NEWS

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microbiome 1.32.2 (2025-07-17)

• Fixed NEWS file

microbiome 1.23.1 (2023-05-31)

• Removed compositional transformation as part of CLR

microbiome 1.17.2 (2022-02-15)

• Bug fix error in transform when taxa_are_rows is FALSE
• 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
• alr transformation added

microbiome 1.17.1 (2022-01-11)

• Fixed bug in plot_core
• bfratio function removed

microbiome 1.15.3 (2021-10-27)

• Deprecated bfratio function

microbiome 1.14.1 (2021-09-29)

• Removed categorical method from associate function

microbiome 1.1.2 (2020-07-01)

• Core heatmap labeling improved
• aggregate_top_taxa deprecated
• bimodality and potential_analysis functions fixed

microbiome 1.1.1 (2020-04-06)

• Added overlap function

microbiome 0.9.9 (2020-04-05)

• noncore_members removed
• Added aggregate_rare function
• Bioc polishing

microbiome 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

microbiome 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