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.
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CRAN Check Status
Show all 14 flavors
| Flavor | Status |
|---|---|
| r-devel-linux-x86_64-debian-clang | OK |
| r-devel-linux-x86_64-debian-gcc | OK |
| r-devel-linux-x86_64-fedora-clang | OK |
| r-devel-linux-x86_64-fedora-gcc | OK |
| r-devel-macos-arm64 | OK |
| r-devel-windows-x86_64 | OK |
| r-oldrel-macos-arm64 | OK |
| r-oldrel-macos-x86_64 | OK |
| r-oldrel-windows-x86_64 | OK |
| r-patched-linux-x86_64 | OK |
| r-release-linux-x86_64 | OK |
| r-release-macos-arm64 | OK |
| r-release-macos-x86_64 | OK |
| r-release-windows-x86_64 | OK |
Check History
OK 14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 16, 2026
ERROR 13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Mar 12, 2026
package dependencies
Package required but not available: ‘phyloseq’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
OK 14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 11, 2026
ERROR 13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Mar 10, 2026
package dependencies
Package required but not available: ‘phyloseq’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.