# Microbiome Analytics

## 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