R: Microbiome Analysis Tools

# Microbiome Analysis Tools

## Documentation for package ‘holobiont’ version 0.1.3

- DESCRIPTION file

## Help Pages

basic_branch | Branch-based Core Community Phylogeny Using Thresholds
basic_np | Non-phylogenetic Core Community Phylogeny Using Thresholds
basic_tip | Tip-based Core Community Phylogeny Using Thresholds
coreEdges | Edges of the Tree Included in the Core Community Phylogeny
coreFaithsPD | Faiths PD of the Core Microbiome
coreJaccard | Jaccard Distance Between Core Microbiomes from Two Habitats
corePhyloVenn | Phylogenetic Venn Diagram Comparing Core Microbiomes from Multiple Habitats
coreRichness | Richness of the Core Microbiome
coreTaxa | Taxa Included in the Core Microbiome
coreTree | The Core Community Phylogeny
coreUniFrac | UniFrac Distance Between Core Microbiomes from Two Habitats
coreVenn | Venn Diagram Comparing (Non-Phylogenetic) Core Microbiomes from Multiple Habitats
coreVennTree | Phylogeny with Branches Colored Based on Venn Diagram
ggvenn2 | A modified version of functions from the ggvenn package for plotting phylogenetic venn diagrams.
shade_branch | Branch-based Core Community Phylogeny Using the Shade & Stopnisek (2019) algorithm.
shade_np | Non-phylogenetic Core Community Using the Shade & Stopnisek (2019) algorithm.
shade_tip | Tip-based Core Community Phylogeny Using the Shade & Stopnisek (2019) algorithm.