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 o Color order in plot_landscape legend now follows the factor levels of the col argument o Fixed example in remove_samples CHANGES IN VERSION 0.1.2 # New features o Added plot_abundances 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 # Major changes o Abundance matrices (otu tables) for all example data sets now starting from 0 without pseudocount # Minor changes o Changed the default for the detection argument in the richness function to detection=0 o Color order in plot_landscape legend now follows the factor levels of the col argument o Various minor fixes; see github commits for many more details