DAssemble 0.99.4
=================

* Extended the main `DAssemble()` API with support for `coVars`,
  `random_effects`, and open-ended `method_args` controls for forwarding
  additional arguments to supported underlying methods and enhancers.
* Updated the `LR` enhancer to serve as the package's prevalence-oriented
  presence/absence logistic model, using MaAsLin3-style augmented logistic
  fitting by default and supporting an opt-in fixed-effects `"firth"` mode
  via `method_args$LR$separation_method` using `brglm2`.
* Preserved standard `Maaslin3` wrapper behavior rather than forcing a
  prevalence-only analysis path.
* Added an optional MaAsLin2 median-comparison path that operates on raw
  `fit$results` before returning the standardized exposure-specific table.
* Enabled or expanded multi-covariate support across compatible wrappers,
  including `DESeq2`, `edgeR`, `limmaVOOM`, `metagenomeSeq`, `MAST`,
  `Robseq`, `LinDA`, `Tweedieverse`, `Maaslin2`, and `Maaslin3`.
* Exposed longitudinal support through the original `DAssemble()` entry point
  for `Maaslin2`, `Maaslin3`, `Tweedieverse`, and the `LR` enhancer.
* Removed the temporary `Prevalence` core path so prevalence-oriented modeling
  is handled consistently through the `LR` enhancer.
* Clarified documentation for hurdle and two-part core methods so sensitivity
  analyses recommend `WLX` or `KS`, but not `LR`, to avoid reintroducing
  overlapping prevalence-style evidence.
* Made method-specific arguments override DAssemble wrapper defaults before
  MaAsLin2, MaAsLin3, and other wrapped model calls are evaluated.
* Updated the README, vignette, examples, and man pages to document the new
  API, supported method matrix, longitudinal workflows, and `method_args`
  pass-through mechanism.

DAssemble 0.99.3
=================

* Updated package metadata for Bioconductor resubmission.
* Added .DS_Store to .gitignore and cleaned temporary build artifacts.

DAssemble 0.99.2
=================

* Updated NEWS for the latest Bioconductor resubmission version.

DAssemble 0.99.1
=================

* Added Bioconductor-ready vignette examples for bulk RNA-seq, microbiome, and
  single-cell workflows.
* Expanded unit test coverage across core methods, enhancers, normalization,
  CCT utilities, and internal helper functions.
* Added package-level documentation and improved reviewer-requested
  attribution for incorporated Robseq and Tweedieverse code.

DAssemble 0.99.0
=================

* Initial Bioconductor submission.
* Added MultiAssayExperiment input support.
* Added conditional backend support for differential analysis methods.
