Man pages for RAM
R for Amplicon-Sequencing-Based Microbial-Ecology
| alignment | Sample Alignment |
| assist.ado | Perform ADONIS Analysis for OTU Tables Or Taxonomic Abundance... |
| assist.NB | Negative Binomial Test For OTUID or Taxon |
| 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... |
| data.revamp | Transform OTU Table |
| 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... |
| factor.abundance | Plot the Abundance of OTUs by Classification at a Given... |
| filter.META | Select METADATA Variables |
| filter.OTU | Filter OTU |
| filter.Taxa | Filter Taxonomic Abundance Matrix by Total Counts Or Maximum... |
| fread.meta | Load Metadata Table |
| fread.OTU | Fast Load Large OTU Table |
| get.rank | Get OTUs Classified at Taxonomic Rank(s) |
| group.abundance | Plot the Abundance of OTUs by Classification at a Given... |
| group.abundance.meta | Plot the Abundance of OTUs by Classification at a Given... |
| group.abund.Taxa | Barplot Of Distribution Of Taxa In Groups |
| 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... |
| 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... |
| group.spatial | Plot Spatial Collection Trends for Taxon Groups |
| group.spec | Boxplot Of Richness For Each Level Of A Given Metadata... |
| 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.venn | Plot Venn Diagram For Two To Five Sets With Item Labels |
| ITS1_and_ITS2 | Sample ITS1 and ITS2 Data |
| LCA.OTU | Lowest Common Ancestor (LCA) OF EACH OTU |
| location.formatting | Location Formatting |
| match.data | Match Samples In Ecology Data Sets and Metadata |
| meta | Sample Metadata for ITS1/ITS2 |
| META.clust | Plot Hierarchical Cluster Of Metadata |
| network_data | Creates Nodes and Edge-List For An OTU Table |
| 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 |
| OTU.subsets | Subset OTU And Metadata |
| pcoa.plot | Create a PCoA plot for an OTU Table |
| percent.classified | Calculate Percent of OTUs Classified at a Given Taxonomic... |
| phylog_taxonomy | Plot Hierarchical Taxonomic Tree |
| phylo_taxonomy | Plot Hierarchical Taxonomic Tree with Relative Abundance |
| RAM.dates | Date Formatting for RAM |
| RAM.factors | Factor Formatting for RAM |
| RAM.input.formatting | Data Input Formatting |
| RAM-package | Analysis of Amplicon-Based Metagenomic Data |
| 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 |
| 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 |
| Taxa.ord | Ordination Plot For Taxa Groups Using CCA or RDA Analysis |
| tax.fill | Fill Missing Taxonomic Information |
| tax.split | Split OTU Tables By Taxonomic Rank |
| theme_ggplot | Customized Themes For GGPLOT |
| 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 |
