotes: data-wise/medfit; medfit now resolves
from CRAN. Pinned Suggests: medfit (>= 0.2.0).
ci() for medfit
MediationData/SerialMediationData now extracts
the path covariance by parameter name and uses the full covariance
matrix (including off-diagonals) for both simple and serial mediation.
Removed the previous positional/value-matching heuristics and the
independence/diagonal fallbacks, which could silently produce incorrect
intervals; unresolved path labels now raise an informative error.- The serial-mediation pipeline is now verified end-to-end against
medfit’s released serial extractor (medfit >= 0.2.0):
medfit::extract_mediation() produces a
SerialMediationData for both lavaan (ordered
mediator vector) and lm/glm (mediator_models)
chains, and ci() consumes it via the documented
d1, d2, ... path-name contract. Added integration tests
that fit a real model, extract, and run ci() end-to-end
(skipped when medfit < 0.2.0).
Workflow
Optimization & Standardization (2025-12-05)
- 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
Workflow
Optimization & Standardization (2025-12-05)
- 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.
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.
- 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).
- 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.
- Fixed an issue where the type=“all” in the medci function would
generate incorrect labels for CIs.
- Fixed issues to meet CRAN submission requirements.
New parametric and non-parametric MBCO test, using
mbco function. Fixed an error with printing medci,
‘(1-alpha)% CI’
- Fixed the issue with ‘medic’ function that printed ‘(1-alpha/2)% CI’
instead of ‘(1-alpha)% CI’
‘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’.
- 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.
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.