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