{ "_id": "6ac75fdcde46216d5edcf0f9", "Package": "holobiont", "Type": "Package", "Title": "Microbiome Analysis Tools", "Version": "0.1.3", "Authors@R": "c(person(given = \"Sharon\",\nfamily = \"Bewick\",\nemail = \"sbewick@clemson.edu\",\nrole = c(\"aut\",\"cre\")),\nperson(given = \"Benjamin\",\nfamily = \"Camper\",\nrole = c(\"aut\")),\nperson(given=\"National Science Foundation Division of Integrative Organismal Systems (award #2104605)\",\nrole=\"fnd\"))", "Description": "We provide functions for identifying the core community\nphylogeny in any microbiome, drawing phylogenetic Venn\ndiagrams, calculating the core Faith’s PD for a set of\ncommunities, and calculating the core UniFrac distance between\ntwo sets of communities. All functions rely on construction of\na core community phylogeny, which is a phylogeny where branches\nare defined based on their presence in multiple samples from a\nsingle type of habitat. Our package provides two options for\nconstructing the core community phylogeny, a tip-based\napproach, where the core community phylogeny is identified\nbased on incidence of leaf nodes and a branch-based approach,\nwhere the core community phylogeny is identified based on\nincidence of individual branches. We suggest use of the\nmicroViz package.", "License": "GPL-2", "Encoding": "UTF-8", "biocViews": "Software, phyloseq", "RoxygenNote": "7.3.2", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-08 09:05:50 UTC", "User": "root" }, "Author": "Sharon Bewick [aut, cre], Benjamin Camper [aut], National\nScience Foundation Division of Integrative Organismal Systems\n(award #2104605) [fnd]", "Maintainer": "Sharon Bewick ", "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", "_user": "bewicklab", "_type": "src", "_file": "holobiont_0.1.3.tar.gz", "_fileid": "https://r2.ropensci.org/326608da022af2edf3ae422ea1ae56178ae17281123460ac7acdc7579cf86bac", "_filesize": 186013, "_sha256": "326608da022af2edf3ae422ea1ae56178ae17281123460ac7acdc7579cf86bac", 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"package": "dplyr", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "tibble", "role": "Imports" }, { "package": "castor", "role": "Imports" }, { "package": "vegan", "role": "Imports" }, { "package": "data.table", "role": "Imports" } ], "_owner": "cran", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_topics": [ "software", "phyloseq" ], "_stars": 0, "_contributors": [ { "user": "bewicklab", "count": 2, "uuid": 68816453 } ], "_userbio": { "uuid": 68816453, "type": "user", "name": "bewicklab", "followers": 0 }, "_downloads": { "count": 298, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/holobiont" }, "_searchresults": 0, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/holobiont.html", "extra/manual.pdf" ], "_realowner": "bewicklab", "_cranurl": false, "_releases": [ { "version": "0.1.2", "date": "2024-10-16" }, { "version": "0.1.3", "date": "2025-07-21" } ], "_exports": [ "basic_branch", "basic_np", "basic_tip", "coreEdges", "coreFaithsPD", "coreJaccard", "corePhyloVenn", "coreRichness", "coreTaxa", "coreTree", "coreUniFrac", "coreVenn", "coreVennTree", "ggvenn2", "shade_branch", "shade_np", "shade_tip" ], "_help": [ { "page": "basic_branch", "title": "Branch-based Core Community Phylogeny Using Thresholds", "topics": [ "basic_branch" ] }, { "page": "basic_np", "title": "Non-phylogenetic Core Community Phylogeny Using Thresholds", "topics": [ "basic_np" ] }, { "page": "basic_tip", "title": "Tip-based Core Community Phylogeny Using Thresholds", "topics": [ "basic_tip" ] }, { "page": "coreEdges", "title": "Edges of the Tree Included in the Core Community Phylogeny", "topics": [ "coreEdges" ] }, { "page": "coreFaithsPD", "title": "Faiths PD of the Core Microbiome", "topics": [ "coreFaithsPD" ] }, { "page": "coreJaccard", "title": "Jaccard Distance Between Core Microbiomes from Two Habitats", "topics": [ "coreJaccard" ] }, { "page": "corePhyloVenn", "title": "Phylogenetic Venn Diagram Comparing Core Microbiomes from Multiple Habitats", "topics": [ "corePhyloVenn" ] }, { "page": "coreRichness", "title": "Richness of the Core Microbiome", "topics": [ "coreRichness" ] }, { "page": "coreTaxa", "title": "Taxa Included in the Core Microbiome", "topics": [ "coreTaxa" ] }, { "page": "coreTree", "title": "The Core Community Phylogeny", "topics": [ "coreTree" ] }, { "page": "coreUniFrac", "title": "UniFrac Distance Between Core Microbiomes from Two Habitats", "topics": [ "coreUniFrac" ] }, { "page": "coreVenn", "title": "Venn Diagram Comparing (Non-Phylogenetic) Core Microbiomes from Multiple Habitats", "topics": [ "coreVenn" ] }, { "page": "coreVennTree", "title": "Phylogeny with Branches Colored Based on Venn Diagram", "topics": [ "coreVennTree" ] }, { "page": "ggvenn2", "title": "A modified version of functions from the ggvenn package for plotting phylogenetic venn diagrams.", 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