NEWS

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microbiomeutilities 1.00.16 (2021-04-14)

• Fix 'format_to_besthit' to return all slots present in input.

microbiomeutilities 1.00.15 (2021-01-21)

• Fix 'plot_taxa_cv' to deal with taxa_are_rows==FALSE.

microbiomeutilities 1.00.14 (2021-01-21)

• Added utilities within 'peak-methods'.

microbiomeutilities 1.00.12 (2021-01-18)

• Removed prevalence option 'plot_taxa_heatmap'.
• Bug fix 'format_to_besthit'.

microbiomeutilities 1.00.11 (2020-11-09)

• Small improvement in error handling.
• Phyloseq slots to tibble
• 'add_refseq' for storing ASV sequences

microbiomeutilities 1.00.10 (2020-11-02)

• Improve 'get_group_abundances' documentation and code

microbiomeutilities 1.00.09 (2020-10-21)

• Added longitudinal page to website
• Added new function plot_area
• Added new function plot_paired_abundances
• Added new function plot_spaghetti

microbiomeutilities 1.00.08 (2020-10-17)

• Cosmetic updates

microbiomeutilities 1.00.07 (2020-10-15)

• Update to 'plot_taxa_heatmap'
• Fixed 'plot_abund_prev' options
• Added 'plot_alpha_rcurve'

microbiomeutilities 1.00.06 (2020-10-11)

• Added new function dominant_taxa
• Removed plot_ternary due to clash between ggplot2 and ggtern
• Added new function find_samples_taxa

microbiomeutilities 1.00.05 (2020-10-11)

• Added new function dominant_taxa
• Added new function get_group_abundances
• removed microbiome_pipeline

microbiomeutilities 1.00.04 (2020-10-11)

• Added new function plasticity
• modified theme_biome_utils

microbiomeutilities 1.00.03 (2020-10-04)

• Added new function plot_ternary
• Deprecated plot_select_taxa

microbiomeutilities 1.00.02 (2020-10-04)

• Added new function plot_listed_taxa
• Deprecated plot_select_taxa
• Added option for half violin in boxplots

microbiomeutilities 1.00.01 (2020-10-03)

• Added new function plot_abund_prev
• Added new function simple_heatmap
• Added new function taxa_distribution
• Added a custom theme theme_biome_utils
• Added gghalves to imports
• Fixed microbiome_pipeline report

microbiomeutilities 1.00.00 (2020-10-01)

• Version tested with R version 4.0.2 (2020-06-22)
• Fix typos in documentation
• Add prefix option to format_to_besthit
• Edited phy_to_ldf to speed up conversion
• Removed format_phyloseq function as it is redundant
• Speedup taxa_summary function
• Free up pheatmap option in plot_taxa_heatmap
• Updated for more info from print_ps output
• plot_taxa_boxplot now returns a faceted plot
• Added new function plot_diversity_stats
• R code styling styler::tidyverse_style()

microbiomeutilities 0.99.02 (2020-02-02)

• diversities to alpha in plot_alpha_diversities function
• fix typos in documentation

microbiomeutilities 0.99.01 (2018-04-09)

• Cosmetic changes to report generator

microbiomeutilities 0.99.0 (2018-20-04)

• Added print_ps (utility and alternative to print(ps))
• Added taxa_summary, returns table with mean, max, median, standard deviation relative abundance
• Use of abundance to extract otu_table to avoid bugs
• Fixes for other bugs in examples and documentation