# R for Amplicon-Sequencing-Based Microbial-Ecology

## Documentation for package ‘RAM’ version 1.2.1.3

- DESCRIPTION file.
- Package NEWS.

## Help Pages

A C D E F G I L M N O P R S T V W

RAM-package | Analysis of Amplicon-Based Metagenomic Data

## -- A --

alignment | Sample Alignment
assist.ado | Perform ADONIS Analysis for OTU Tables Or Taxonomic Abundance Matrix
assist.cca | Perform CCA and RDA Analysis for OTU Tables
assist.NB | Negative Binomial Test For OTUID or Taxon
assist.ordination | Perform CCA and RDA Analysis for OTU Tables
assist.rda | Perform CCA and RDA Analysis for OTU Tables

## -- C --

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

## -- D --

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.alleig.plot | Plot Dissimilarity Matrix Data for Different Methods
dissim.clust | Calculate Dissimilarity Matrix Data
dissim.clust.plot | Plot Dissimilarity Matrix Data for Different Methods
dissim.eig | Calculate Dissimilarity Matrix Data
dissim.eig.plot | Plot Dissimilarity Matrix Data for Different Methods
dissim.GOF | Calculate Dissimilarity Matrix Data
dissim.GOF.plot | Plot Dissimilarity Matrix Data for Different Methods
dissim.heatmap | Plot Distance Matrix Heatmap for OTU Samples
dissim.ord | Calculate Dissimilarity Matrix Data
dissim.ord.plot | Plot Dissimilarity Matrix Data for Different Methods
dissim.plot | Plot Dissimilarity Matrix Data for Different Methods
dissim.pvar | Calculate Dissimilarity Matrix Data
dissim.pvar.plot | Plot Dissimilarity Matrix Data for Different Methods
dissim.tree | Calculate Dissimilarity Matrix Data
dissim.tree.plot | Plot Dissimilarity Matrix Data for Different Methods
diversity.indices | Calculate True Diversity and Evenness

## -- E --

envis.NB | Visualize The Negative Binomial Model OF A Given Taxon OR OTUID
evenness | Calculate True Diversity and Evenness

## -- F --

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.meta | Load Metadata Table
fread.OTU | Fast Load Large OTU Table

## -- G --

get.rank | Get OTUs Classified at Taxonomic Rank(s)
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.OTU | Plot Distribution of OTUs
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.Taxa.bar | Barplot Of Taxa Distribution In Groups
group.Taxa.box | Boxplot Of Taxa In Each Level of A Metadata Variable
group.temporal | Plot Temporal Trends for Metadata and Taxon Groups
group.top.number | Plot the Top Taxon Groups
group.top.percent | Plot the Top Taxon Groups
group.venn | Plot Venn Diagram For Two To Five Sets With Item Labels

## -- I --

ITS1 | Sample ITS1 and ITS2 Data
ITS1/ITS2 | Sample ITS1 and ITS2 Data
ITS2 | Sample ITS1 and ITS2 Data

## -- L --

LCA.OTU | Lowest Common Ancestor (LCA) OF EACH OTU
location.formatting | Location Formatting

## -- M --

match.data | Match Samples In Ecology Data Sets and Metadata
meta | Sample Metadata for ITS1/ITS2
META.clust | Plot Hierarchical Cluster Of Metadata

## -- N --

network_data | Creates Nodes and Edge-List For An OTU Table

## -- O --

OTU.cca | Ordination Plot For OTUs Using CCA or RDA Analysis
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.rda | Ordination Plot For OTUs Using CCA or RDA Analysis
OTU.recap | Summarize OTU

## -- P --

pcoa.plot | Create a PCoA plot for an OTU Table
percent.classified | Calculate Percent of OTUs Classified at a Given Taxonomic Rank
phylog_taxonomy | Plot Hierarchical Taxonomic Tree
phylo_taxonomy | Plot Hierarchical Taxonomic Tree with Relative Abundance

## -- R --

RAM | Analysis of Amplicon-Based Metagenomic Data
RAM.border | Customized Themes For GGPLOT
RAM.color | 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
read.meta | Open Metadata Table
read.OTU | Open OTU Table
reformat.taxonomy | Validate And Reformat The OTU Taxonomy Column
reset.META | Reset OTU

## -- S --

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

## -- T --

tax.abund | Aggregate OTU Data Based on Taxonomy
tax.fill | Fill Missing Taxonomic Information
tax.split | Split OTU Tables By Taxonomic Rank
Taxa.cca | Ordination Plot For Taxa Groups Using CCA or RDA Analysis
Taxa.ord | Ordination Plot For Taxa Groups Using CCA or RDA Analysis
Taxa.rda | Ordination Plot For Taxa Groups Using CCA or RDA Analysis
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
true.diversity | Calculate True Diversity and Evenness

## -- V --

valid.OTU | Validate an OTU Table
valid.taxonomy | Validate And Reformat The OTU Taxonomy Column

## -- W --

write.data | Write Data To CSV File