We provide functions for identifying the core community phylogeny in any microbiome, drawing phylogenetic Venn diagrams, calculating the core Faithâs PD for a set of communities, and calculating the core UniFrac distance between two sets of communities. All functions rely on construction of a core community phylogeny, which is a phylogeny where branches are defined based on their presence in multiple samples from a single type of habitat. Our package provides two options for constructing the core community phylogeny, a tip-based approach, where the core community phylogeny is identified based on incidence of leaf nodes and a branch-based approach, where the core community phylogeny is identified based on incidence of individual branches. We suggest use of the microViz package.
Version: 0.1.3 Imports: ape, phyloseq, phytools, ggplot2, dplyr, utils, tibble, castor, vegan, data.table Published: 2025-07-21 DOI: 10.32614/CRAN.package.holobiont Author: Sharon Bewick [aut, cre], Benjamin Camper [aut], National Science Foundation Division of Integrative Organismal Systems (award #2104605) [fnd] Maintainer: Sharon Bewick <sbewick at clemson.edu> License: GPL-2 NeedsCompilation: no CRAN checks: holobiont results Documentation: Downloads: Linking:Please use the canonical form https://CRAN.R-project.org/package=holobiont to link to this page.
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