TibbleUtilites          Utilities For 'phyloseq-class' Slots to Tibbles
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
core                    Core Microbiota
core_abundance          Core Abundance
core_heatmap            Core Heatmap
core_matrix             Core Matrix
core_members            Core Taxa
coverage                Coverage Index
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
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-package      R package for microbiome studies
multimodality           Multimodality Score
neat                    Neatmap Sorting
neatsort                Neatmap Sorting
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
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
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
readcount               Total Read Count
remove_samples          Exclude Samples
remove_taxa             Exclude Taxa
richness                Richness Index
spreadplot              Abundance Spread Plot
summarize_phyloseq      Summarize phyloseq object
taxa                    Taxa Names
time_normalize          Normalize Phyloseq Metadata Time Field
time_sort               Temporal Sorting Within Subjects
timesplit               Time Split
top                     Identify Top Entries
top_taxa                Top Taxa
transform               Data Transformations for phyloseq Objects
