Changes in version 1.35.2 (2026-10-25)
+ Fixed Camargo evenness (#231). Zeroes were not removed, so the index
  was computed on the wrong entries and depended on the order of taxa.
  All Camargo values change; samples with no observed taxa now return
  NA instead of an error
+ Documented that the zeroes argument of evenness() has no effect

Changes in version 1.35.1 (2026-08-10)
+ Added support for TreeSummarizedExperiment and other
  SummarizedExperiment-derived objects
  * abundances(), meta() and taxa() now accept these objects alongside
    phyloseq objects, which extends support to most of the package
  * abundances() gains an assay.type argument, defaulting to the counts
    assay when present and otherwise the first assay
  * transform() stores its result as a new named assay and leaves the
    original assays untouched, following the mia transformAssay
    convention. It gains a name argument to control that assay name, and
    the result is read back with abundances(x, assay.type = name) rather
    than abundances(x)
  * Functions that manipulate the taxonomy table (aggregate_taxa,
    plot_composition, map_levels, psmelt2, the tibble utilities and the
    read_* family) remain phyloseq only
+ We recommend switching from phyloseq to the TreeSummarizedExperiment
  based methods described in the Orchestrating Microbiome Analysis (OMA)
  online book, https://bioconductor.org/books/release/OMA/, which is
  where method development now takes place
+ Passing a phyloseq object now emits a one-time deprecation notice per
  session, recommending the (Tree)SummarizedExperiment framework and the
  mia package. Silence it with
  options(microbiome.phyloseq_deprecation = FALSE)
+ Fixed low_abundance returning an unnamed vector for phyloseq input
+ Fixed collapse_replicates failing when given a single replicate field

Changes in version 1.32.2 (2025-07-17)
+ Fixed NEWS file

Changes in version 1.23.1 (2023-05-31)
+ Removed compositional transformation as part of CLR

Changes in version 1.17.2 (2022-02-15)
+ Bug fix error in transform when taxa_are_rows is FALSE

Changes in version 1.17.2 (2022-02-03)
+ Merge microbiomeutilites functionality
  * Convert phyloseq slots to tibbles
  * Combine_otu_tax joins otu_table and tax_table
  * Merged add_besthit a fine tuned version from format_to_besthit 
  * Merged psmelt2 a fine tuned version from phy_to_ldf 
  * Bug fix in transform method alr 

Changes in version 1.17.2 (2022-01-15)
+ alr transformation added

Changes in version 1.17.1 (2022-01-11)
+ Fixed bug in plot_core
+ bfratio function removed

Changes in version 1.15.3 (2021-10-27)
+ Deprecated bfratio function

Changes in version 1.14.1 (2021-09-29)
+ Removed categorical method from associate function

Changes in version 1.1.2 (2020-07-01)
+ Core heatmap labeling improved
+ aggregate_top_taxa deprecated
+ bimodality and potential_analysis functions fixed

Changes in version 1.1.1 (2020-04-06)
+ Added overlap function

Changes in version 0.9.9 (2020-04-05)
+ noncore_members removed
+ Added aggregate_rare function
+ Bioc polishing

Changes in version 0.9.2 (2019-12-25)
+ Divergence function rewritten for clarity
* Switched from sapply to vapply
+ Removed noncore_abundance
+ Fixing plot_core axis labeling
+ is.compositional function added
+ spreadplot function added
+ removed ready made themes from functions
+ Renamed is.compositional to is_compositional
+ Fixed a bug in core_members (also non-compositional detection now allowed)
+ removed rm.na option from aggregate_taxa
+ Deprecating noncore_* functions (replacing with rare_* functions everywhere)
+ Removed variable_members function
+ Support removed from R-3.3.3 and lower

Changes in version 0.5.4 (2018-11-20)
+ Removed theme() commands from functions to give the choice to user
+ Fixed bug in merge_taxa2
+ Fixed bug in Pielou's evenness
+ New functions: readcount, bfratio, aggregate_top_taxa
+ rewritten aggregate_taxa and moved the top argument in the new function aggregate_top_taxa 
+ plot_composition function: new options for sample.sort and otu.sort
+ Added Phylum level to taxonomy tables in example data sets 
* New function: dominant
+ The diversities function is now replaces by alpha function. The alpha is more
  generic and can return also other alpha diversity indices.
+ plot_frequencies function now only returns the ggplot object
+ Renamed the global function into alpha
+ Renamed arguments rarity.detection and rarity.prevalence into
  detection and prevalence in the rarity function
+ Added Chao1 index in richness function
+ In atlas1006 data set, pseudocount of +1 in otu table has been
  removed to facilitate comparison with sequencing data sets and to
  avoid confusion
+ In atlas1006 data set, only a single replicate per subject-time
  combination is chosen (at random)
+ New function collapse_replicates has been added
+ Abundance matrices (otu tables) for all example data sets now
  starting from 0 without pseudocount
+ Changed the default for the detection argument in the richness function to
  detection=0
+ removed rarity.threshold and rarity.prevalence options from the alpha function
+ Various minor fixes; see github commits for many more details
+ Color order in plot_landscape legend now follows the factor levels
  of the col argument
+ Fixed example in remove_samples