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: 2026-10-08 09:05:50 UTC; root
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>
Config/pak/sysreqs: libglpk-dev libicu-dev libxml2-dev zlib1g-dev
Repository: https://bewicklab.r-universe.dev
Date/Publication: 2025-07-21 22:50:02 UTC
RemoteUrl: https://github.com/cran/holobiont
RemoteRef: HEAD
RemoteSha: f02a232655df80c01889400f0c4ac47fd59af037