CHANGES IN VERSION 2.2.0
-------------------------

NEW FEATURES

    o Added design and metadata diagnostics, grouped missing-value filtering
      and plots, and t-SNE and UMAP plots for matrices and ProBatchFeatures.

    o Added unified long/wide centering and batch correction, plus
      provider-aware registered transformations for ProBatchFeatures.

SIGNIFICANT USER-VISIBLE CHANGES

    o Batch correction now errors on missing values by default; use "keep",
      "drop_features", or "fill" explicitly. Invalid or conflicting
      identifiers, assay selections, lineage, and result names now also error.

DEPRECATED

    o Deprecated center_feature_batch_medians_df(),
      center_feature_batch_means_df(), center_feature_batch_medians_dm(),
      center_feature_batch_means_dm(), correct_with_ComBat_df(),
      correct_with_ComBat_dm(), correct_batch_effects_df(),
      correct_batch_effects_dm(), and correct_with_removeBatchEffect_dm(); use
      center_feature_batch(), correct_with_ComBat(), correct_batch_effects(),
      or correct_with_removeBatchEffect().

BUG FIXES

    o Fixed edge cases in batch correction, sample matching, CV and nonlinear
      fitting, date parsing, and diagnostic plots.


CHANGES IN VERSION 1.99.0
--------------------------

NEW FEATURES

    o Added ProBatchFeatures support, including multiple assays and feature
      levels, across correction and plotting functions.

    o Added limma batch correction and missing-value heatmap, density, and
      frequency plots for ProBatchFeatures objects.


CHANGES IN VERSION 1.1.0
-------------------------

NEW FEATURES

    o Added matrix and long-format transformation APIs with sample consistency
      checks and preservation of original long-format measurements.

    o Added generic heatmaps and consistent missing-value and colour handling
      across diagnostic plots.

SIGNIFICANT USER-VISIBLE CHANGES

    o Renamed center_peptide_batch_medians() to
      center_feature_batch_medians(), normalize_custom_fit() to
      adjust_batch_trend(), and plot_heatmap() to plot_heatmap_diagnostic().
