NEWS

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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.