Changes in version 0.99.0
+ Submitted to Bioconductor

Changes in version 1.1.x
+ split transformAssay into transformSamples and transformFeatures
+ added log_modulo_skewness as a diversity index
+ added functions for summarizing dominant taxa information
+ added wrapper for adding dominant taxa information to colData
+ added specialized subsetting function for subsetting by prevalence (subsetByPrevalentTaxa/subsetByRareTaxa)
+ added mapTaxonomy
+ added estimateDivergence
+ bugfix: makePhyloseqFromTreeSummarizedExperiment checks now for rowTree be compatible
+ bugfix: meltAssay supports Matrix types
+ bugfix: meltAssay is able to include rowData also when there are duplicated rownames
+ added subsampleCounts for Subsampling/Rarefying data
+ added getExperimentCrossCorrelation for calculatting cross-correlation between features
+ added calculateOverlap
+ getUniqueTaxa & getTopTaxa: added option for alphabetical order

Changes in version 1.3.x
+ name change: testForExperimentCrossCorrelation to testExperimentCrossCorrelation
+ getExperimentCrossCorrelation: Filtering disabled by default, option to suppress warnings
+ bugfix: taxonomyTree gave error if taxa were agglomerated at highest level (taxa name mismatch)
+ bugfix: subsampleCounts errors if no samples are found after subsampling
+ added loadFromMetaphlan
+ renamed calculateUniFrac to calculateUnifrac
+ added na.rm option to getTopTaxa function
+ bugfix: makeTreeSEFromPseq -- orientation of assay is taken into account
+ bugfix: getExperimentCrossCorrelation's "matrix"" mode works with features named equally
+ bugfix: getExperimentCrossCorrelation's calculates correlations correctly with features named equally
+ getExperimentCrossCorrelation name changed to getExperimentCrossAssociation
+ getExperimentCrossAssociation: user's own function supported, sort in mode == table enabled
+ getExperimentCrossAssociation: added MARGIN & paired options, efficiency of algorithm improved
+ Added *Features aliases for *Taxa functions
+ *RDA functions utilize vegan:dbrda instead of vegan:rda
+ Sped up estimateDivergence by removing unnecessary pairwise comparisons
+ Added new internal function .calculate_reference_distance to calculate distance to a single reference sample
+ added new skin microbiome example data set 'peerj13075'
+ added splitOn and unsplitOn functions
+ CLR transformation: remove internal relative transformation
+ Replace 'abund_values' argument with 'assay_name'
+ getExpCrossCorr: added altExp option
+ added detection threshold option to getTopTaxa
+ makeSummarizedExperimentFromBiom is now makeTreeSummarizedExperimentFromBiom
+ Added mergeSE function
+ bugfix: loadFromBiom

Changes in version 1.5.x
+ Added HintikkaXOData
+ Added sample metadata option to getExperimentCrossAssociation
+ estimateFaith: add support for multiple rowTrees
+ calculateRDA/CCA: added variable argument & replaced altexp argument with altExp
+ getExpCrossCorr: bugfix; samples should match when correlations between features are calculated
+ getExpCrossCorr: Kendall's tau is the default method
+ mergeSEs: bugfix; links between trees and rows/cols were wrong & rowData did not include all info
+ calculateDPCoA, calculateUnifrac & merge: add support for multiple trees
+ altExp parameter to altexp
+ agglomerateByRank: make rownames unique by default
+ removed calculateDistance and calculateUniFrac alias
+ calculateUnifrac bugfix

Changes in version 1.7.x
+ Deprecated assay_name arguments, replaced with assay.type
+ Removed abund_values argument
+ makePhyloseqFromTreeSE: added option for choosing a tree from multiple rowTrees
+ mergeSEs: match rows based on all available taxonomy level data on rowData
+ mergeSEs: fix bug related to equally named variables that are different class
+ mergeSEs: option for merging multiple assays
+ calculateUnifrac: option for specifying the tree from TreeSE
+ transformAssay: utilize vegan package
+ calculateUnifrac: subset tree based on data
+ agglomerateByRank: take into account multiple trees
+ loadFromBiom: name columns of rowData based on prefixes
+ Deprecate transformSamples, *Features, relabundance, ZTransform, relAbundanceCounts
+ mergeSEs: faster tree merging
+ Faith's index: fix bug that occurred when only one taxon is present

Changes in version 1.9.x
+ loadFromMetaphlan: Bugfix, not all files include ID column.
+ cluster: added wrapper for bluster's clusterRows function
+ Added loadFromHumann
+ calculateDMM: deprecated/updated outdated functions
+ Added Tengeler2020 dataset
+ *RDA & *CCA: calculate also statistical significance
+ altExp support for meltAssay
+ Deprecate mergeRows, mergeCols, agglomerateByRank, agglomerateByPrevalence
+ Removed  getAbundanceSample and getAbundanceFeature
+ Updated test to avoid warning from deprecated functions
+ Export mergeFeaturesByRank
+ *RDA & *CCA: scores parameter for specifying output
+ Improve mergeSEs and loadFromBiom
+ Faith index: bugfix
+ runRDA bugfix: vegan::dbrda and vegan::vegdist have different parameter for dissimilarity --> taken into account
+ Add support for Metaphlan v2
+ loadFromHumann: Improved speed

Changes in version 1.11.x
+ loadFromMetaphlan: support strain rank
+ agglomerateByRank: agglomerate tree fix
+ Replace taxonomyTree and addTaxonomyTree with getHierarchyTree and addHierarchyTree
+ splitOn: update rowTree fix
+ perSampleDominantFeatures: add new arguments (n, other.name, complete)
+ loadFromMetaphlan: support "taxonomy" column for specifying taxonomy
+ cluster: Overwrite old results instead of failing
+ getPrevalence: bugfix, if assay contains NA values, it does not end up to NA anymore.
+ getExperimentCrossCorrelation fix: enable using of sampleMap in MAE.
+ Implemented the setTaxonomyRanks function to specify which ranks are recognized as taxonomy ranks.
+ Rename cluster to addCluster
+ rename importers loadFromBiom, loadFromQIIME2, readQZA, loadFromMothur, loadFromMetaphlan, loadFromHumann
+ fix typo in loadFromBiom definition (deprecate file)
+ deprecate subsetSamples, subsetFeatures and subsetTaxa
+ deprecate plotNMDS after moving it to miaViz
+ rename estimateDivergence to addDivergence
+ Add details to documentation of function agglomerateByPrevalence

Changes in version 1.13.x
+ Added new functions getMediation and addMediation
+ replace getExperiment* and testExperiment* functions with getCrossAssociation
+ Replace mergeRows and mergeCols with new function agglomerateByVariable
+ agglomerateByRank: bugfix related to agglomeration of non-existing tree
+ getHierarchyTree: bugfix related to empty cells in rowData
+ agglomerateByRank: bugfix: trees was not pruned correctly
+ rename meltAssay to meltSE
+ Rename countDominantFeatures and countDominantTaxa to summarizeDominance
+ rename subsetByPrevalent* and subsetByRare* to subsetByPrevalent and subsetByRare
+ Deprecate transformFeatures, transformSamples, transformCounts, Ztransform,
  relAbundanceCounts
+ rename getRare* functions to getRare, getUnique* functions to getUnique,
  getTop* functions to getTop and getPrevalent* functions to getPrevalent
+ Rename subsampleCounts to rarefyAssay
+ Rename perSampleDominant* functions to getDominant and addPerSampleDominant*
  functions to addDominant
+ Rename splitByRanks to agglomerateByRanks and add option as.list
+ Explain that rarefyAssay returns a new SummarizedExperiment object that
  includes the newly added subsampled assay.
+ Fix bug in mergeFeaturesByPrevalence
+ new aliases calculateDPCoA to getDPCoA, calculateNMDS to getNMDS, calculateRDA to getRDA,
calculateCCA to getCCA
+ add informative error message in rarefyAssay on assays with strictly-negative values
+ Use rbiom package in unifrac implementation
+ Updated parameter names to follow naming convention "parameter.name"
+ rename converters makeTreeSEFrom* to convertFrom* and makePhyloseqFromTreeSE to
convertToPhyloseq
+ add rowTree agglomeration and RefSeq agglomeration in agglomerateByPrevalence
+ Fix tree merging in unsplit and mergeSEs functions
+ Added addAlpha; a wrapper for calculating all alpha diversity indices
+ Added importTaxpasta
+ Changes in default taxonomy ranks; more ranks supported
+ Added Tito2024QMP dataset
+ Added convertToBIOM
+ new methods getLDA and addLDA for LDA ordination with feature loadings
computation
+ new methods getNMF and addNMF for NMF ordination with feature loadings
computation
+ If missing values, give informative error in *RDA/*CCA functions
+ transformAssay can apply transformation to altExp
+ Added CSS transformation
+ In agglomerateByVariable, splitOn and getDominant, use 'group' to specify grouping variable.

Changes in version 1.15.x
+ subsetBy*: added update.tree argument
+ agglomerateBy*: Add na.rm option for excluding NA counts
+ Added getPERMANOVA and addPERMANOVA functions to calculate PERMANOVA
+ update.tree = TRUE by default
+ Add functions for classifying taxa based on their average abundance
+ Add addPrevalence function that adds results of getPrevalence to rowData
+ Added support for dimred to getCrossAssociation
+ Add wrapper for PhILR transformation
+ Support rarefaction when applying unifrac
+ Added getMDS and addMDS: wrappers for scater::calculateMDS and scater::runMDS
+ Fix tree merging and agglomeration
+ getReducedDimAttribute: function for fetching elements from attributes of reducedDim
+ Improve decontam functions
+ Support precalculated dissimilarity matrix in dbRDA
+ Calculate standard, binary Jaccard index by default

Changes in version 1.17.x
+ Added add.dimred parameter to meltSE() (2025-04-29)
+ Added transformation method that replaces values <= threshold with NA (2025-05-09)
