Package: holobiont
Type: Package
Title: Microbiome Analysis Tools
Version: 0.1.3
Authors@R: 
  c(person(given = "Sharon",
           family = "Bewick",
           email = "sbewick@clemson.edu",
           role = c("aut","cre")),
    person(given = "Benjamin",
           family = "Camper",
           role = c("aut")),
           person(given="National Science Foundation Division of Integrative Organismal Systems (award #2104605)",
           role="fnd"))
Description: We provide functions for identifying the core community phylogeny in any microbiome, drawing phylogenetic Venn diagrams, calculating the core Faith’s 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.
License: GPL-2
Encoding: UTF-8
biocViews: Software, phyloseq
Imports: ape, phyloseq, phytools, ggplot2, dplyr, utils, tibble,
        castor, vegan, data.table
RoxygenNote: 7.3.2
NeedsCompilation: no
Packaged: 2025-07-21 22:31:04 UTC; sbewick
Author: Sharon Bewick [aut, cre],
  Benjamin Camper [aut],
  National Science Foundation Division of Integrative Organismal Systems
    (award #2104605) [fnd]
Maintainer: Sharon Bewick <sbewick@clemson.edu>
Repository: CRAN
Date/Publication: 2025-07-21 22:50:02 UTC
Built: R 4.6.0; ; 2026-04-26 13:28:10 UTC; unix
