ITS1/ITS2               Sample ITS1 and ITS2 Data
LCA.OTU                 Lowest Common Ancestor (LCA) OF EACH OTU
META.clust              Plot Hierarchical Cluster Of Metadata
OTU.diversity           Summarize Diversity Indices for OTU Tables
OTU.ord                 Ordination Plot For OTUs Using CCA or RDA
                        Analysis
OTU.rarefy              Create Rarefied OTU Tables
OTU.recap               Summarize OTU
RAM-package             Analysis of Amplicon-Based Metagenomic Data
RAM.border              Customized Themes For GGPLOT
RAM.dates               Date Formatting for RAM
RAM.factors             Factor Formatting for RAM
RAM.input.formatting    Data Input Formatting
RAM.pal                 Creat Color Palette
RAM.plotting            Creating Plots with RAM
RAM.rank.formatting     Taxonomic Rank Formatting
Taxa.ord                Ordination Plot For Taxa Groups Using CCA or
                        RDA Analysis
alignment               Sample Alignment
assist.NB               Negative Binomial Test For OTUID or Taxon
assist.ado              Perform ADONIS Analysis for OTU Tables Or
                        Taxonomic Abundance Matrix
assist.ordination       Perform CCA and RDA Analysis for OTU Tables
col.splitup             Split Column Of Data Frame
combine.OTU             Combine Non Overlapped OTU tables From The Same
                        Community
core.OTU                Summary Of Core OTUs
core.OTU.rank           Summary Of Core OTUs
core.Taxa               Show Summary of Core Taxa
correlation             Plot Of Correlation Coefficient
data.clust              Plot Hierarchical Cluster Of Samples Based on
                        OTU Table or Taxonomic Abundance Matrix
data.revamp             Transform OTU Table
data.subset             Subset OTU And Metadata
dissim                  Calculate Dissimilarity Matrix Data
dissim.heatmap          Plot Distance Matrix Heatmap for OTU Samples
dissim.plot             Plot Dissimilarity Matrix Data for Different
                        Methods
diversity.indices       Calculate True Diversity and Evenness
envis.NB                Visualize The Negative Binomial Model OF A
                        Given Taxon OR OTUID
factor.abundance        Plot the Abundance of OTUs by Classification at
                        a Given Taxonomic Rank For Each Level of A
                        Metadata Category Variable.
filter.META             Select METADATA Variables
filter.OTU              Filter OTU
filter.Taxa             Filter Taxonomic Abundance Matrix by Total
                        Counts Or Maximum Relative Abundance
fread.OTU               Fast Load Large OTU Table
fread.meta              Load Metadata Table
get.rank                Get OTUs Classified at Taxonomic Rank(s)
group.OTU               Plot Distribution of OTUs
group.Taxa.bar          Barplot Of Taxa Distribution In Groups
group.Taxa.box          Boxplot Of Taxa In Each Level of A Metadata
                        Variable
group.abund.Taxa        Barplot Of Distribution Of Taxa In Groups
group.abundance         Plot the Abundance of OTUs by Classification at
                        a Given Taxonomic Rank
group.abundance.meta    Plot the Abundance of OTUs by Classification at
                        a Given Taxonomic Rank
group.diversity         Boxplot To Compare Diversity Indices Among
                        Groups
group.heatmap           Plot OTU Abundance at a Given Rank with
                        Metadata Annotation
group.heatmap.simple    Plot a Heatmap Showing OTU Abundance by
                        Taxonomic Classification
group.indicators        Plot Indicator Taxon Groups for Metadata Trends
group.rich              Barplot Of Richness For Each Level Of A Given
                        Metadata Variable
group.spatial           Plot Spatial Collection Trends for Taxon Groups
group.spec              Boxplot Of Richness For Each Level Of A Given
                        Metadata Variable
group.temporal          Plot Temporal Trends for Metadata and Taxon
                        Groups
group.venn              Plot Venn Diagram For Two To Five Sets With
                        Item Labels
location.formatting     Location Formatting
match.data              Match Samples In Ecology Data Sets and Metadata
meta                    Sample Metadata for ITS1/ITS2
network_data            Creates Nodes and Edge-List For An OTU Table
pcoa.plot               Create a PCoA plot for an OTU Table
percent.classified      Calculate Percent of OTUs Classified at a Given
                        Taxonomic Rank
phylo_taxonomy          Plot Hierarchical Taxonomic Tree with Relative
                        Abundance
phylog_taxonomy         Plot Hierarchical Taxonomic Tree
read.OTU                Open OTU Table
read.meta               Open Metadata Table
reset.META              Reset OTU
sample.locations        Plot the Geographic Location of Samples
sample.map              Plot The Geographic Location of Samples
sample.sites            Plot The Geographic Location of Samples
seq_var                 Plot Intra And Inter Specific Variation For An
                        Alignment
shared.OTU              Summary of Shared OTUs Across ALL Subjects
shared.Taxa             Summary of Shared Taxa Across ALL Subjects
tax.abund               Aggregate OTU Data Based on Taxonomy
tax.fill                Fill Missing Taxonomic Information
tax.split               Split OTU Tables By Taxonomic Rank
top.groups.plot         Plot the Top Taxon Groups
transpose.LCA           Transpose OTU Tables With LCA Annotation For
                        Each OTU
transpose.OTU           Take the Transpose of an OTU Table
valid.OTU               Validate an OTU Table
valid.taxonomy          Validate And Reformat The OTU Taxonomy Column
write.data              Write Data To CSV File
