Microbiome Analytics

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Documentation for package ‘microbiome’ version 1.28.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

microbiome-package	R package for microbiome studies
ab,	Abundance Matrix from Phyloseq
abundances	Abundance Matrix from Phyloseq
add_besthit	Adds 'best_hist' to a 'phyloseq-class' Object
add_refseq	Add 'refseq' Slot for 'dada2' based 'phyloseq' Object
aggregate_rare	Aggregate Rare Groups
aggregate_taxa	Aggregate Taxa
alpha	Global Ecosystem State Variables
associate	Cross Correlation Wrapper
atlas1006	HITChip Atlas with 1006 Western Adults
baseline	Pick Baseline Timepoint Samples
bimodality	Bimodality Analysis
bimodality_sarle	Sarle's Bimodality Coefficient
boxplot_abundance	Abundance Boxplot
boxplot_alpha	Alpha Boxplot
cmat2table	Convert Correlation Matrix into a Table
collapse_replicates	Collapse Replicate Samples
combine_otu_tax	Utilities For 'phyloseq-class' Slots to Tibbles
core	Core Microbiota
core_abundance	Core Abundance
core_heatmap	Core Heatmap
core_matrix	Core Matrix
core_members	Core Taxa
coverage	Coverage Index
cross_correlate	Cross Correlation Wrapper
default_colors	Default Colors
densityplot	Density Plot
dietswap	Diet Swap Data
divergence	Divergence within a Sample Group
diversity	Diversity Index
dominance	Dominance Index
dominant	Dominant taxa
evenness	Evenness Index
filter_prevalent	Core Microbiota
find_optima	Find Optima
gktau	gktau
group_age	Age Classes
group_bmi	Body-Mass Index (BMI) Classes
heat	Association Heatmap
hitchip.taxonomy	HITChip Taxonomy
hotplot	Univariate Bimodality Plot
inequality	Gini Index
intermediate_stability	Intermediate Stability
is_compositional	Test Compositionality
log_modulo_skewness	Log-Modulo Skewness Rarity Index
low_abundance	Low Abundance Index
map_levels	Map Taxonomic Levels
merge_taxa2	Merge Taxa
meta	Retrieve Phyloseq Metadata as Data Frame
microbiome	R package for microbiome studies
multimodality	Multimodality Score
neat	Neatmap Sorting
neatsort	Neatmap Sorting
otu	Abundance Matrix from Phyloseq
otu_tibble	Utilities For 'phyloseq-class' Slots to Tibbles
overlap	Overlap Measure
peerj32	Probiotics Intervention Data
plot_atlas	Visualize Samples of a Microbiota Atlas
plot_composition	Taxonomic Composition Plot
plot_core	Visualize OTU Core
plot_density	Plot Density
plot_frequencies	Plot Frequencies
plot_landscape	Landscape Plot
plot_regression	Visually Weighted Regression Plot
plot_taxa_prevalence	Visualize Prevalence Distributions for Taxa
plot_tipping	Variation Line Plot
potential_analysis	Bootstrapped Potential Analysis
potential_univariate	Potential Analysis for Univariate Data
prevalence	OTU Prevalence
prevalent_taxa	Core Taxa
psmelt2	Convert 'phyloseq-class' object to long data format
rare	Rare Microbiota
rare_abundance	Rare (Non-Core) Abundance Index
rare_members	Rare Taxa
rarity	Rarity Index
readcount	Total Read Count
read_biom2phyloseq	Read BIOM File into a Phyloseq Object
read_csv2phyloseq	Read Simple OTU Tables into a Phyloseq Object
read_mothur2phyloseq	Read Mothur Output into a Phyloseq Object
read_phyloseq	Import phyloseq Data
remove_samples	Exclude Samples
remove_taxa	Exclude Taxa
richness	Richness Index
sample_tibble	Utilities For 'phyloseq-class' Slots to Tibbles
spreadplot	Abundance Spread Plot
summarize_phyloseq	Summarize phyloseq object
taxa	Taxa Names
tax_tibble	Utilities For 'phyloseq-class' Slots to Tibbles
TibbleUtilites	Utilities For 'phyloseq-class' Slots to Tibbles
timesplit	Time Split
time_normalize	Normalize Phyloseq Metadata Time Field
time_sort	Temporal Sorting Within Subjects
top	Identify Top Entries
top_taxa	Top Taxa
transform	Data Transformations for phyloseq Objects