Changes in version 1.32.2 (2025-07-17)                 

    o   Fixed NEWS file

                 Changes in version 1.23.1 (2023-05-31)                 

    o   Removed compositional transformation as part of CLR

                 Changes in version 1.17.2 (2022-02-15)                 

    o   Bug fix error in transform when taxa_are_rows is FALSE

    o   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 

    o   alr transformation added

                 Changes in version 1.17.1 (2022-01-11)                 

    o   Fixed bug in plot_core

    o   bfratio function removed

                 Changes in version 1.15.3 (2021-10-27)                 

    o   Deprecated bfratio function

                 Changes in version 1.14.1 (2021-09-29)                 

    o   Removed categorical method from associate function

                 Changes in version 1.1.2 (2020-07-01)                  

    o   Core heatmap labeling improved

    o   aggregate_top_taxa deprecated

    o   bimodality and potential_analysis functions fixed

                 Changes in version 1.1.1 (2020-04-06)                  

    o   Added overlap function

                 Changes in version 0.9.9 (2020-04-05)                  

    o   noncore_members removed

    o   Added aggregate_rare function

    o   Bioc polishing

                 Changes in version 0.9.2 (2019-12-25)                  

    o   Divergence function rewritten for clarity
	* Switched from sapply to vapply

    o   Removed noncore_abundance

    o   Fixing plot_core axis labeling

    o   is.compositional function added

    o   spreadplot function added

    o   removed ready made themes from functions

    o   Renamed is.compositional to is_compositional

    o   Fixed a bug in core_members (also non-compositional detection now allowed)

    o   removed rm.na option from aggregate_taxa

    o   Deprecating noncore_* functions (replacing with rare_* functions everywhere)

    o   Removed variable_members function

    o   Support removed from R-3.3.3 and lower

                 Changes in version 0.5.4 (2018-11-20)                  

    o   Removed theme() commands from functions to give the choice to user

    o   Fixed bug in merge_taxa2

    o   Fixed bug in Pielou's evenness

    o   New functions: readcount, bfratio, aggregate_top_taxa

    o   rewritten aggregate_taxa and moved the top argument in the new function aggregate_top_taxa 

    o   plot_composition function: new options for sample.sort and otu.sort

    o   Added Phylum level to taxonomy tables in example data sets 
	* New function: dominant

    o   The diversities function is now replaces by alpha function. The alpha is more
	generic and can return also other alpha diversity indices.

    o   plot_frequencies function now only returns the ggplot object

    o   Renamed the global function into alpha

    o   Renamed arguments rarity.detection and rarity.prevalence into
	detection and prevalence in the rarity function

    o   Added Chao1 index in richness function

    o   In atlas1006 data set, pseudocount of +1 in otu table has been
	removed to facilitate comparison with sequencing data sets and to
	avoid confusion

    o   In atlas1006 data set, only a single replicate per subject-time
	combination is chosen (at random)

    o   New function collapse_replicates has been added

    o   Abundance matrices (otu tables) for all example data sets now
	starting from 0 without pseudocount

    o   Changed the default for the detection argument in the richness function to
	detection=0

    o   removed rarity.threshold and rarity.prevalence options from the alpha function

    o   Various minor fixes; see github commits for many more details

    o   Color order in plot_landscape legend now follows the factor levels
	of the col argument

    o   Fixed example in remove_samples