NEWS

---

mia 1.15

• subsetBy*: added update.tree argument
• agglomerateBy*: Add na.rm option for excluding NA counts
• Added getPERMANOVA and addPERMANOVA functions to calculate PERMANOVA

mia 1.13

• 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.

mia 1.11

• 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

mia 1.9

• 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

mia 1.7

• 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

mia 1.5

• 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

mia 1.3

• 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

mia 1.1

• 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

mia 0.99.0

• Submitted to Bioconductor