abundances              Abundance Matrix from Phyloseq
aggregate_taxa          Aggregate Taxa
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
cmat2table              Convert Correlation Matrix into a Table
core                    Core Microbiota
core_abundance          Core Abundance
core_heatmap            Core Heatmap
core_matrix             Core Matrix
core_members            Core Taxa
coverage                Coverage Index
densityplot             Density Plot
dietswap                Diet Swap Data
divergence              Diversity within a Sample Group
diversities             Diversity Index
dominance               Dominance Index
evenness                Evenness Index
find_optima             Find Optima
gktau                   gktau
global                  Global Ecosystem State Variables
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
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-package      R package for microbiome studies
multimodality           Multimodality Score
neat                    Neatmap Sorting
neatsort                Neatmap Sorting
noncore_abundance       Non-Core Abundance Index
noncore_members         Select Non-Core Taxa
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
rare_members            Rare Taxa
rarity                  Rarity Index
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
summarize_phyloseq      Summarize phyloseq object
taxa                    Taxa Names
time_normalize          Normalize Phyloseq Metadata Time Field
time_sort               Temporal Sorting Within Subjects
top_taxa                Top Taxa
transform               Data Transformations for phyloseq Objects
variable_members        Variable Microbiota
write_phyloseq          Exporting phyloseq Data in CSV Files
